Starting phenix.real_space_refine on Thu Jul 25 04:46:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pid_17681/07_2024/8pid_17681_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pid_17681/07_2024/8pid_17681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pid_17681/07_2024/8pid_17681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pid_17681/07_2024/8pid_17681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pid_17681/07_2024/8pid_17681_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pid_17681/07_2024/8pid_17681_neut.cif" } resolution = 3.0 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 89 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 17460 2.51 5 N 5013 2.21 5 O 5620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I GLU 415": "OE1" <-> "OE2" Residue "I GLU 504": "OE1" <-> "OE2" Residue "I ASP 674": "OD1" <-> "OD2" Residue "J GLU 175": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J ASP 248": "OD1" <-> "OD2" Residue "J TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 443": "OE1" <-> "OE2" Residue "J ASP 462": "OD1" <-> "OD2" Residue "J ASP 751": "OD1" <-> "OD2" Residue "J ASP 802": "OD1" <-> "OD2" Residue "J GLU 913": "OE1" <-> "OE2" Residue "J PHE 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 204": "OE1" <-> "OE2" 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: 28297 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1294 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 150} Chain: "I" Number of atoms: 10450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 bond proxies already assigned to first conformer: 10558 Chain: "J" Number of atoms: 10450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10450 Classifications: {'peptide': 1343} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1287} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "G" Number of atoms: 1807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Conformer: "B" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} bond proxies already assigned to first conformer: 1812 Chain: "H" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 784 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} Chain: "R" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 303 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12193 SG CYS J 70 24.334 70.291 85.576 1.00 90.31 S ATOM 12207 SG CYS J 72 23.326 66.614 85.192 1.00 91.52 S ATOM 12315 SG CYS J 85 21.696 68.777 87.827 1.00 90.44 S ATOM 12339 SG CYS J 88 25.403 67.813 88.170 1.00 87.37 S ATOM 18027 SG CYS J 814 56.468 126.456 93.755 1.00 74.29 S ATOM 18592 SG CYS J 888 58.541 123.452 93.071 1.00 72.59 S ATOM 18643 SG CYS J 895 57.575 126.019 90.253 1.00 67.71 S ATOM 18664 SG CYS J 898 60.271 126.753 92.762 1.00 68.41 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE I 156 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE I 156 " occ=0.50 Time building chain proxies: 21.73, per 1000 atoms: 0.77 Number of scatterers: 28297 At special positions: 0 Unit cell: (139.776, 169.728, 158.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 112 16.00 P 89 15.00 Mg 1 11.99 O 5620 8.00 N 5013 7.00 C 17460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.54 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " Number of angles added : 12 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6244 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 50 sheets defined 38.9% alpha, 18.1% beta 40 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 10.29 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 71 Processing helix chain 'P' and resid 89 through 100 removed outlier: 3.552A pdb=" N ILE P 93 " --> pdb=" O PRO P 89 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL P 98 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 124 removed outlier: 3.704A pdb=" N PHE P 123 " --> pdb=" O GLU P 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.639A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.990A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.708A 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 163 through 167 removed outlier: 3.983A pdb=" N SER I 166 " --> pdb=" O LYS I 163 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 163 through 167' Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 removed outlier: 3.775A pdb=" N ILE I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 295 removed outlier: 3.738A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.950A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.552A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.782A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (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 608 through 612 removed outlier: 4.020A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 624 through 628 removed outlier: 3.849A pdb=" N HIS I 628 " --> pdb=" O GLU I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.514A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.133A 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 825 Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 991 Processing helix chain 'I' and resid 993 through 998 removed outlier: 3.534A pdb=" N TRP I 997 " --> pdb=" O ARG I 994 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.582A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.322A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.566A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 4.117A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.591A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.747A 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 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.570A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.661A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.702A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.556A 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 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.502A pdb=" N ILE J 416 " --> pdb=" O LEU J 412 " (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 485 through 489 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.722A 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 581 removed outlier: 3.955A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.936A 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: 4.041A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.936A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.066A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.653A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 926 through 930 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: 3.537A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.347A 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: 3.730A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN J1326 " --> pdb=" O ALA J1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.730A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 4.169A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA J1375 " --> pdb=" O ARG J1371 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.557A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.609A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 removed outlier: 4.136A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.566A 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 159 Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.169A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.576A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 160 removed outlier: 3.609A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 166 removed outlier: 3.767A pdb=" N ASP H 164 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG H 166 " --> pdb=" O GLU H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 228 through 232 Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'P' and resid 149 through 155 removed outlier: 3.543A pdb=" N SER P 139 " --> pdb=" O VAL P 154 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N MET P 140 " --> pdb=" O THR P 131 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR P 131 " --> pdb=" O MET P 140 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE P 129 " --> pdb=" O LEU P 142 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASN P 144 " --> pdb=" O GLN P 127 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN P 127 " --> pdb=" O ASN P 144 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE P 126 " --> pdb=" O ILE P 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.608A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.805A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA7, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.307A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 154 through 159 removed outlier: 4.951A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB1, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB2, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.020A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.559A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.811A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB6, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.671A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.239A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 755 through 758 Processing sheet with id=AB9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.371A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 830 through 841 removed outlier: 4.024A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.589A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.224A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC6, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC7, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AC8, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.713A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.261A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.807A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 253 through 254 Processing sheet with id=AD2, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD3, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AD4, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD6, first strand: chain 'J' and resid 825 through 827 removed outlier: 7.261A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP J 830 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 842 through 843 removed outlier: 4.009A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.528A 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: 4.851A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.362A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.262A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE4, first strand: chain 'J' and resid 1046 through 1050 Processing sheet with id=AE5, first strand: chain 'J' and resid 1188 through 1191 removed outlier: 6.946A pdb=" N LYS J1172 " --> pdb=" O GLU J1168 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU J1168 " --> pdb=" O LYS J1172 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG J1174 " --> pdb=" O GLY J1166 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.673A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.781A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.585A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.215A 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 91 Processing sheet with id=AF1, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.948A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=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: 6.662A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 98 through 105 removed outlier: 3.899A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.605A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) 1141 hydrogen bonds defined for protein. 3188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 14.41 Time building geometry restraints manager: 12.47 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: 9135 1.34 - 1.46: 4057 1.46 - 1.58: 15362 1.58 - 1.70: 176 1.70 - 1.81: 194 Bond restraints: 28924 Sorted by residual: bond pdb=" CD GLU K 76 " pdb=" OE1 GLU K 76 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.35e+00 bond pdb=" CB ASN H 137 " pdb=" CG ASN H 137 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" CB LYS J 964 " pdb=" CG LYS J 964 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CB GLU K 76 " pdb=" CG GLU K 76 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CB LYS J1151 " pdb=" CG LYS J1151 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 ... (remaining 28919 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.08: 815 105.08 - 112.30: 14990 112.30 - 119.52: 9666 119.52 - 126.73: 13506 126.73 - 133.95: 500 Bond angle restraints: 39477 Sorted by residual: angle pdb=" CA GLU K 76 " pdb=" CB GLU K 76 " pdb=" CG GLU K 76 " ideal model delta sigma weight residual 114.10 121.99 -7.89 2.00e+00 2.50e-01 1.56e+01 angle pdb=" C GLN K 75 " pdb=" N GLU K 76 " pdb=" CA GLU K 76 " ideal model delta sigma weight residual 121.14 114.91 6.23 1.75e+00 3.27e-01 1.27e+01 angle pdb=" CB ARG I 996 " pdb=" CG ARG I 996 " pdb=" CD ARG I 996 " ideal model delta sigma weight residual 111.30 119.29 -7.99 2.30e+00 1.89e-01 1.21e+01 angle pdb=" N GLY H 108 " pdb=" CA GLY H 108 " pdb=" C GLY H 108 " ideal model delta sigma weight residual 112.34 118.99 -6.65 2.04e+00 2.40e-01 1.06e+01 angle pdb=" CB LYS J1151 " pdb=" CG LYS J1151 " pdb=" CD LYS J1151 " ideal model delta sigma weight residual 111.30 118.51 -7.21 2.30e+00 1.89e-01 9.83e+00 ... (remaining 39472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 16733 35.09 - 70.17: 829 70.17 - 105.26: 39 105.26 - 140.35: 0 140.35 - 175.43: 2 Dihedral angle restraints: 17603 sinusoidal: 7899 harmonic: 9704 Sorted by residual: dihedral pdb=" C4' DC B 28 " pdb=" C3' DC B 28 " pdb=" O3' DC B 28 " pdb=" P DC B 29 " ideal model delta sinusoidal sigma weight residual 220.00 44.57 175.43 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC A 39 " pdb=" C3' DC A 39 " pdb=" O3' DC A 39 " pdb=" P DC A 40 " ideal model delta sinusoidal sigma weight residual 220.00 74.24 145.76 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA ASN I 314 " pdb=" C ASN I 314 " pdb=" N MET I 315 " pdb=" CA MET I 315 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 17600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2913 0.027 - 0.055: 955 0.055 - 0.082: 342 0.082 - 0.109: 231 0.109 - 0.137: 67 Chirality restraints: 4508 Sorted by residual: chirality pdb=" CA LYS I 236 " pdb=" N LYS I 236 " pdb=" C LYS I 236 " pdb=" CB LYS I 236 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE J1190 " pdb=" N ILE J1190 " pdb=" C ILE J1190 " pdb=" CB ILE J1190 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE J1090 " pdb=" N ILE J1090 " pdb=" C ILE J1090 " pdb=" CB ILE J1090 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 4505 not shown) Planarity restraints: 4852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO I 190 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET I 488 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO I 489 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 489 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 489 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 153 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO G 154 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO G 154 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 154 " 0.020 5.00e-02 4.00e+02 ... (remaining 4849 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 200 2.53 - 3.12: 20579 3.12 - 3.71: 45657 3.71 - 4.31: 61162 4.31 - 4.90: 103643 Nonbonded interactions: 231241 Sorted by model distance: nonbonded pdb=" OD2 ASP J 460 " pdb=" OP1 U R 17 " model vdw 1.935 3.040 nonbonded pdb=" P U R 17 " pdb="MG MG J1503 " model vdw 2.054 2.530 nonbonded pdb=" OP1 U R 17 " pdb="MG MG J1503 " model vdw 2.067 2.170 nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG J1503 " model vdw 2.081 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.086 2.170 ... (remaining 231236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 4 through 218 or resid 220 through 233)) selection = (chain 'H' and (resid 4 through 218 or resid 220 through 233)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 98.360 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28924 Z= 0.137 Angle : 0.457 8.659 39477 Z= 0.242 Chirality : 0.038 0.137 4508 Planarity : 0.003 0.045 4852 Dihedral : 18.104 175.432 11359 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 0.28 % Allowed : 18.47 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 3359 helix: 2.38 (0.16), residues: 1138 sheet: 0.38 (0.24), residues: 510 loop : -0.16 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 997 HIS 0.003 0.000 HIS P 152 PHE 0.005 0.001 PHE I1025 TYR 0.009 0.001 TYR J 631 ARG 0.012 0.000 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.6867 (tmm) cc_final: 0.6463 (tmm) REVERT: I 741 MET cc_start: 0.8463 (mmt) cc_final: 0.8141 (mmt) REVERT: J 1034 PHE cc_start: 0.8380 (m-80) cc_final: 0.7999 (m-80) REVERT: J 1040 MET cc_start: 0.6087 (ptt) cc_final: 0.5314 (pmt) REVERT: G 93 GLN cc_start: 0.8244 (pp30) cc_final: 0.7921 (pp30) outliers start: 5 outliers final: 2 residues processed: 187 average time/residue: 1.4262 time to fit residues: 312.7835 Evaluate side-chains 170 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain G residue 90 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 175 optimal weight: 0.0980 chunk 138 optimal weight: 7.9990 chunk 268 optimal weight: 2.9990 chunk 104 optimal weight: 0.0570 chunk 163 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 311 optimal weight: 0.7980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I1116 HIS I1257 GLN K 15 ASN G 117 HIS H 41 ASN H 147 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28924 Z= 0.193 Angle : 0.472 8.337 39477 Z= 0.249 Chirality : 0.039 0.170 4508 Planarity : 0.003 0.056 4852 Dihedral : 15.622 174.656 4749 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 1.70 % Allowed : 19.65 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 3359 helix: 2.39 (0.16), residues: 1164 sheet: 0.32 (0.24), residues: 507 loop : -0.18 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 997 HIS 0.010 0.001 HIS G 117 PHE 0.011 0.001 PHE I 405 TYR 0.012 0.001 TYR J 631 ARG 0.013 0.000 ARG I 996 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 3.461 Fit side-chains revert: symmetry clash REVERT: I 741 MET cc_start: 0.8581 (mmt) cc_final: 0.8248 (mmt) REVERT: J 1034 PHE cc_start: 0.8407 (m-80) cc_final: 0.8081 (m-80) REVERT: J 1040 MET cc_start: 0.6055 (ptt) cc_final: 0.5349 (pmt) REVERT: G 93 GLN cc_start: 0.8261 (pp30) cc_final: 0.7861 (pp30) outliers start: 46 outliers final: 14 residues processed: 207 average time/residue: 1.3589 time to fit residues: 333.1243 Evaluate side-chains 175 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 312 optimal weight: 4.9990 chunk 337 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 250 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 HIS J 910 ASN K 15 ASN G 117 HIS H 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 28924 Z= 0.442 Angle : 0.612 9.305 39477 Z= 0.322 Chirality : 0.044 0.161 4508 Planarity : 0.004 0.058 4852 Dihedral : 15.910 170.993 4747 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 3.33 % Allowed : 18.99 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3359 helix: 1.89 (0.15), residues: 1165 sheet: 0.08 (0.23), residues: 515 loop : -0.38 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 409 HIS 0.010 0.001 HIS G 117 PHE 0.019 0.002 PHE I1164 TYR 0.020 0.002 TYR J 631 ARG 0.016 0.001 ARG I 996 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 173 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 136 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: J 862 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8849 (p) REVERT: J 875 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7839 (t0) REVERT: J 895 CYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6731 (p) REVERT: J 1034 PHE cc_start: 0.8448 (m-80) cc_final: 0.8080 (m-80) REVERT: J 1040 MET cc_start: 0.6578 (ptt) cc_final: 0.5864 (pmt) REVERT: G 93 GLN cc_start: 0.8449 (pp30) cc_final: 0.8025 (pp30) outliers start: 93 outliers final: 37 residues processed: 243 average time/residue: 1.1702 time to fit residues: 341.5084 Evaluate side-chains 202 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 209 optimal weight: 0.9990 chunk 313 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 60 GLN ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28924 Z= 0.205 Angle : 0.502 9.418 39477 Z= 0.263 Chirality : 0.040 0.148 4508 Planarity : 0.003 0.051 4852 Dihedral : 15.776 173.795 4747 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 2.64 % Allowed : 19.86 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3359 helix: 2.05 (0.16), residues: 1175 sheet: 0.10 (0.23), residues: 511 loop : -0.31 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 997 HIS 0.012 0.001 HIS G 117 PHE 0.012 0.001 PHE I 405 TYR 0.013 0.001 TYR J 631 ARG 0.013 0.000 ARG I 996 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 168 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 84 SER cc_start: 0.9133 (t) cc_final: 0.8931 (m) REVERT: I 101 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8420 (mtm-85) REVERT: J 136 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: J 895 CYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6813 (p) REVERT: J 1034 PHE cc_start: 0.8412 (m-80) cc_final: 0.8040 (m-80) REVERT: J 1040 MET cc_start: 0.6554 (ptt) cc_final: 0.6009 (pmt) REVERT: J 1095 MET cc_start: 0.7705 (tmt) cc_final: 0.7359 (tmm) REVERT: J 1101 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8034 (mp) REVERT: G 93 GLN cc_start: 0.8382 (pp30) cc_final: 0.7941 (pp30) REVERT: H 65 LEU cc_start: 0.9399 (mm) cc_final: 0.9147 (tt) outliers start: 73 outliers final: 33 residues processed: 230 average time/residue: 1.2675 time to fit residues: 348.4074 Evaluate side-chains 194 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 4 optimal weight: 0.0770 chunk 246 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN G 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28924 Z= 0.234 Angle : 0.503 10.243 39477 Z= 0.263 Chirality : 0.040 0.213 4508 Planarity : 0.003 0.052 4852 Dihedral : 15.755 173.821 4747 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 2.60 % Allowed : 20.52 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 3359 helix: 2.14 (0.16), residues: 1160 sheet: 0.12 (0.23), residues: 502 loop : -0.33 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 997 HIS 0.012 0.001 HIS G 117 PHE 0.012 0.001 PHE I 405 TYR 0.013 0.001 TYR J 631 ARG 0.016 0.000 ARG I 996 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 161 time to evaluate : 3.184 Fit side-chains revert: symmetry clash REVERT: P 84 SER cc_start: 0.9146 (t) cc_final: 0.8926 (m) REVERT: I 315 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7626 (ptp) REVERT: J 725 MET cc_start: 0.8765 (ptp) cc_final: 0.8409 (ptp) REVERT: J 895 CYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6816 (p) REVERT: J 1034 PHE cc_start: 0.8423 (m-80) cc_final: 0.8045 (m-80) REVERT: J 1040 MET cc_start: 0.6628 (ptt) cc_final: 0.6103 (pmt) REVERT: J 1101 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8013 (mp) REVERT: K 4 VAL cc_start: 0.9448 (p) cc_final: 0.9245 (p) REVERT: G 93 GLN cc_start: 0.8395 (pp30) cc_final: 0.7944 (pp30) REVERT: G 156 SER cc_start: 0.9349 (m) cc_final: 0.9114 (t) REVERT: H 65 LEU cc_start: 0.9373 (mm) cc_final: 0.9146 (tt) outliers start: 72 outliers final: 40 residues processed: 220 average time/residue: 1.2622 time to fit residues: 332.3922 Evaluate side-chains 201 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 158 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 331 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 174 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN G 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28924 Z= 0.164 Angle : 0.494 12.118 39477 Z= 0.258 Chirality : 0.040 0.180 4508 Planarity : 0.003 0.055 4852 Dihedral : 15.695 175.076 4747 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.59 % Favored : 97.38 % Rotamer: Outliers : 2.19 % Allowed : 21.35 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3359 helix: 2.20 (0.16), residues: 1161 sheet: 0.12 (0.23), residues: 516 loop : -0.29 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 997 HIS 0.020 0.001 HIS G 117 PHE 0.012 0.001 PHE I 405 TYR 0.012 0.001 TYR J 631 ARG 0.017 0.000 ARG I 996 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 165 time to evaluate : 3.321 Fit side-chains revert: symmetry clash REVERT: P 84 SER cc_start: 0.9150 (t) cc_final: 0.8931 (m) REVERT: I 101 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8383 (mtm-85) REVERT: J 1034 PHE cc_start: 0.8401 (m-80) cc_final: 0.8016 (m-80) REVERT: J 1040 MET cc_start: 0.6638 (ptt) cc_final: 0.6091 (pmt) REVERT: J 1095 MET cc_start: 0.7545 (tmt) cc_final: 0.7305 (tmm) REVERT: J 1101 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8002 (mp) REVERT: G 93 GLN cc_start: 0.8381 (pp30) cc_final: 0.7928 (pp30) REVERT: G 156 SER cc_start: 0.9349 (m) cc_final: 0.9111 (t) REVERT: H 65 LEU cc_start: 0.9362 (mm) cc_final: 0.9154 (tt) outliers start: 60 outliers final: 35 residues processed: 216 average time/residue: 1.3415 time to fit residues: 342.8339 Evaluate side-chains 196 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 0.0370 chunk 37 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 279 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 330 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 ASN J 875 ASN K 15 ASN G 117 HIS H 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28924 Z= 0.178 Angle : 0.498 13.617 39477 Z= 0.258 Chirality : 0.040 0.168 4508 Planarity : 0.003 0.058 4852 Dihedral : 15.676 175.388 4747 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.33 % Allowed : 21.25 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.15), residues: 3359 helix: 2.23 (0.16), residues: 1160 sheet: 0.17 (0.23), residues: 509 loop : -0.29 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 4 HIS 0.016 0.001 HIS G 117 PHE 0.012 0.001 PHE I 405 TYR 0.017 0.001 TYR I1053 ARG 0.019 0.000 ARG I 996 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 164 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 84 SER cc_start: 0.9166 (t) cc_final: 0.8947 (m) REVERT: I 101 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8364 (mtm-85) REVERT: J 169 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9143 (pt) REVERT: J 895 CYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6805 (p) REVERT: J 1034 PHE cc_start: 0.8412 (m-80) cc_final: 0.8025 (m-80) REVERT: J 1040 MET cc_start: 0.6625 (ptt) cc_final: 0.6071 (pmt) REVERT: J 1095 MET cc_start: 0.7600 (tmt) cc_final: 0.7277 (tmm) REVERT: J 1101 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7975 (mp) REVERT: G 93 GLN cc_start: 0.8376 (pp30) cc_final: 0.7916 (pp30) REVERT: G 156 SER cc_start: 0.9355 (m) cc_final: 0.9119 (t) REVERT: H 65 LEU cc_start: 0.9333 (mm) cc_final: 0.9074 (tt) REVERT: H 168 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8279 (tp) outliers start: 64 outliers final: 36 residues processed: 219 average time/residue: 1.3462 time to fit residues: 353.2010 Evaluate side-chains 199 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 168 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 0.0670 chunk 132 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 259 optimal weight: 4.9990 chunk 300 optimal weight: 4.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28924 Z= 0.209 Angle : 0.511 12.856 39477 Z= 0.264 Chirality : 0.040 0.156 4508 Planarity : 0.003 0.065 4852 Dihedral : 15.682 175.097 4747 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.40 % Allowed : 21.32 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3359 helix: 2.20 (0.16), residues: 1166 sheet: 0.09 (0.23), residues: 522 loop : -0.29 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 997 HIS 0.005 0.001 HIS I 273 PHE 0.012 0.001 PHE I 972 TYR 0.016 0.001 TYR I1053 ARG 0.018 0.000 ARG I 996 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 159 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 84 SER cc_start: 0.9176 (t) cc_final: 0.8960 (m) REVERT: I 101 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8375 (mtm-85) REVERT: J 895 CYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6807 (p) REVERT: J 964 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8828 (mtmt) REVERT: J 1034 PHE cc_start: 0.8437 (m-80) cc_final: 0.8042 (m-80) REVERT: J 1040 MET cc_start: 0.6670 (ptt) cc_final: 0.6101 (pmt) REVERT: J 1101 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7947 (mp) REVERT: G 93 GLN cc_start: 0.8394 (pp30) cc_final: 0.7928 (pp30) REVERT: G 156 SER cc_start: 0.9353 (m) cc_final: 0.9126 (t) REVERT: H 65 LEU cc_start: 0.9328 (mm) cc_final: 0.9076 (tt) REVERT: H 168 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8283 (tp) outliers start: 66 outliers final: 45 residues processed: 217 average time/residue: 1.3073 time to fit residues: 339.3844 Evaluate side-chains 206 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 157 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 168 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 241 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 291 optimal weight: 7.9990 chunk 306 optimal weight: 0.2980 chunk 202 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 HIS ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28924 Z= 0.262 Angle : 0.540 13.603 39477 Z= 0.278 Chirality : 0.040 0.150 4508 Planarity : 0.004 0.074 4852 Dihedral : 15.724 174.222 4747 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.29 % Allowed : 21.49 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 3359 helix: 2.13 (0.16), residues: 1167 sheet: 0.03 (0.23), residues: 526 loop : -0.33 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 997 HIS 0.005 0.001 HIS I 273 PHE 0.013 0.001 PHE I 972 TYR 0.017 0.001 TYR I1053 ARG 0.019 0.000 ARG I 996 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 161 time to evaluate : 3.163 Fit side-chains revert: symmetry clash REVERT: P 84 SER cc_start: 0.9180 (t) cc_final: 0.8965 (m) REVERT: I 101 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8387 (mtm-85) REVERT: J 895 CYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6806 (p) REVERT: J 964 LYS cc_start: 0.9316 (mmmt) cc_final: 0.8930 (mtmt) REVERT: J 1034 PHE cc_start: 0.8463 (m-80) cc_final: 0.8059 (m-80) REVERT: J 1040 MET cc_start: 0.6782 (ptt) cc_final: 0.6277 (pmt) REVERT: J 1101 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7942 (mp) REVERT: J 1196 LEU cc_start: 0.8903 (mp) cc_final: 0.8339 (tp) REVERT: K 4 VAL cc_start: 0.9407 (p) cc_final: 0.9172 (p) REVERT: G 93 GLN cc_start: 0.8412 (pp30) cc_final: 0.7941 (pp30) REVERT: G 156 SER cc_start: 0.9348 (OUTLIER) cc_final: 0.9135 (t) REVERT: H 65 LEU cc_start: 0.9338 (mm) cc_final: 0.8983 (tt) REVERT: H 168 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8309 (tp) outliers start: 63 outliers final: 47 residues processed: 216 average time/residue: 1.2735 time to fit residues: 328.0094 Evaluate side-chains 210 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 158 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 94 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 168 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 314 optimal weight: 9.9990 chunk 272 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN H 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 28924 Z= 0.320 Angle : 0.575 14.541 39477 Z= 0.295 Chirality : 0.041 0.165 4508 Planarity : 0.004 0.074 4852 Dihedral : 15.769 173.379 4747 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.15 % Allowed : 21.67 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3359 helix: 2.06 (0.16), residues: 1162 sheet: -0.02 (0.22), residues: 532 loop : -0.38 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 997 HIS 0.004 0.001 HIS I 273 PHE 0.013 0.001 PHE I 812 TYR 0.018 0.001 TYR I1053 ARG 0.019 0.000 ARG I 996 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 165 time to evaluate : 3.213 Fit side-chains revert: symmetry clash REVERT: P 84 SER cc_start: 0.9198 (t) cc_final: 0.8978 (m) REVERT: J 725 MET cc_start: 0.8786 (ptp) cc_final: 0.8440 (ptp) REVERT: J 895 CYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6796 (p) REVERT: J 964 LYS cc_start: 0.9307 (mmmt) cc_final: 0.8928 (mtmt) REVERT: J 1034 PHE cc_start: 0.8512 (m-80) cc_final: 0.8121 (m-80) REVERT: J 1040 MET cc_start: 0.6752 (ptt) cc_final: 0.6219 (pmt) REVERT: J 1101 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7937 (mp) REVERT: J 1196 LEU cc_start: 0.8968 (mp) cc_final: 0.8397 (tp) REVERT: K 4 VAL cc_start: 0.9450 (p) cc_final: 0.9229 (p) REVERT: K 69 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8132 (ttp80) REVERT: G 93 GLN cc_start: 0.8435 (pp30) cc_final: 0.7959 (pp30) REVERT: G 156 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.9134 (t) REVERT: H 65 LEU cc_start: 0.9379 (mm) cc_final: 0.9102 (tt) REVERT: H 168 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8306 (tp) outliers start: 59 outliers final: 46 residues processed: 216 average time/residue: 1.2407 time to fit residues: 322.0148 Evaluate side-chains 210 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 160 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 888 CYS Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 168 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 250 optimal weight: 50.0000 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 0.0070 chunk 272 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 239 optimal weight: 0.7980 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051194 restraints weight = 145899.870| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 4.25 r_work: 0.2695 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28924 Z= 0.215 Angle : 0.547 14.508 39477 Z= 0.279 Chirality : 0.040 0.143 4508 Planarity : 0.004 0.069 4852 Dihedral : 15.730 174.119 4747 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.08 % Allowed : 21.88 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3359 helix: 2.08 (0.16), residues: 1163 sheet: 0.09 (0.23), residues: 508 loop : -0.36 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 997 HIS 0.004 0.001 HIS I 273 PHE 0.041 0.001 PHE I 972 TYR 0.014 0.001 TYR I1053 ARG 0.019 0.000 ARG I 996 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7891.26 seconds wall clock time: 140 minutes 4.12 seconds (8404.12 seconds total)