Starting phenix.real_space_refine on Thu Jul 25 01:59:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pib_17679/07_2024/8pib_17679_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pib_17679/07_2024/8pib_17679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pib_17679/07_2024/8pib_17679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pib_17679/07_2024/8pib_17679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pib_17679/07_2024/8pib_17679_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pib_17679/07_2024/8pib_17679_neut.cif" } resolution = 2.6 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= 0.007 sd= 0.057 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 1 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 17170 2.51 5 N 4934 2.21 5 O 5542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 19": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P GLU 132": "OE1" <-> "OE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "I GLU 106": "OE1" <-> "OE2" Residue "I TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 249": "OE1" <-> "OE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 441": "OE1" <-> "OE2" Residue "I GLU 461": "OE1" <-> "OE2" Residue "I ASP 842": "OD1" <-> "OD2" Residue "I GLU 849": "OE1" <-> "OE2" Residue "I GLU 867": "OE1" <-> "OE2" Residue "I GLU 876": "OE1" <-> "OE2" Residue "I ASP 937": "OD1" <-> "OD2" Residue "I GLU 940": "OE1" <-> "OE2" Residue "I GLU 949": "OE1" <-> "OE2" Residue "I GLU 1005": "OE1" <-> "OE2" Residue "I ASP 1126": "OD1" <-> "OD2" Residue "I TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1310": "OD1" <-> "OD2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 301": "OE1" <-> "OE2" Residue "J GLU 402": "OE1" <-> "OE2" Residue "J GLU 404": "OE1" <-> "OE2" Residue "J GLU 658": "OE1" <-> "OE2" Residue "J ASP 785": "OD1" <-> "OD2" Residue "J ASP 902": "OD1" <-> "OD2" Residue "J PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1143": "OD1" <-> "OD2" Residue "K ASP 8": "OD1" <-> "OD2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K ASP 44": "OD1" <-> "OD2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27848 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 10423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Chain: "J" Number of atoms: 10249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1318, 10249 Classifications: {'peptide': 1318} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1262} Chain breaks: 3 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: 1811 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 223} Conformer: "B" Number of residues, atoms: 233, 1803 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 223} bond proxies already assigned to first conformer: 1816 Chain: "H" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1741 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 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: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 826 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 808 Classifications: {'DNA': 40} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 39} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17579 SG CYS J 814 58.060 125.179 93.358 1.00 99.44 S ATOM 18144 SG CYS J 888 59.993 122.325 92.265 1.00 96.47 S ATOM 18195 SG CYS J 895 58.920 125.138 89.708 1.00 90.42 S ATOM 18216 SG CYS J 898 61.786 125.619 92.033 1.00 96.47 S Time building chain proxies: 17.21, per 1000 atoms: 0.62 Number of scatterers: 27848 At special positions: 0 Unit cell: (140.608, 169.728, 157.248, 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 1 29.99 S 110 16.00 P 90 15.00 Mg 1 11.99 O 5542 8.00 N 4934 7.00 C 17170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS P 51 " - pdb=" SG CYS P 139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.26 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 898 " Number of angles added : 6 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6132 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 52 sheets defined 40.3% alpha, 17.9% beta 41 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 15.23 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 72 removed outlier: 3.538A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 99 Processing helix chain 'P' and resid 121 through 132 Processing helix chain 'P' and resid 134 through 153 Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.730A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.528A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.776A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.138A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.949A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 289 through 294 removed outlier: 3.956A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 289 through 294' 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: 4.119A 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 480 removed outlier: 3.954A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 481 through 482 No H-bonds generated for 'chain 'I' and resid 481 through 482' Processing helix chain 'I' and resid 483 through 487 removed outlier: 3.850A pdb=" N THR I 486 " --> pdb=" O ASP I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 492 removed outlier: 3.676A pdb=" N ASP I 491 " --> pdb=" O MET I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 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: 4.109A 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: 4.206A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 990 Processing helix chain 'I' and resid 993 through 1000 removed outlier: 3.718A pdb=" N TRP I 997 " --> pdb=" O PRO I 993 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU I 998 " --> pdb=" O ARG I 994 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.515A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.179A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.629A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.904A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.725A 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 96 through 101 Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.547A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.737A pdb=" N TYR J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.514A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.663A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.580A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) 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 327 through 331 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.558A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 403 removed outlier: 3.962A pdb=" N ARG J 403 " --> pdb=" O LYS J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.060A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.902A 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 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 removed outlier: 4.062A 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: 3.501A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 647 through 671 removed outlier: 3.863A pdb=" N HIS J 651 " --> pdb=" O PRO J 647 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.633A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 729 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.597A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 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 930 Processing helix chain 'J' and resid 1068 through 1073 removed outlier: 3.583A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) 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: 3.865A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.259A 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: 3.564A 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 removed outlier: 3.535A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1361 through 1375 removed outlier: 4.352A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 55 removed outlier: 3.795A pdb=" N GLU K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.611A 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 160 Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.353A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.546A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 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 removed outlier: 3.588A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.635A pdb=" N ILE H 217 " --> pdb=" O PRO H 213 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 235 removed outlier: 4.487A pdb=" N LEU H 234 " --> pdb=" O ALA H 230 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 removed outlier: 3.597A pdb=" N ASN P 27 " --> pdb=" O GLU P 58 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS P 77 " --> pdb=" O TYR P 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 33 removed outlier: 3.920A pdb=" N ILE P 33 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU P 48 " --> pdb=" O ILE P 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'P' and resid 80 through 81 Processing sheet with id=AA4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.654A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.533A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA7, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.180A 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 160 removed outlier: 3.788A pdb=" N ASP I 160 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 226 through 229 removed outlier: 4.678A pdb=" N GLU I 226 " --> pdb=" O PHE I 337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 239 through 240 removed outlier: 4.061A pdb=" N MET I 239 " --> pdb=" O ILE I 285 " (cutoff:3.500A) removed outlier: 4.228A 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 250 through 251 removed outlier: 3.916A pdb=" N ALA I 251 " --> pdb=" O ARG I 267 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG I 267 " --> pdb=" O ALA I 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.006A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.793A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.738A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB7, first strand: chain 'I' and resid 633 through 637 Processing sheet with id=AB8, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.501A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.064A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC2, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC3, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.360A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.823A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.638A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.856A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.651A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC9, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.727A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.687A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.095A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.801A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.885A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD4, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AD5, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD6, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD7, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.077A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.844A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.305A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.670A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 4.482A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AE4, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.792A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1186 through 1190 removed outlier: 4.348A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.570A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.714A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.527A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AF1, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.756A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AF3, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.589A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N THR H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL H 192 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 97 through 105 removed outlier: 3.654A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AF6, first strand: chain 'H' and resid 110 through 111 removed outlier: 7.570A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 152 through 153 1145 hydrogen bonds defined for protein. 3236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 15.93 Time building geometry restraints manager: 13.23 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: 9171 1.34 - 1.46: 5166 1.46 - 1.58: 13754 1.58 - 1.70: 180 1.70 - 1.82: 192 Bond restraints: 28463 Sorted by residual: bond pdb=" CB PRO P 133 " pdb=" CG PRO P 133 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.65e+00 bond pdb=" C3' DA A 2 " pdb=" O3' DA A 2 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.65e+00 bond pdb=" CB GLN K 62 " pdb=" CG GLN K 62 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CA GLU P 132 " pdb=" C GLU P 132 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.26e-02 6.30e+03 1.83e+00 bond pdb=" CB LYS J 395 " pdb=" CG LYS J 395 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.75e+00 ... (remaining 28458 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.77: 984 105.77 - 112.87: 15509 112.87 - 119.96: 9726 119.96 - 127.05: 12216 127.05 - 134.15: 419 Bond angle restraints: 38854 Sorted by residual: angle pdb=" CA PRO P 133 " pdb=" N PRO P 133 " pdb=" CD PRO P 133 " ideal model delta sigma weight residual 112.00 102.89 9.11 1.40e+00 5.10e-01 4.23e+01 angle pdb=" CB MET I 488 " pdb=" CG MET I 488 " pdb=" SD MET I 488 " ideal model delta sigma weight residual 112.70 128.44 -15.74 3.00e+00 1.11e-01 2.75e+01 angle pdb=" N PRO P 133 " pdb=" CA PRO P 133 " pdb=" C PRO P 133 " ideal model delta sigma weight residual 112.47 121.37 -8.90 2.06e+00 2.36e-01 1.87e+01 angle pdb=" CB MET J1095 " pdb=" CG MET J1095 " pdb=" SD MET J1095 " ideal model delta sigma weight residual 112.70 125.66 -12.96 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CB MET I 1 " pdb=" CG MET I 1 " pdb=" SD MET I 1 " ideal model delta sigma weight residual 112.70 124.77 -12.07 3.00e+00 1.11e-01 1.62e+01 ... (remaining 38849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 16323 35.59 - 71.18: 934 71.18 - 106.77: 37 106.77 - 142.36: 0 142.36 - 177.95: 4 Dihedral angle restraints: 17298 sinusoidal: 7773 harmonic: 9525 Sorted by residual: dihedral pdb=" O4' U R 6 " pdb=" C1' U R 6 " pdb=" N1 U R 6 " pdb=" C2 U R 6 " ideal model delta sinusoidal sigma weight residual 200.00 42.49 157.51 1 1.50e+01 4.44e-03 8.21e+01 dihedral pdb=" CA VAL H 192 " pdb=" C VAL H 192 " pdb=" N GLU H 193 " pdb=" CA GLU H 193 " ideal model delta harmonic sigma weight residual -180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CB CYS P 51 " pdb=" SG CYS P 51 " pdb=" SG CYS P 139 " pdb=" CB CYS P 139 " ideal model delta sinusoidal sigma weight residual 93.00 57.75 35.25 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 17295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4043 0.073 - 0.147: 392 0.147 - 0.220: 5 0.220 - 0.293: 1 0.293 - 0.367: 1 Chirality restraints: 4442 Sorted by residual: chirality pdb=" CG LEU P 143 " pdb=" CB LEU P 143 " pdb=" CD1 LEU P 143 " pdb=" CD2 LEU P 143 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA PRO P 133 " pdb=" N PRO P 133 " pdb=" C PRO P 133 " pdb=" CB PRO P 133 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA GLU P 132 " pdb=" N GLU P 132 " pdb=" C GLU P 132 " pdb=" CB GLU P 132 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 4439 not shown) Planarity restraints: 4762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU P 132 " -0.097 5.00e-02 4.00e+02 1.43e-01 3.27e+01 pdb=" N PRO P 133 " 0.247 5.00e-02 4.00e+02 pdb=" CA PRO P 133 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO P 133 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 10 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO H 11 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO H 11 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 11 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 11 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" CD GLU K 11 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU K 11 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU K 11 " 0.012 2.00e-02 2.50e+03 ... (remaining 4759 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 235 2.57 - 3.15: 21386 3.15 - 3.73: 45732 3.73 - 4.32: 61290 4.32 - 4.90: 102050 Nonbonded interactions: 230693 Sorted by model distance: nonbonded pdb=" OP1 U R 17 " pdb="MG MG J1502 " model vdw 1.982 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1502 " model vdw 2.052 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1502 " model vdw 2.053 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1502 " model vdw 2.069 2.170 nonbonded pdb=" O3' G R 16 " pdb="MG MG J1502 " model vdw 2.102 2.170 ... (remaining 230688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 3 through 159 or resid 167 through 218 or resid 220 throug \ h 235)) selection = (chain 'H' and (resid 3 through 218 or resid 220 through 235)) } 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 99.690 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 28463 Z= 0.170 Angle : 0.577 15.745 38854 Z= 0.292 Chirality : 0.041 0.367 4442 Planarity : 0.004 0.143 4762 Dihedral : 19.352 177.947 11163 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.30 % Rotamer: Outliers : 2.65 % Allowed : 25.35 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3293 helix: 1.98 (0.16), residues: 1166 sheet: 0.52 (0.24), residues: 491 loop : -0.33 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J1193 HIS 0.002 0.000 HIS J1366 PHE 0.011 0.001 PHE P 130 TYR 0.020 0.001 TYR G 185 ARG 0.012 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 263 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 GLN cc_start: 0.8861 (tt0) cc_final: 0.8614 (tp40) REVERT: P 22 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8302 (mm-30) REVERT: P 33 ILE cc_start: 0.7072 (tp) cc_final: 0.6801 (pp) REVERT: P 150 ILE cc_start: 0.6695 (mm) cc_final: 0.6373 (tp) REVERT: J 714 GLU cc_start: 0.8753 (tp30) cc_final: 0.8299 (tp30) REVERT: G 93 GLN cc_start: 0.7971 (mp10) cc_final: 0.7439 (mp10) REVERT: H 25 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8543 (tttp) REVERT: H 65 LEU cc_start: 0.9145 (pp) cc_final: 0.8828 (pt) outliers start: 75 outliers final: 67 residues processed: 330 average time/residue: 1.3303 time to fit residues: 516.8184 Evaluate side-chains 316 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 249 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 995 ASP Chi-restraints excluded: chain I residue 1155 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 670 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1088 VAL Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 0.2980 chunk 256 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 136 optimal weight: 0.5980 chunk 264 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 161 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 306 optimal weight: 0.7980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN J 875 ASN J 962 ASN K 43 ASN H 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 28463 Z= 0.160 Angle : 0.503 9.295 38854 Z= 0.263 Chirality : 0.041 0.313 4442 Planarity : 0.004 0.149 4762 Dihedral : 16.783 178.055 4788 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 4.00 % Allowed : 23.54 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.99 (0.15), residues: 3293 helix: 2.03 (0.16), residues: 1198 sheet: 0.53 (0.24), residues: 497 loop : -0.33 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 4 HIS 0.002 0.000 HIS H 37 PHE 0.012 0.001 PHE P 78 TYR 0.012 0.001 TYR J 631 ARG 0.006 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 271 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 33 ILE cc_start: 0.7216 (tp) cc_final: 0.7013 (pp) REVERT: P 150 ILE cc_start: 0.6705 (mm) cc_final: 0.6358 (tp) REVERT: I 315 MET cc_start: 0.6904 (pmt) cc_final: 0.6629 (pmm) REVERT: I 694 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7815 (mtp85) REVERT: J 136 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: J 166 LEU cc_start: 0.9313 (mm) cc_final: 0.8984 (pp) REVERT: J 404 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: K 3 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8090 (ttm-80) REVERT: K 55 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7870 (mm-30) REVERT: G 93 GLN cc_start: 0.8004 (mp10) cc_final: 0.7553 (mp-120) REVERT: H 65 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9022 (pt) outliers start: 113 outliers final: 47 residues processed: 363 average time/residue: 1.4258 time to fit residues: 603.8707 Evaluate side-chains 302 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 250 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1088 VAL Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 255 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 246 optimal weight: 30.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 15 GLN P 95 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN G 186 ASN H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 28463 Z= 0.465 Angle : 0.635 9.176 38854 Z= 0.331 Chirality : 0.045 0.318 4442 Planarity : 0.005 0.141 4762 Dihedral : 16.940 179.720 4734 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 4.92 % Allowed : 23.40 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.57 (0.15), residues: 3293 helix: 1.62 (0.15), residues: 1202 sheet: 0.20 (0.24), residues: 490 loop : -0.48 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 868 HIS 0.005 0.001 HIS J 450 PHE 0.016 0.002 PHE J 763 TYR 0.019 0.002 TYR J 631 ARG 0.006 0.001 ARG J 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 274 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 22 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8372 (mm-30) REVERT: P 26 VAL cc_start: 0.9066 (t) cc_final: 0.8813 (p) REVERT: P 33 ILE cc_start: 0.7170 (tp) cc_final: 0.6781 (pp) REVERT: P 58 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: P 123 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7574 (t80) REVERT: I 83 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8630 (mm-40) REVERT: I 241 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6380 (tm) REVERT: I 315 MET cc_start: 0.7462 (pmt) cc_final: 0.7074 (pmm) REVERT: I 641 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: I 654 ASP cc_start: 0.8755 (m-30) cc_final: 0.8554 (m-30) REVERT: I 694 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7964 (mtp85) REVERT: I 1329 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: J 136 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: J 166 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8990 (pp) REVERT: J 206 ASN cc_start: 0.9119 (m110) cc_final: 0.8745 (m110) REVERT: J 354 VAL cc_start: 0.9395 (OUTLIER) cc_final: 0.9097 (t) REVERT: J 398 LYS cc_start: 0.8814 (mttp) cc_final: 0.8543 (mttp) REVERT: K 67 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7308 (ttm110) REVERT: G 93 GLN cc_start: 0.8070 (mp10) cc_final: 0.7542 (mp10) REVERT: H 65 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8600 (pp) REVERT: H 66 HIS cc_start: 0.8591 (m90) cc_final: 0.8043 (m90) outliers start: 139 outliers final: 66 residues processed: 375 average time/residue: 1.4835 time to fit residues: 648.8756 Evaluate side-chains 334 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 257 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 439 LYS Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 889 ASP Chi-restraints excluded: chain J residue 909 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1088 VAL Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 chunk 326 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 292 optimal weight: 0.0020 chunk 88 optimal weight: 0.7980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 43 ASN H 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28463 Z= 0.181 Angle : 0.528 9.270 38854 Z= 0.275 Chirality : 0.041 0.293 4442 Planarity : 0.004 0.140 4762 Dihedral : 16.827 179.823 4727 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 3.82 % Allowed : 24.92 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3293 helix: 1.81 (0.15), residues: 1202 sheet: 0.27 (0.23), residues: 511 loop : -0.41 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 4 HIS 0.002 0.000 HIS I 447 PHE 0.013 0.001 PHE P 78 TYR 0.012 0.001 TYR J 631 ARG 0.012 0.000 ARG I 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 280 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 58 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: P 123 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7877 (t80) REVERT: I 83 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8630 (mm-40) REVERT: I 241 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6393 (tm) REVERT: I 315 MET cc_start: 0.7288 (pmt) cc_final: 0.7003 (pmt) REVERT: I 694 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7944 (mtp85) REVERT: J 136 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: J 166 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8976 (pp) REVERT: J 206 ASN cc_start: 0.9109 (m110) cc_final: 0.8817 (m110) REVERT: K 3 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.8124 (ttm-80) REVERT: K 55 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: K 67 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7368 (ttm110) REVERT: G 93 GLN cc_start: 0.8043 (mp10) cc_final: 0.7475 (mp10) REVERT: G 95 LYS cc_start: 0.8964 (pttm) cc_final: 0.8698 (ptpp) REVERT: H 192 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7558 (p) outliers start: 108 outliers final: 51 residues processed: 363 average time/residue: 1.4222 time to fit residues: 601.6510 Evaluate side-chains 322 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 262 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 243 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 278 optimal weight: 0.7980 chunk 225 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 293 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 95 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN G 186 ASN H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 28463 Z= 0.217 Angle : 0.537 11.310 38854 Z= 0.279 Chirality : 0.041 0.282 4442 Planarity : 0.004 0.143 4762 Dihedral : 16.785 179.847 4721 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 3.82 % Allowed : 25.45 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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 (0.15), residues: 3293 helix: 1.83 (0.15), residues: 1203 sheet: 0.24 (0.23), residues: 527 loop : -0.39 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 409 HIS 0.004 0.001 HIS H 66 PHE 0.012 0.001 PHE P 78 TYR 0.014 0.001 TYR J 631 ARG 0.010 0.000 ARG J 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 269 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 58 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: P 123 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7570 (t80) REVERT: I 83 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8630 (mm-40) REVERT: I 241 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6353 (tm) REVERT: I 315 MET cc_start: 0.7360 (pmt) cc_final: 0.6969 (pmm) REVERT: I 694 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7913 (mtp85) REVERT: I 1329 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: J 136 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: J 166 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8970 (pp) REVERT: J 206 ASN cc_start: 0.9097 (m110) cc_final: 0.8814 (m110) REVERT: K 67 ARG cc_start: 0.7789 (ttm110) cc_final: 0.7352 (ttm110) REVERT: K 79 GLU cc_start: 0.3077 (OUTLIER) cc_final: 0.2725 (tt0) REVERT: G 93 GLN cc_start: 0.8026 (mp10) cc_final: 0.7463 (mp10) REVERT: G 95 LYS cc_start: 0.8990 (pttm) cc_final: 0.8705 (ptpp) REVERT: H 65 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8905 (pt) outliers start: 108 outliers final: 57 residues processed: 347 average time/residue: 1.4878 time to fit residues: 602.3386 Evaluate side-chains 330 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 263 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 9.9990 chunk 294 optimal weight: 0.0270 chunk 64 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 327 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 15 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 43 ASN H 93 GLN H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 28463 Z= 0.197 Angle : 0.549 13.248 38854 Z= 0.282 Chirality : 0.041 0.270 4442 Planarity : 0.004 0.140 4762 Dihedral : 16.764 179.813 4721 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 3.75 % Allowed : 25.70 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.82 (0.15), residues: 3293 helix: 1.89 (0.15), residues: 1199 sheet: 0.26 (0.23), residues: 529 loop : -0.38 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 4 HIS 0.003 0.000 HIS I 447 PHE 0.012 0.001 PHE P 78 TYR 0.013 0.001 TYR J 631 ARG 0.011 0.000 ARG I 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 277 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 58 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: P 123 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7530 (t80) REVERT: P 138 ARG cc_start: 0.8723 (mtm110) cc_final: 0.8465 (mtm110) REVERT: I 83 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8628 (mm-40) REVERT: I 241 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6293 (tm) REVERT: I 315 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6986 (pmm) REVERT: I 694 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7938 (mtp85) REVERT: I 1329 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: J 136 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: J 166 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8959 (pp) REVERT: J 206 ASN cc_start: 0.9092 (m110) cc_final: 0.8808 (m110) REVERT: J 300 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: K 3 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.8388 (ttm-80) REVERT: K 79 GLU cc_start: 0.3324 (OUTLIER) cc_final: 0.3016 (tt0) REVERT: G 93 GLN cc_start: 0.8039 (mp10) cc_final: 0.7469 (mp10) REVERT: G 95 LYS cc_start: 0.8989 (pttm) cc_final: 0.8707 (ptpp) outliers start: 106 outliers final: 62 residues processed: 356 average time/residue: 1.4568 time to fit residues: 602.7612 Evaluate side-chains 339 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 266 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 333 ILE Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1038 GLN Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 238 optimal weight: 10.0000 chunk 185 optimal weight: 0.7980 chunk 275 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 325 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN G 186 ASN H 93 GLN H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28463 Z= 0.269 Angle : 0.577 14.175 38854 Z= 0.295 Chirality : 0.042 0.269 4442 Planarity : 0.004 0.137 4762 Dihedral : 16.780 179.395 4720 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.22 % Favored : 96.72 % Rotamer: Outliers : 3.89 % Allowed : 25.35 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3293 helix: 1.82 (0.15), residues: 1202 sheet: 0.25 (0.23), residues: 530 loop : -0.42 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 4 HIS 0.003 0.001 HIS J1366 PHE 0.011 0.001 PHE P 59 TYR 0.015 0.001 TYR J 631 ARG 0.011 0.000 ARG J 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 271 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 58 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: P 123 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7603 (t80) REVERT: P 142 LEU cc_start: 0.9213 (tm) cc_final: 0.8992 (tm) REVERT: I 83 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8620 (mm-40) REVERT: I 241 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6438 (tm) REVERT: I 315 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7071 (pmm) REVERT: I 694 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7924 (mtp85) REVERT: I 834 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: I 1329 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: J 136 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: J 166 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8961 (pp) REVERT: J 206 ASN cc_start: 0.9087 (m110) cc_final: 0.8717 (m110) REVERT: J 762 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7983 (m110) REVERT: J 1084 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7579 (pp30) REVERT: K 3 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8416 (ttm-80) REVERT: K 79 GLU cc_start: 0.3273 (OUTLIER) cc_final: 0.2963 (tt0) REVERT: G 93 GLN cc_start: 0.8084 (mp10) cc_final: 0.7521 (mp10) REVERT: G 95 LYS cc_start: 0.8996 (pttm) cc_final: 0.8704 (ptpp) outliers start: 110 outliers final: 58 residues processed: 352 average time/residue: 1.4427 time to fit residues: 592.3948 Evaluate side-chains 334 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 263 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 CYS Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 834 GLN Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1084 GLN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 98 optimal weight: 0.0670 chunk 64 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 256 optimal weight: 6.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 46 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 43 ASN H 93 GLN H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 28463 Z= 0.197 Angle : 0.576 14.770 38854 Z= 0.294 Chirality : 0.041 0.256 4442 Planarity : 0.004 0.135 4762 Dihedral : 16.736 179.365 4718 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 3.43 % Allowed : 26.37 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3293 helix: 1.91 (0.15), residues: 1193 sheet: 0.25 (0.23), residues: 520 loop : -0.38 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 4 HIS 0.003 0.000 HIS J1366 PHE 0.013 0.001 PHE P 78 TYR 0.013 0.001 TYR J 631 ARG 0.013 0.000 ARG J 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 272 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 2 GLN cc_start: 0.5322 (tm-30) cc_final: 0.4859 (tm-30) REVERT: P 51 CYS cc_start: 0.5242 (t) cc_final: 0.4902 (t) REVERT: P 123 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7436 (t80) REVERT: P 139 CYS cc_start: 0.6854 (t) cc_final: 0.6462 (t) REVERT: P 142 LEU cc_start: 0.9243 (tm) cc_final: 0.9011 (tm) REVERT: I 241 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6390 (tm) REVERT: I 275 ARG cc_start: 0.9237 (mmm160) cc_final: 0.8810 (tpm-80) REVERT: I 315 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7218 (pmt) REVERT: I 834 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8527 (pt0) REVERT: I 1154 ASP cc_start: 0.7842 (t0) cc_final: 0.7598 (t0) REVERT: J 136 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: J 166 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8947 (pp) REVERT: J 206 ASN cc_start: 0.9088 (m110) cc_final: 0.8804 (m110) REVERT: J 1084 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7575 (pp30) REVERT: J 1101 LEU cc_start: 0.8728 (mp) cc_final: 0.8359 (mp) REVERT: K 67 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7598 (ttm110) REVERT: K 79 GLU cc_start: 0.3341 (OUTLIER) cc_final: 0.3018 (tt0) REVERT: G 93 GLN cc_start: 0.8045 (mp10) cc_final: 0.7472 (mp10) REVERT: G 95 LYS cc_start: 0.8990 (pttm) cc_final: 0.8710 (ptpp) outliers start: 97 outliers final: 60 residues processed: 347 average time/residue: 1.4746 time to fit residues: 600.4105 Evaluate side-chains 333 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 265 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 834 GLN Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1084 GLN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 2.9990 chunk 312 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 303 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 274 optimal weight: 0.7980 chunk 287 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN G 186 ASN H 93 GLN H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 28463 Z= 0.243 Angle : 0.589 15.358 38854 Z= 0.301 Chirality : 0.042 0.250 4442 Planarity : 0.004 0.133 4762 Dihedral : 16.732 179.308 4718 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 2.65 % Allowed : 27.26 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % 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: 0.81 (0.15), residues: 3293 helix: 1.89 (0.15), residues: 1199 sheet: 0.27 (0.23), residues: 530 loop : -0.40 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 409 HIS 0.003 0.001 HIS J1366 PHE 0.013 0.001 PHE P 78 TYR 0.038 0.001 TYR I 262 ARG 0.013 0.000 ARG J 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 270 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 123 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7464 (t80) REVERT: P 142 LEU cc_start: 0.9244 (tm) cc_final: 0.9001 (tm) REVERT: I 241 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6405 (tm) REVERT: I 275 ARG cc_start: 0.9243 (mmm160) cc_final: 0.8667 (tpt90) REVERT: I 315 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7102 (pmm) REVERT: I 834 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8540 (pt0) REVERT: I 1154 ASP cc_start: 0.7870 (t0) cc_final: 0.7632 (t0) REVERT: I 1329 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: J 136 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: J 166 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8950 (pp) REVERT: J 206 ASN cc_start: 0.9096 (m110) cc_final: 0.8820 (m110) REVERT: J 1084 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7566 (pp30) REVERT: K 11 GLU cc_start: 0.7925 (pp20) cc_final: 0.7682 (mt-10) REVERT: K 12 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8568 (ttmm) REVERT: K 79 GLU cc_start: 0.3586 (OUTLIER) cc_final: 0.3357 (tt0) REVERT: G 93 GLN cc_start: 0.8073 (mp10) cc_final: 0.7508 (mp10) REVERT: G 95 LYS cc_start: 0.9006 (pttm) cc_final: 0.8716 (ptpp) outliers start: 75 outliers final: 59 residues processed: 327 average time/residue: 1.4264 time to fit residues: 545.3898 Evaluate side-chains 331 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 263 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 834 GLN Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1084 GLN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 0.9990 chunk 321 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 164 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 43 ASN H 93 GLN H 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28463 Z= 0.217 Angle : 0.596 15.823 38854 Z= 0.304 Chirality : 0.042 0.243 4442 Planarity : 0.004 0.133 4762 Dihedral : 16.726 179.205 4717 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 2.83 % Allowed : 27.15 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3293 helix: 1.91 (0.15), residues: 1199 sheet: 0.27 (0.24), residues: 506 loop : -0.38 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 4 HIS 0.003 0.001 HIS J1366 PHE 0.021 0.001 PHE P 59 TYR 0.030 0.001 TYR I 262 ARG 0.015 0.000 ARG J 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6586 Ramachandran restraints generated. 3293 Oldfield, 0 Emsley, 3293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 264 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 123 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7444 (t80) REVERT: I 83 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8626 (mm-40) REVERT: I 241 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6404 (tm) REVERT: I 275 ARG cc_start: 0.9255 (mmm160) cc_final: 0.8685 (tpt90) REVERT: I 315 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7243 (pmt) REVERT: I 834 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8534 (pt0) REVERT: I 1154 ASP cc_start: 0.7860 (t0) cc_final: 0.7631 (t0) REVERT: J 136 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: J 166 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8945 (pp) REVERT: J 206 ASN cc_start: 0.9106 (m110) cc_final: 0.8817 (m110) REVERT: J 1084 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7560 (pp30) REVERT: J 1101 LEU cc_start: 0.8720 (mp) cc_final: 0.8345 (mp) REVERT: K 11 GLU cc_start: 0.7941 (pp20) cc_final: 0.7715 (mt-10) REVERT: K 79 GLU cc_start: 0.3557 (OUTLIER) cc_final: 0.3351 (tt0) REVERT: G 93 GLN cc_start: 0.8045 (mp10) cc_final: 0.7470 (mp10) REVERT: G 95 LYS cc_start: 0.8998 (pttm) cc_final: 0.8713 (ptpp) outliers start: 80 outliers final: 61 residues processed: 323 average time/residue: 1.4033 time to fit residues: 531.5174 Evaluate side-chains 329 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 259 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 123 PHE Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 834 GLN Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1084 GLN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 0.5980 chunk 285 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 247 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 268 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 275 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1114 GLN K 43 ASN G 186 ASN H 93 GLN H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.098337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.067822 restraints weight = 77160.500| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.85 r_work: 0.3014 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 28463 Z= 0.179 Angle : 0.575 15.487 38854 Z= 0.294 Chirality : 0.041 0.232 4442 Planarity : 0.004 0.131 4762 Dihedral : 16.676 179.195 4717 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 2.58 % Allowed : 27.50 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 3293 helix: 2.01 (0.15), residues: 1186 sheet: 0.29 (0.24), residues: 507 loop : -0.36 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 4 HIS 0.003 0.000 HIS J1366 PHE 0.020 0.001 PHE J1034 TYR 0.026 0.001 TYR I 262 ARG 0.014 0.000 ARG J 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10272.98 seconds wall clock time: 183 minutes 21.78 seconds (11001.78 seconds total)