Starting phenix.real_space_refine on Mon Jun 23 06:36:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8egb_28113/06_2025/8egb_28113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8egb_28113/06_2025/8egb_28113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8egb_28113/06_2025/8egb_28113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8egb_28113/06_2025/8egb_28113.map" model { file = "/net/cci-nas-00/data/ceres_data/8egb_28113/06_2025/8egb_28113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8egb_28113/06_2025/8egb_28113.cif" } resolution = 3.8 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= 0.000 sd= 0.006 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 69 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 16356 2.51 5 N 4653 2.21 5 O 5233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26419 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 548 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 236 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "G" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1684 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10555 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 10360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10360 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1278} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 79} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 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 15796 SG CYS J 70 111.274 60.694 69.590 1.00 94.03 S ATOM 15810 SG CYS J 72 112.697 57.286 69.070 1.00 98.26 S ATOM 15918 SG CYS J 85 113.603 60.145 66.663 1.00 97.17 S ATOM 15942 SG CYS J 88 110.111 58.865 66.547 1.00 95.31 S ATOM 21618 SG CYS J 814 85.843 121.267 78.728 1.00 66.05 S ATOM 22183 SG CYS J 888 85.083 117.612 77.772 1.00 61.83 S ATOM 22234 SG CYS J 895 85.780 118.577 81.374 1.00 58.10 S ATOM 22255 SG CYS J 898 82.613 119.711 79.946 1.00 57.60 S Time building chain proxies: 15.45, per 1000 atoms: 0.58 Number of scatterers: 26419 At special positions: 0 Unit cell: (143, 159.9, 166.4, 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 105 16.00 P 69 15.00 Mg 1 11.99 O 5233 8.00 N 4653 7.00 C 16356 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 - 3.00 Amino acid : True - 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: 8.05 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5900 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 44 sheets defined 37.7% alpha, 14.9% beta 30 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 9.47 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 87 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 212 through 229 Processing helix chain 'G' and resid 230 through 232 No H-bonds generated for 'chain 'G' and resid 230 through 232' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.750A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.526A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.638A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.543A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.862A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.146A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 290 through 295 removed outlier: 3.716A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.730A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.831A 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 451 removed outlier: 3.958A pdb=" N ARG I 451 " --> pdb=" O LEU I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.670A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (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 removed outlier: 3.863A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 613 removed outlier: 3.643A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 613' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.865A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 898 through 907 Processing helix chain 'I' and resid 942 through 980 Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.816A 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 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.629A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.538A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 4.165A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.506A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.832A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.629A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 removed outlier: 3.517A pdb=" N LEU J 128 " --> pdb=" O ILE J 124 " (cutoff:3.500A) 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 Processing helix chain 'J' and resid 193 through 209 removed outlier: 3.648A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN J 209 " --> pdb=" O LEU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 removed outlier: 3.589A pdb=" N LYS J 222 " --> pdb=" O THR J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 307 Processing helix chain 'J' and resid 326 through 331 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.502A 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 407 through 417 removed outlier: 3.688A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (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 453 through 458 Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.692A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 581 Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.641A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.669A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 removed outlier: 3.929A pdb=" N ILE J 653 " --> pdb=" O LYS J 649 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 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: 4.594A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.537A pdb=" N TYR J 899 " --> pdb=" O CYS J 895 " (cutoff:3.500A) Processing helix chain 'J' and resid 915 through 930 Proline residue: J 926 - end of helix removed outlier: 3.564A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.522A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.395A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1325 removed outlier: 4.047A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1373 removed outlier: 3.523A pdb=" N ARG J1373 " --> pdb=" O ARG J1369 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 removed outlier: 4.438A pdb=" N GLY K 33 " --> pdb=" O GLN K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 84 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 16 removed outlier: 5.138A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.547A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.953A pdb=" N GLY G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.580A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 18 removed outlier: 5.338A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 104 removed outlier: 7.837A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY H 53 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.781A pdb=" N GLY H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU H 133 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.585A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.322A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 147 through 148 removed outlier: 6.353A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.633A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 256 removed outlier: 3.594A pdb=" N ILE I 255 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.254A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.524A pdb=" N THR I 589 " --> pdb=" O LEU I 606 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.558A pdb=" N ILE I 616 " --> pdb=" O ARG I 637 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 3.869A pdb=" N ALA I 784 " --> pdb=" O ALA I 716 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 750 through 751 removed outlier: 6.786A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 3.527A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET I1230 " --> pdb=" O MET I 800 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET I 800 " --> pdb=" O MET I1230 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 3.527A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 841 removed outlier: 6.556A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 887 through 888 removed outlier: 3.737A pdb=" N THR I 888 " --> pdb=" O LYS I 914 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS I 914 " --> pdb=" O THR I 888 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.514A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1269 through 1270 removed outlier: 3.521A pdb=" N LYS J 345 " --> pdb=" O PHE I1270 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 1335 through 1339 removed outlier: 3.515A pdb=" N GLU I1338 " --> pdb=" O LYS J 21 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.071A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.655A pdb=" N VAL J 145 " --> pdb=" O LYS J 179 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'J' and resid 848 through 849 removed outlier: 7.385A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 949 through 951 removed outlier: 6.961A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.691A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id=AE5, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.573A pdb=" N VAL J1081 " --> pdb=" O PHE J1034 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.708A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1187 through 1189 removed outlier: 3.578A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.623A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) 1014 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 13.22 Time building geometry restraints manager: 8.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4461 1.29 - 1.43: 6499 1.43 - 1.56: 15655 1.56 - 1.69: 153 1.69 - 1.83: 188 Bond restraints: 26956 Sorted by residual: bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.822 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.728 -0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.728 -0.196 2.00e-02 2.50e+03 9.59e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.702 -0.160 2.00e-02 2.50e+03 6.41e+01 ... (remaining 26951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 36212 2.18 - 4.35: 462 4.35 - 6.53: 40 6.53 - 8.71: 11 8.71 - 10.88: 2 Bond angle restraints: 36727 Sorted by residual: angle pdb=" CA PRO I 897 " pdb=" N PRO I 897 " pdb=" CD PRO I 897 " ideal model delta sigma weight residual 112.00 103.37 8.63 1.40e+00 5.10e-01 3.80e+01 angle pdb=" N ASP I 915 " pdb=" CA ASP I 915 " pdb=" C ASP I 915 " ideal model delta sigma weight residual 108.23 117.37 -9.14 1.72e+00 3.38e-01 2.82e+01 angle pdb=" C3' DC A 5 " pdb=" O3' DC A 5 " pdb=" P DC A 6 " ideal model delta sigma weight residual 120.20 128.03 -7.83 1.50e+00 4.44e-01 2.72e+01 angle pdb=" N ALA J 315 " pdb=" CA ALA J 315 " pdb=" C ALA J 315 " ideal model delta sigma weight residual 109.59 102.29 7.30 1.47e+00 4.63e-01 2.47e+01 angle pdb=" C4' DG A 7 " pdb=" C3' DG A 7 " pdb=" O3' DG A 7 " ideal model delta sigma weight residual 110.00 116.58 -6.58 1.50e+00 4.44e-01 1.92e+01 ... (remaining 36722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 16164 35.86 - 71.72: 350 71.72 - 107.57: 22 107.57 - 143.43: 0 143.43 - 179.29: 2 Dihedral angle restraints: 16538 sinusoidal: 7365 harmonic: 9173 Sorted by residual: dihedral pdb=" N ASN J 309 " pdb=" C ASN J 309 " pdb=" CA ASN J 309 " pdb=" CB ASN J 309 " ideal model delta harmonic sigma weight residual 122.80 111.70 11.10 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" CA SER H 20 " pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta harmonic sigma weight residual -180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" C PRO I 897 " pdb=" N PRO I 897 " pdb=" CA PRO I 897 " pdb=" CB PRO I 897 " ideal model delta harmonic sigma weight residual -120.70 -130.91 10.21 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 16535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3949 0.094 - 0.187: 262 0.187 - 0.281: 8 0.281 - 0.374: 2 0.374 - 0.468: 1 Chirality restraints: 4222 Sorted by residual: chirality pdb=" CA PRO I 897 " pdb=" N PRO I 897 " pdb=" C PRO I 897 " pdb=" CB PRO I 897 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.85 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -2.85 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 4219 not shown) Planarity restraints: 4556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 896 " 0.097 5.00e-02 4.00e+02 1.44e-01 3.30e+01 pdb=" N PRO I 897 " -0.248 5.00e-02 4.00e+02 pdb=" CA PRO I 897 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO I 897 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 892 " -0.026 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU I 892 " 0.088 2.00e-02 2.50e+03 pdb=" O GLU I 892 " -0.033 2.00e-02 2.50e+03 pdb=" N THR I 893 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 515 " -0.384 9.50e-02 1.11e+02 1.73e-01 1.94e+01 pdb=" NE ARG J 515 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG J 515 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG J 515 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG J 515 " -0.007 2.00e-02 2.50e+03 ... (remaining 4553 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 277 2.58 - 3.16: 22696 3.16 - 3.74: 40014 3.74 - 4.32: 54669 4.32 - 4.90: 91498 Nonbonded interactions: 209154 Sorted by model distance: nonbonded pdb=" O LEU J 930 " pdb=" OG1 THR J 931 " model vdw 2.001 3.040 nonbonded pdb=" O GLN I1288 " pdb=" OG1 THR I1292 " model vdw 2.011 3.040 nonbonded pdb=" O3' G R 16 " pdb="MG MG J1501 " model vdw 2.014 2.170 nonbonded pdb=" OE1 GLU I 50 " pdb=" OH TYR I 70 " model vdw 2.027 3.040 nonbonded pdb=" O ASP I 516 " pdb=" OG SER I 522 " model vdw 2.038 3.040 ... (remaining 209149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 158 or resid 169 through 232)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.130 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: 1.070 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 74.950 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 0.006 0.295 26964 Z= 0.296 Angle : 0.627 10.884 36739 Z= 0.345 Chirality : 0.045 0.468 4222 Planarity : 0.005 0.173 4556 Dihedral : 14.583 179.289 10638 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.72 % Favored : 95.25 % Rotamer: Outliers : 0.11 % Allowed : 0.18 % Favored : 99.70 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % 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: -0.39 (0.15), residues: 3179 helix: 1.47 (0.16), residues: 1086 sheet: -0.38 (0.28), residues: 364 loop : -1.42 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 115 HIS 0.011 0.001 HIS I1023 PHE 0.015 0.001 PHE J 719 TYR 0.015 0.001 TYR I1281 ARG 0.024 0.001 ARG J 311 Details of bonding type rmsd hydrogen bonds : bond 0.16859 ( 1087) hydrogen bonds : angle 6.55739 ( 3002) metal coordination : bond 0.00674 ( 8) metal coordination : angle 3.23173 ( 12) covalent geometry : bond 0.00556 (26956) covalent geometry : angle 0.62481 (36727) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 352 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.7933 (m110) cc_final: 0.7373 (m110) REVERT: I 286 GLU cc_start: 0.6824 (mt-10) cc_final: 0.5475 (pm20) REVERT: I 337 PHE cc_start: 0.8182 (t80) cc_final: 0.7973 (t80) REVERT: I 403 MET cc_start: 0.8097 (ttt) cc_final: 0.7896 (ttp) REVERT: I 515 MET cc_start: 0.8131 (ttp) cc_final: 0.7771 (ttt) REVERT: J 869 CYS cc_start: 0.8264 (m) cc_final: 0.7901 (m) REVERT: J 870 ASP cc_start: 0.7505 (m-30) cc_final: 0.7274 (m-30) outliers start: 3 outliers final: 1 residues processed: 355 average time/residue: 0.3432 time to fit residues: 200.1245 Evaluate side-chains 266 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 917 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 2.9990 chunk 245 optimal weight: 8.9990 chunk 136 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN H 37 HIS H 66 HIS H 75 GLN H 132 HIS H 194 GLN I 69 GLN I 150 HIS I 165 HIS ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN I 649 GLN I 799 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 HIS J 777 HIS J1023 HIS J1244 GLN K 61 ASN K 73 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102530 restraints weight = 43111.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.104556 restraints weight = 24174.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.104809 restraints weight = 17401.480| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 26964 Z= 0.185 Angle : 0.601 10.081 36739 Z= 0.312 Chirality : 0.043 0.190 4222 Planarity : 0.005 0.142 4556 Dihedral : 13.641 174.887 4432 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.12 % Rotamer: Outliers : 1.03 % Allowed : 7.57 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % 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: -0.36 (0.15), residues: 3179 helix: 1.39 (0.16), residues: 1106 sheet: -0.50 (0.27), residues: 373 loop : -1.34 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 115 HIS 0.024 0.001 HIS I 165 PHE 0.011 0.002 PHE J 620 TYR 0.020 0.002 TYR J1365 ARG 0.005 0.001 ARG J1148 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 1087) hydrogen bonds : angle 4.84625 ( 3002) metal coordination : bond 0.01044 ( 8) metal coordination : angle 3.10678 ( 12) covalent geometry : bond 0.00437 (26956) covalent geometry : angle 0.59859 (36727) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 293 time to evaluate : 2.773 Fit side-chains revert: symmetry clash REVERT: H 66 HIS cc_start: 0.6823 (OUTLIER) cc_final: 0.6400 (m-70) REVERT: H 84 ASN cc_start: 0.8319 (m110) cc_final: 0.7632 (m110) REVERT: H 145 LYS cc_start: 0.8468 (tptp) cc_final: 0.8144 (tptt) REVERT: I 115 LYS cc_start: 0.6235 (mtmt) cc_final: 0.5480 (mtmm) REVERT: I 286 GLU cc_start: 0.7085 (mt-10) cc_final: 0.5585 (pm20) REVERT: I 370 MET cc_start: 0.7932 (mmm) cc_final: 0.7182 (mmm) REVERT: I 488 MET cc_start: 0.2497 (mmt) cc_final: 0.2223 (mmt) REVERT: I 545 PHE cc_start: 0.7459 (m-80) cc_final: 0.7230 (m-80) REVERT: I 1088 ASP cc_start: 0.8601 (p0) cc_final: 0.8346 (p0) REVERT: I 1170 MET cc_start: 0.8209 (tpt) cc_final: 0.7951 (tpp) REVERT: J 52 GLU cc_start: 0.5751 (mm-30) cc_final: 0.5491 (mm-30) REVERT: J 100 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7817 (tm-30) REVERT: J 130 MET cc_start: 0.8164 (ttp) cc_final: 0.7751 (ttp) REVERT: J 198 CYS cc_start: 0.8082 (t) cc_final: 0.7698 (t) REVERT: J 236 TRP cc_start: 0.9068 (m-10) cc_final: 0.8028 (m-10) REVERT: J 484 MET cc_start: 0.8882 (mtt) cc_final: 0.8471 (mtt) REVERT: J 869 CYS cc_start: 0.8453 (m) cc_final: 0.7977 (m) REVERT: J 870 ASP cc_start: 0.7267 (m-30) cc_final: 0.7024 (m-30) REVERT: J 1349 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6998 (mt-10) REVERT: K 60 ASN cc_start: 0.7981 (p0) cc_final: 0.7673 (p0) outliers start: 28 outliers final: 14 residues processed: 309 average time/residue: 0.3616 time to fit residues: 179.6421 Evaluate side-chains 274 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 259 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 188 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 297 optimal weight: 0.4980 chunk 159 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 313 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS H 75 GLN I 69 GLN J 424 ASN K 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105525 restraints weight = 43023.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107244 restraints weight = 32360.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.107561 restraints weight = 23096.211| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 26964 Z= 0.125 Angle : 0.533 9.859 36739 Z= 0.276 Chirality : 0.041 0.197 4222 Planarity : 0.004 0.135 4556 Dihedral : 13.645 173.909 4431 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 1.62 % Allowed : 9.67 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % 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: -0.19 (0.15), residues: 3179 helix: 1.60 (0.16), residues: 1109 sheet: -0.35 (0.28), residues: 362 loop : -1.30 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 115 HIS 0.005 0.001 HIS H 66 PHE 0.010 0.001 PHE I 405 TYR 0.018 0.001 TYR J1365 ARG 0.005 0.000 ARG I 202 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 1087) hydrogen bonds : angle 4.49488 ( 3002) metal coordination : bond 0.00598 ( 8) metal coordination : angle 2.47388 ( 12) covalent geometry : bond 0.00289 (26956) covalent geometry : angle 0.53146 (36727) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 3.026 Fit side-chains revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8240 (m110) cc_final: 0.7462 (m110) REVERT: H 181 GLU cc_start: 0.7669 (tp30) cc_final: 0.7425 (tp30) REVERT: I 119 GLU cc_start: 0.7266 (pm20) cc_final: 0.6868 (pm20) REVERT: I 202 ARG cc_start: 0.8102 (ttp-110) cc_final: 0.7551 (ttp-110) REVERT: I 218 GLU cc_start: 0.7792 (pp20) cc_final: 0.7537 (pp20) REVERT: I 286 GLU cc_start: 0.6947 (mt-10) cc_final: 0.5422 (pm20) REVERT: I 370 MET cc_start: 0.7288 (mmm) cc_final: 0.6944 (mmm) REVERT: I 427 ASP cc_start: 0.7948 (m-30) cc_final: 0.7478 (m-30) REVERT: I 488 MET cc_start: 0.2522 (mmt) cc_final: 0.2096 (mmt) REVERT: I 545 PHE cc_start: 0.7376 (m-80) cc_final: 0.7135 (m-80) REVERT: I 962 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: I 1088 ASP cc_start: 0.8621 (p0) cc_final: 0.8344 (p0) REVERT: I 1170 MET cc_start: 0.8259 (tpt) cc_final: 0.7935 (tpp) REVERT: I 1281 TYR cc_start: 0.8440 (m-10) cc_final: 0.8013 (m-80) REVERT: I 1304 MET cc_start: 0.9014 (tpp) cc_final: 0.8755 (tpp) REVERT: J 21 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7649 (ptpp) REVERT: J 52 GLU cc_start: 0.5858 (mm-30) cc_final: 0.5517 (mm-30) REVERT: J 100 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7750 (tm-30) REVERT: J 130 MET cc_start: 0.8178 (ttp) cc_final: 0.7705 (ttp) REVERT: J 198 CYS cc_start: 0.8155 (t) cc_final: 0.7694 (t) REVERT: J 236 TRP cc_start: 0.8974 (m-10) cc_final: 0.7876 (m-10) REVERT: J 293 ARG cc_start: 0.7667 (mpt90) cc_final: 0.7328 (mtt90) REVERT: J 298 MET cc_start: 0.7566 (mmp) cc_final: 0.7361 (mmt) REVERT: J 484 MET cc_start: 0.9036 (mtt) cc_final: 0.8426 (mtt) REVERT: J 743 MET cc_start: 0.8836 (ptp) cc_final: 0.8603 (ptm) REVERT: J 762 ASN cc_start: 0.8691 (p0) cc_final: 0.8447 (p0) REVERT: J 777 HIS cc_start: 0.8132 (m-70) cc_final: 0.7637 (t-90) REVERT: J 822 MET cc_start: 0.8427 (tpp) cc_final: 0.8161 (tpp) REVERT: J 869 CYS cc_start: 0.8655 (m) cc_final: 0.8195 (m) REVERT: J 870 ASP cc_start: 0.7406 (m-30) cc_final: 0.7119 (m-30) REVERT: J 983 LYS cc_start: 0.6280 (mmtt) cc_final: 0.6049 (mmtt) REVERT: J 1344 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8550 (pp) REVERT: J 1349 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6844 (mt-10) REVERT: K 61 ASN cc_start: 0.7943 (t0) cc_final: 0.7469 (t0) outliers start: 44 outliers final: 21 residues processed: 316 average time/residue: 0.3914 time to fit residues: 201.8042 Evaluate side-chains 283 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 274 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 293 optimal weight: 0.9990 chunk 269 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 260 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS H 75 GLN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100944 restraints weight = 43359.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101179 restraints weight = 25669.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.101714 restraints weight = 20132.627| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 26964 Z= 0.218 Angle : 0.603 12.489 36739 Z= 0.311 Chirality : 0.043 0.199 4222 Planarity : 0.005 0.130 4556 Dihedral : 13.813 173.691 4431 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 1.92 % Allowed : 12.48 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % 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: -0.34 (0.15), residues: 3179 helix: 1.40 (0.16), residues: 1115 sheet: -0.62 (0.27), residues: 374 loop : -1.29 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 686 HIS 0.008 0.001 HIS I 165 PHE 0.017 0.002 PHE J 620 TYR 0.023 0.002 TYR J1365 ARG 0.007 0.001 ARG J 744 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 1087) hydrogen bonds : angle 4.53757 ( 3002) metal coordination : bond 0.01123 ( 8) metal coordination : angle 2.81562 ( 12) covalent geometry : bond 0.00508 (26956) covalent geometry : angle 0.60049 (36727) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 2.803 Fit side-chains revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8367 (m110) cc_final: 0.7648 (m110) REVERT: I 70 TYR cc_start: 0.7898 (t80) cc_final: 0.7532 (t80) REVERT: I 115 LYS cc_start: 0.6246 (mtmt) cc_final: 0.5816 (mtmt) REVERT: I 286 GLU cc_start: 0.6946 (mt-10) cc_final: 0.5271 (pm20) REVERT: I 369 MET cc_start: 0.7726 (tmm) cc_final: 0.6944 (tmm) REVERT: I 370 MET cc_start: 0.7273 (mmm) cc_final: 0.6895 (mmm) REVERT: I 962 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: I 1170 MET cc_start: 0.8230 (tpt) cc_final: 0.8012 (tpp) REVERT: J 52 GLU cc_start: 0.5967 (mm-30) cc_final: 0.5552 (mm-30) REVERT: J 100 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7832 (tm-30) REVERT: J 130 MET cc_start: 0.8077 (ttp) cc_final: 0.7663 (ttp) REVERT: J 198 CYS cc_start: 0.8219 (t) cc_final: 0.7752 (t) REVERT: J 236 TRP cc_start: 0.9033 (m-10) cc_final: 0.7988 (m-10) REVERT: J 484 MET cc_start: 0.9185 (mtt) cc_final: 0.8866 (mtt) REVERT: J 576 ARG cc_start: 0.8256 (mtt90) cc_final: 0.7805 (mtt180) REVERT: J 777 HIS cc_start: 0.8119 (m-70) cc_final: 0.7831 (t-90) REVERT: J 822 MET cc_start: 0.8379 (tpp) cc_final: 0.8166 (tpp) REVERT: J 869 CYS cc_start: 0.8642 (m) cc_final: 0.8165 (m) REVERT: J 870 ASP cc_start: 0.7392 (m-30) cc_final: 0.7099 (m-30) REVERT: J 1344 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8601 (pp) REVERT: J 1349 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6894 (mt-10) outliers start: 52 outliers final: 34 residues processed: 304 average time/residue: 0.3800 time to fit residues: 189.2309 Evaluate side-chains 286 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 178 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 190 optimal weight: 0.2980 chunk 138 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 308 optimal weight: 7.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100706 restraints weight = 43136.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101649 restraints weight = 25399.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.102132 restraints weight = 18779.981| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 26964 Z= 0.195 Angle : 0.581 12.139 36739 Z= 0.299 Chirality : 0.042 0.188 4222 Planarity : 0.004 0.128 4556 Dihedral : 13.840 173.722 4431 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.68 % Rotamer: Outliers : 2.10 % Allowed : 13.92 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % 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: -0.36 (0.15), residues: 3179 helix: 1.38 (0.16), residues: 1115 sheet: -0.67 (0.27), residues: 374 loop : -1.29 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 686 HIS 0.005 0.001 HIS G 23 PHE 0.019 0.001 PHE I 405 TYR 0.023 0.001 TYR J1365 ARG 0.005 0.000 ARG J 311 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 1087) hydrogen bonds : angle 4.45450 ( 3002) metal coordination : bond 0.00951 ( 8) metal coordination : angle 2.55823 ( 12) covalent geometry : bond 0.00455 (26956) covalent geometry : angle 0.57962 (36727) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8391 (m110) cc_final: 0.7594 (m110) REVERT: H 181 GLU cc_start: 0.7701 (tp30) cc_final: 0.7369 (tp30) REVERT: I 115 LYS cc_start: 0.6263 (mtmt) cc_final: 0.5833 (mtmt) REVERT: I 119 GLU cc_start: 0.7368 (pm20) cc_final: 0.7066 (pm20) REVERT: I 202 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.7746 (ttp-110) REVERT: I 286 GLU cc_start: 0.6942 (mt-10) cc_final: 0.5201 (pm20) REVERT: I 488 MET cc_start: 0.2499 (mmt) cc_final: 0.1870 (mmt) REVERT: I 962 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: J 52 GLU cc_start: 0.5969 (mm-30) cc_final: 0.5509 (mm-30) REVERT: J 100 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7791 (tm-30) REVERT: J 130 MET cc_start: 0.8070 (ttp) cc_final: 0.7667 (ttp) REVERT: J 198 CYS cc_start: 0.8214 (t) cc_final: 0.7725 (t) REVERT: J 236 TRP cc_start: 0.9027 (m-10) cc_final: 0.7961 (m-10) REVERT: J 484 MET cc_start: 0.9215 (mtt) cc_final: 0.8823 (mtt) REVERT: J 576 ARG cc_start: 0.8237 (mtt90) cc_final: 0.7790 (mtt180) REVERT: J 765 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: J 777 HIS cc_start: 0.8117 (m-70) cc_final: 0.7825 (t-90) REVERT: J 822 MET cc_start: 0.8313 (tpp) cc_final: 0.8107 (tpp) REVERT: J 869 CYS cc_start: 0.8624 (m) cc_final: 0.8130 (m) REVERT: J 870 ASP cc_start: 0.7564 (m-30) cc_final: 0.7188 (m-30) REVERT: J 1344 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8594 (pp) REVERT: J 1349 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7076 (mt-10) outliers start: 57 outliers final: 42 residues processed: 312 average time/residue: 0.3747 time to fit residues: 192.3267 Evaluate side-chains 301 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 581 MET Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 131 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 280 optimal weight: 30.0000 chunk 217 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN I 65 ASN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.138528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102574 restraints weight = 42994.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102996 restraints weight = 25351.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103718 restraints weight = 19043.585| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 26964 Z= 0.153 Angle : 0.555 11.236 36739 Z= 0.284 Chirality : 0.042 0.188 4222 Planarity : 0.004 0.125 4556 Dihedral : 13.833 173.583 4431 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 2.10 % Allowed : 14.99 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % 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: -0.28 (0.15), residues: 3179 helix: 1.53 (0.16), residues: 1109 sheet: -0.60 (0.28), residues: 364 loop : -1.30 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 686 HIS 0.005 0.001 HIS I 165 PHE 0.016 0.001 PHE I 337 TYR 0.022 0.001 TYR I 70 ARG 0.005 0.000 ARG I 368 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1087) hydrogen bonds : angle 4.34723 ( 3002) metal coordination : bond 0.00710 ( 8) metal coordination : angle 2.30674 ( 12) covalent geometry : bond 0.00357 (26956) covalent geometry : angle 0.55309 (36727) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 2.802 Fit side-chains REVERT: H 84 ASN cc_start: 0.8338 (m110) cc_final: 0.7551 (m110) REVERT: H 181 GLU cc_start: 0.7674 (tp30) cc_final: 0.7372 (tp30) REVERT: I 115 LYS cc_start: 0.6267 (mtmt) cc_final: 0.5823 (mtmt) REVERT: I 119 GLU cc_start: 0.7359 (pm20) cc_final: 0.6954 (pm20) REVERT: I 369 MET cc_start: 0.7227 (ppp) cc_final: 0.6713 (ppp) REVERT: I 488 MET cc_start: 0.3427 (mmt) cc_final: 0.3119 (mmt) REVERT: I 962 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: J 52 GLU cc_start: 0.6092 (mm-30) cc_final: 0.5650 (mm-30) REVERT: J 100 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7769 (tm-30) REVERT: J 130 MET cc_start: 0.8013 (ttp) cc_final: 0.7610 (ttp) REVERT: J 198 CYS cc_start: 0.8205 (t) cc_final: 0.7714 (t) REVERT: J 236 TRP cc_start: 0.9023 (m-10) cc_final: 0.7887 (m-10) REVERT: J 270 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8283 (ttp80) REVERT: J 412 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8501 (tt) REVERT: J 484 MET cc_start: 0.9175 (mtt) cc_final: 0.8760 (mtt) REVERT: J 747 MET cc_start: 0.6550 (mmt) cc_final: 0.6323 (mmt) REVERT: J 765 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: J 777 HIS cc_start: 0.8044 (m-70) cc_final: 0.7793 (t-90) REVERT: J 869 CYS cc_start: 0.8629 (m) cc_final: 0.8123 (m) REVERT: J 870 ASP cc_start: 0.7397 (m-30) cc_final: 0.7015 (m-30) REVERT: J 1344 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8534 (pp) REVERT: J 1349 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7098 (mt-10) REVERT: K 55 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7517 (tm-30) outliers start: 57 outliers final: 40 residues processed: 318 average time/residue: 0.3595 time to fit residues: 186.8996 Evaluate side-chains 308 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 581 MET Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 294 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 chunk 247 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS K 61 ASN K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.140651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104693 restraints weight = 43004.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105617 restraints weight = 24488.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.106295 restraints weight = 18439.416| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 26964 Z= 0.113 Angle : 0.530 10.970 36739 Z= 0.272 Chirality : 0.041 0.210 4222 Planarity : 0.004 0.122 4556 Dihedral : 13.788 173.415 4431 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 1.59 % Allowed : 16.35 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % 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: -0.15 (0.15), residues: 3179 helix: 1.69 (0.16), residues: 1112 sheet: -0.55 (0.28), residues: 356 loop : -1.27 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 686 HIS 0.004 0.001 HIS J1366 PHE 0.017 0.001 PHE I 337 TYR 0.020 0.001 TYR J1365 ARG 0.006 0.000 ARG I 202 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 1087) hydrogen bonds : angle 4.22081 ( 3002) metal coordination : bond 0.00452 ( 8) metal coordination : angle 2.06399 ( 12) covalent geometry : bond 0.00261 (26956) covalent geometry : angle 0.52850 (36727) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.8326 (mttt) cc_final: 0.8066 (mtmt) REVERT: H 84 ASN cc_start: 0.8278 (m110) cc_final: 0.7497 (m110) REVERT: H 181 GLU cc_start: 0.7578 (tp30) cc_final: 0.7252 (tp30) REVERT: I 32 LEU cc_start: 0.8367 (mm) cc_final: 0.8132 (mm) REVERT: I 119 GLU cc_start: 0.7164 (pm20) cc_final: 0.6691 (pm20) REVERT: I 202 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7665 (ttp-110) REVERT: I 337 PHE cc_start: 0.8057 (t80) cc_final: 0.7844 (t80) REVERT: I 427 ASP cc_start: 0.7887 (m-30) cc_final: 0.7465 (m-30) REVERT: I 488 MET cc_start: 0.3996 (mmt) cc_final: 0.3588 (mmt) REVERT: I 545 PHE cc_start: 0.7270 (m-80) cc_final: 0.7033 (m-80) REVERT: I 562 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8389 (tm-30) REVERT: I 962 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: I 1088 ASP cc_start: 0.8520 (p0) cc_final: 0.7979 (p0) REVERT: I 1170 MET cc_start: 0.8256 (tpt) cc_final: 0.8000 (tpp) REVERT: J 52 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5976 (mm-30) REVERT: J 100 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7669 (tm-30) REVERT: J 130 MET cc_start: 0.7950 (ttp) cc_final: 0.7527 (ttp) REVERT: J 198 CYS cc_start: 0.8181 (t) cc_final: 0.7713 (t) REVERT: J 236 TRP cc_start: 0.8998 (m-10) cc_final: 0.7834 (m-10) REVERT: J 270 ARG cc_start: 0.8677 (ttm110) cc_final: 0.8208 (ttp80) REVERT: J 285 LEU cc_start: 0.8208 (pp) cc_final: 0.7779 (mt) REVERT: J 291 ILE cc_start: 0.8250 (mt) cc_final: 0.8017 (tp) REVERT: J 412 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8526 (tt) REVERT: J 484 MET cc_start: 0.9182 (mtt) cc_final: 0.8724 (mtt) REVERT: J 777 HIS cc_start: 0.8164 (m-70) cc_final: 0.7723 (t-90) REVERT: J 822 MET cc_start: 0.8428 (tpp) cc_final: 0.8133 (tpp) REVERT: J 869 CYS cc_start: 0.8648 (m) cc_final: 0.8145 (m) REVERT: J 870 ASP cc_start: 0.7337 (m-30) cc_final: 0.7000 (m-30) REVERT: J 1344 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8541 (pp) REVERT: K 55 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7487 (tm-30) outliers start: 43 outliers final: 30 residues processed: 314 average time/residue: 0.3669 time to fit residues: 188.0966 Evaluate side-chains 302 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 258 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 286 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 275 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 ASN J1098 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.103284 restraints weight = 43061.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.104616 restraints weight = 25077.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105697 restraints weight = 17403.628| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 26964 Z= 0.149 Angle : 0.552 11.188 36739 Z= 0.283 Chirality : 0.041 0.194 4222 Planarity : 0.004 0.120 4556 Dihedral : 13.825 173.221 4431 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.87 % Rotamer: Outliers : 1.85 % Allowed : 16.57 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % 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: -0.19 (0.15), residues: 3179 helix: 1.62 (0.16), residues: 1112 sheet: -0.62 (0.27), residues: 384 loop : -1.24 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 686 HIS 0.004 0.001 HIS J1366 PHE 0.014 0.001 PHE I 337 TYR 0.023 0.001 TYR J1365 ARG 0.004 0.000 ARG J 311 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 1087) hydrogen bonds : angle 4.23670 ( 3002) metal coordination : bond 0.00687 ( 8) metal coordination : angle 2.14577 ( 12) covalent geometry : bond 0.00349 (26956) covalent geometry : angle 0.55078 (36727) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 270 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.8260 (mttt) cc_final: 0.7991 (mtmt) REVERT: H 84 ASN cc_start: 0.8342 (m110) cc_final: 0.7655 (m-40) REVERT: H 181 GLU cc_start: 0.7628 (tp30) cc_final: 0.7280 (tp30) REVERT: I 119 GLU cc_start: 0.7180 (pm20) cc_final: 0.6696 (pm20) REVERT: I 427 ASP cc_start: 0.7869 (m-30) cc_final: 0.7469 (m-30) REVERT: I 488 MET cc_start: 0.3865 (mmt) cc_final: 0.3291 (mmt) REVERT: I 545 PHE cc_start: 0.7277 (m-80) cc_final: 0.7021 (m-80) REVERT: I 562 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8384 (tm-30) REVERT: I 962 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: I 1170 MET cc_start: 0.8259 (tpt) cc_final: 0.8009 (tpp) REVERT: J 52 GLU cc_start: 0.6198 (mm-30) cc_final: 0.5699 (mm-30) REVERT: J 100 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7672 (tm-30) REVERT: J 130 MET cc_start: 0.7936 (ttp) cc_final: 0.7539 (ttp) REVERT: J 198 CYS cc_start: 0.8205 (t) cc_final: 0.7723 (t) REVERT: J 236 TRP cc_start: 0.9017 (m-10) cc_final: 0.7888 (m-10) REVERT: J 270 ARG cc_start: 0.8696 (ttm110) cc_final: 0.8232 (ttp80) REVERT: J 285 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7838 (mt) REVERT: J 291 ILE cc_start: 0.8254 (mt) cc_final: 0.8024 (tp) REVERT: J 412 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8497 (tt) REVERT: J 466 MET cc_start: 0.8320 (mtp) cc_final: 0.7889 (ptp) REVERT: J 484 MET cc_start: 0.9202 (mtt) cc_final: 0.8804 (mtt) REVERT: J 777 HIS cc_start: 0.8034 (m-70) cc_final: 0.7774 (t-90) REVERT: J 822 MET cc_start: 0.8404 (tpp) cc_final: 0.8171 (tpp) REVERT: J 831 VAL cc_start: 0.5219 (OUTLIER) cc_final: 0.5016 (m) REVERT: J 869 CYS cc_start: 0.8645 (m) cc_final: 0.8110 (m) REVERT: J 870 ASP cc_start: 0.7478 (m-30) cc_final: 0.7099 (m-30) REVERT: J 1344 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8523 (pp) REVERT: K 55 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7201 (tm-30) outliers start: 50 outliers final: 40 residues processed: 303 average time/residue: 0.3537 time to fit residues: 176.4874 Evaluate side-chains 310 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 265 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 chunk 278 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 282 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 226 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 41 ASN G 66 HIS I 65 ASN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100811 restraints weight = 43525.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.100848 restraints weight = 26534.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.101463 restraints weight = 20391.091| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 26964 Z= 0.223 Angle : 0.614 12.503 36739 Z= 0.315 Chirality : 0.043 0.186 4222 Planarity : 0.004 0.119 4556 Dihedral : 13.966 172.955 4431 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer: Outliers : 1.99 % Allowed : 16.83 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % 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: -0.42 (0.15), residues: 3179 helix: 1.33 (0.16), residues: 1126 sheet: -0.67 (0.27), residues: 364 loop : -1.34 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 686 HIS 0.006 0.001 HIS G 23 PHE 0.021 0.002 PHE I 337 TYR 0.025 0.002 TYR J1365 ARG 0.005 0.000 ARG I 368 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 1087) hydrogen bonds : angle 4.41630 ( 3002) metal coordination : bond 0.01135 ( 8) metal coordination : angle 2.82314 ( 12) covalent geometry : bond 0.00522 (26956) covalent geometry : angle 0.61198 (36727) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8464 (m110) cc_final: 0.7789 (m-40) REVERT: H 181 GLU cc_start: 0.7747 (tp30) cc_final: 0.7425 (tp30) REVERT: I 119 GLU cc_start: 0.7674 (pm20) cc_final: 0.7334 (pm20) REVERT: I 129 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9069 (mm) REVERT: I 445 ILE cc_start: 0.8108 (mm) cc_final: 0.7887 (pt) REVERT: I 488 MET cc_start: 0.3935 (mmt) cc_final: 0.3324 (mmt) REVERT: I 962 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: I 1088 ASP cc_start: 0.8595 (p0) cc_final: 0.8029 (p0) REVERT: J 52 GLU cc_start: 0.6155 (mm-30) cc_final: 0.5619 (mm-30) REVERT: J 100 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7745 (tm-30) REVERT: J 130 MET cc_start: 0.8024 (ttp) cc_final: 0.7632 (ttp) REVERT: J 198 CYS cc_start: 0.8275 (t) cc_final: 0.7779 (t) REVERT: J 236 TRP cc_start: 0.9034 (m-10) cc_final: 0.7975 (m-10) REVERT: J 291 ILE cc_start: 0.8190 (mt) cc_final: 0.7935 (tp) REVERT: J 412 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8506 (tt) REVERT: J 777 HIS cc_start: 0.8242 (m-70) cc_final: 0.7902 (t-90) REVERT: J 869 CYS cc_start: 0.8647 (m) cc_final: 0.8146 (m) REVERT: J 870 ASP cc_start: 0.7474 (m-30) cc_final: 0.7057 (m-30) REVERT: J 983 LYS cc_start: 0.5893 (mmtt) cc_final: 0.5689 (mmtt) outliers start: 54 outliers final: 42 residues processed: 310 average time/residue: 0.3457 time to fit residues: 177.2017 Evaluate side-chains 307 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 262 optimal weight: 6.9990 chunk 307 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 246 optimal weight: 0.0370 chunk 181 optimal weight: 2.9990 chunk 169 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.103710 restraints weight = 42852.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105404 restraints weight = 24730.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105556 restraints weight = 17988.750| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 26964 Z= 0.125 Angle : 0.545 11.476 36739 Z= 0.279 Chirality : 0.041 0.189 4222 Planarity : 0.004 0.118 4556 Dihedral : 13.832 172.020 4431 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.22 % Rotamer: Outliers : 1.62 % Allowed : 17.35 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % 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: -0.24 (0.15), residues: 3179 helix: 1.60 (0.16), residues: 1106 sheet: -0.55 (0.27), residues: 388 loop : -1.32 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I1276 HIS 0.004 0.001 HIS J1366 PHE 0.022 0.001 PHE I 337 TYR 0.022 0.001 TYR J1365 ARG 0.006 0.000 ARG I 478 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 1087) hydrogen bonds : angle 4.24895 ( 3002) metal coordination : bond 0.00523 ( 8) metal coordination : angle 2.11994 ( 12) covalent geometry : bond 0.00289 (26956) covalent geometry : angle 0.54376 (36727) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7916 (tm-30) REVERT: H 84 ASN cc_start: 0.8317 (m110) cc_final: 0.7607 (m-40) REVERT: H 181 GLU cc_start: 0.7626 (tp30) cc_final: 0.7281 (tp30) REVERT: I 32 LEU cc_start: 0.8424 (mm) cc_final: 0.8181 (mm) REVERT: I 119 GLU cc_start: 0.7539 (pm20) cc_final: 0.7184 (pm20) REVERT: I 129 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9036 (mm) REVERT: I 218 GLU cc_start: 0.7845 (pp20) cc_final: 0.7540 (pp20) REVERT: I 427 ASP cc_start: 0.7859 (m-30) cc_final: 0.7443 (m-30) REVERT: I 488 MET cc_start: 0.4194 (mmt) cc_final: 0.3704 (mmt) REVERT: I 545 PHE cc_start: 0.7309 (m-80) cc_final: 0.7061 (m-80) REVERT: I 562 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8338 (tm-30) REVERT: I 947 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: I 962 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: I 1170 MET cc_start: 0.8262 (tpt) cc_final: 0.8011 (tpp) REVERT: J 52 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5626 (mm-30) REVERT: J 100 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7652 (tm-30) REVERT: J 130 MET cc_start: 0.7902 (ttp) cc_final: 0.7500 (ttp) REVERT: J 180 MET cc_start: 0.7823 (tpt) cc_final: 0.7553 (tpt) REVERT: J 198 CYS cc_start: 0.8215 (t) cc_final: 0.7731 (t) REVERT: J 236 TRP cc_start: 0.9033 (m-10) cc_final: 0.7943 (m-10) REVERT: J 285 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7778 (mt) REVERT: J 291 ILE cc_start: 0.8264 (mt) cc_final: 0.8052 (tp) REVERT: J 412 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8441 (tt) REVERT: J 484 MET cc_start: 0.8882 (mtt) cc_final: 0.8401 (mtt) REVERT: J 777 HIS cc_start: 0.8032 (m-70) cc_final: 0.7782 (t-90) REVERT: J 869 CYS cc_start: 0.8644 (m) cc_final: 0.8128 (m) REVERT: J 870 ASP cc_start: 0.7337 (m-30) cc_final: 0.6944 (m-30) REVERT: J 983 LYS cc_start: 0.5888 (mmtt) cc_final: 0.5678 (mmtt) outliers start: 44 outliers final: 33 residues processed: 303 average time/residue: 0.3387 time to fit residues: 169.8522 Evaluate side-chains 305 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 947 GLU Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 10 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 303 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 164 optimal weight: 0.0050 chunk 49 optimal weight: 8.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 41 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1098 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.102185 restraints weight = 43036.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.103766 restraints weight = 24446.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105127 restraints weight = 16372.452| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 26964 Z= 0.149 Angle : 0.556 11.320 36739 Z= 0.284 Chirality : 0.041 0.185 4222 Planarity : 0.004 0.117 4556 Dihedral : 13.869 171.980 4431 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 1.70 % Allowed : 17.39 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % 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: -0.29 (0.15), residues: 3179 helix: 1.51 (0.16), residues: 1119 sheet: -0.63 (0.26), residues: 393 loop : -1.32 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 686 HIS 0.004 0.001 HIS J1366 PHE 0.022 0.001 PHE I 337 TYR 0.023 0.001 TYR J1365 ARG 0.006 0.000 ARG I 478 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 1087) hydrogen bonds : angle 4.24798 ( 3002) metal coordination : bond 0.00670 ( 8) metal coordination : angle 2.19591 ( 12) covalent geometry : bond 0.00348 (26956) covalent geometry : angle 0.55491 (36727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7502.12 seconds wall clock time: 131 minutes 47.32 seconds (7907.32 seconds total)