Starting phenix.real_space_refine on Thu Feb 22 02:30:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftd_29423/02_2024/8ftd_29423_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftd_29423/02_2024/8ftd_29423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftd_29423/02_2024/8ftd_29423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftd_29423/02_2024/8ftd_29423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftd_29423/02_2024/8ftd_29423_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ftd_29423/02_2024/8ftd_29423_updated.pdb" } resolution = 2.76 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= 0.004 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 87 atoms to isotropic. 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 117 5.49 5 Mg 1 5.21 5 S 133 5.16 5 C 20054 2.51 5 N 5751 2.21 5 O 6471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 12": "NH1" <-> "NH2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H GLU 229": "OE1" <-> "OE2" Residue "I GLU 1006": "OE1" <-> "OE2" Residue "J GLU 1168": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32529 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1789 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1681 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10575 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10386 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3812 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 455} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 1252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1252 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain breaks: 1 Chain: "Q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1142 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain breaks: 1 Chain: "R" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain: "Z" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 603 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 6, 'TRANS': 66} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14494 SG CYS J 70 101.969 62.929 73.551 1.00133.93 S ATOM 14508 SG CYS J 72 99.763 60.771 71.305 1.00132.75 S ATOM 14616 SG CYS J 85 103.108 61.951 70.042 1.00132.39 S ATOM 14640 SG CYS J 88 100.313 64.497 70.569 1.00131.77 S ATOM 20328 SG CYS J 814 124.449 117.562 108.315 1.00128.67 S ATOM 20893 SG CYS J 888 121.123 116.038 107.248 1.00127.41 S ATOM 20944 SG CYS J 895 122.722 114.917 110.519 1.00119.54 S ATOM 20965 SG CYS J 898 121.292 118.386 110.225 1.00121.44 S Time building chain proxies: 18.03, per 1000 atoms: 0.55 Number of scatterers: 32529 At special positions: 0 Unit cell: (154.212, 189.144, 193.404, 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 133 16.00 P 117 15.00 Mg 1 11.99 O 6471 8.00 N 5751 7.00 C 20054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.77 Conformation dependent library (CDL) restraints added in 5.5 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 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 36 sheets defined 37.4% alpha, 10.3% beta 33 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 14.76 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 removed outlier: 3.648A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 87 removed outlier: 3.860A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 158 No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 213 through 229 removed outlier: 3.589A pdb=" N ALA G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU G 226 " --> pdb=" O THR G 222 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 removed outlier: 3.580A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 87 removed outlier: 3.861A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 228 Processing helix chain 'I' and resid 5 through 8 No H-bonds generated for 'chain 'I' and resid 5 through 8' Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 207 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 245 No H-bonds generated for 'chain 'I' and resid 243 through 245' Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 289 through 291 No H-bonds generated for 'chain 'I' and resid 289 through 291' Processing helix chain 'I' and resid 319 through 326 Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 4.111A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 448 through 450 No H-bonds generated for 'chain 'I' and resid 448 through 450' Processing helix chain 'I' and resid 456 through 481 removed outlier: 3.614A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 Processing helix chain 'I' and resid 520 through 528 removed outlier: 3.616A pdb=" N LYS I 527 " --> pdb=" O GLU I 523 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 608 through 613 removed outlier: 3.853A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.050A 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 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' Processing helix chain 'I' and resid 665 through 667 No H-bonds generated for 'chain 'I' and resid 665 through 667' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 688 removed outlier: 4.209A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 738 through 740 No H-bonds generated for 'chain 'I' and resid 738 through 740' Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 859 through 861 No H-bonds generated for 'chain 'I' and resid 859 through 861' Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 943 through 981 Processing helix chain 'I' and resid 994 through 997 No H-bonds generated for 'chain 'I' and resid 994 through 997' Processing helix chain 'I' and resid 1008 through 1037 removed outlier: 4.058A pdb=" N LEU I1011 " --> pdb=" O GLN I1008 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLN I1013 " --> pdb=" O GLN I1010 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA I1015 " --> pdb=" O GLU I1012 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU I1016 " --> pdb=" O GLN I1013 " (cutoff:3.500A) Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1106 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 through 1134 Processing helix chain 'I' and resid 1139 through 1150 Processing helix chain 'I' and resid 1166 through 1175 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1241 No H-bonds generated for 'chain 'I' and resid 1239 through 1241' Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1298 through 1310 removed outlier: 3.813A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1332 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 59 through 62 No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 114 through 118 Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 182 through 191 Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 247 through 250 Processing helix chain 'J' and resid 264 through 284 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 4.274A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 457 removed outlier: 4.245A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 581 removed outlier: 4.025A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 592 Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 650 through 669 Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 740 Processing helix chain 'J' and resid 769 through 801 removed outlier: 3.789A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 839 Processing helix chain 'J' and resid 866 through 875 Processing helix chain 'J' and resid 885 through 887 No H-bonds generated for 'chain 'J' and resid 885 through 887' Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 929 Proline residue: J 926 - end of helix removed outlier: 5.458A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1070 through 1073 removed outlier: 4.148A pdb=" N ASP J1073 " --> pdb=" O GLY J1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1070 through 1073' Processing helix chain 'J' and resid 1139 through 1146 Processing helix chain 'J' and resid 1217 through 1244 removed outlier: 7.889A pdb=" N VAL J1226 " --> pdb=" O ARG J1222 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N HIS J1227 " --> pdb=" O LEU J1223 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA J1228 " --> pdb=" O ARG J1224 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1314 Processing helix chain 'J' and resid 1319 through 1325 Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 3.844A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 79 removed outlier: 4.442A pdb=" N GLU K 79 " --> pdb=" O GLN K 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 106 Processing helix chain 'L' and resid 113 through 135 Processing helix chain 'L' and resid 138 through 152 Processing helix chain 'L' and resid 215 through 232 Processing helix chain 'L' and resid 245 through 257 Processing helix chain 'L' and resid 263 through 291 removed outlier: 3.624A pdb=" N CYS L 291 " --> pdb=" O ILE L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 306 Processing helix chain 'L' and resid 331 through 351 removed outlier: 3.981A pdb=" N GLU L 335 " --> pdb=" O HIS L 331 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU L 336 " --> pdb=" O ASP L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 394 removed outlier: 5.115A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS L 393 " --> pdb=" O SER L 389 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR L 394 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 418 removed outlier: 3.530A pdb=" N LYS L 418 " --> pdb=" O LYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 427 through 445 removed outlier: 4.057A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 474 Processing helix chain 'L' and resid 480 through 486 removed outlier: 3.905A pdb=" N ALA L 484 " --> pdb=" O PRO L 480 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG L 486 " --> pdb=" O GLU L 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 480 through 486' Processing helix chain 'L' and resid 493 through 499 Processing helix chain 'L' and resid 519 through 522 Processing helix chain 'L' and resid 531 through 550 Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 580 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'L' and resid 605 through 610 Processing helix chain 'R' and resid 257 through 260 Processing helix chain 'R' and resid 264 through 273 Processing helix chain 'R' and resid 278 through 283 removed outlier: 4.317A pdb=" N GLN R 283 " --> pdb=" O GLY R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 291 Processing helix chain 'R' and resid 297 through 309 Processing helix chain 'Z' and resid 62 through 75 Processing sheet with id= A, first strand: chain 'G' and resid 12 through 15 removed outlier: 3.856A pdb=" N GLU G 29 " --> pdb=" O ARG G 12 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU G 201 " --> pdb=" O LEU G 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 170 through 172 removed outlier: 3.814A pdb=" N GLN G 147 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.566A pdb=" N GLY G 151 " --> pdb=" O TYR G 177 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA G 175 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 109 through 111 removed outlier: 3.658A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 23 through 27 removed outlier: 3.624A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA H 184 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 90 through 92 Processing sheet with id= H, first strand: chain 'H' and resid 97 through 105 removed outlier: 6.015A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 109 through 111 removed outlier: 3.657A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= K, first strand: chain 'I' and resid 116 through 123 removed outlier: 6.015A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= M, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= N, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.633A pdb=" N ASN I 173 " --> pdb=" O ASP I 158 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 227 through 230 Processing sheet with id= P, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= Q, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= R, first strand: chain 'I' and resid 748 through 752 removed outlier: 5.936A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 1227 through 1232 removed outlier: 6.615A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= U, first strand: chain 'I' and resid 1065 through 1067 Processing sheet with id= V, first strand: chain 'I' and resid 255 through 257 removed outlier: 4.316A pdb=" N ILE I 255 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.557A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 19 through 21 Processing sheet with id= Y, first strand: chain 'J' and resid 103 through 106 Processing sheet with id= Z, first strand: chain 'J' and resid 145 through 147 removed outlier: 3.801A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 446 through 448 removed outlier: 8.140A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= AC, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.822A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AE, first strand: chain 'J' and resid 1024 through 1026 removed outlier: 3.847A pdb=" N MET J1025 " --> pdb=" O ILE J1124 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE J1124 " --> pdb=" O MET J1025 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.788A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER J1058 " --> pdb=" O GLN J1049 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 1077 through 1079 Processing sheet with id= AH, first strand: chain 'J' and resid 1162 through 1165 removed outlier: 3.825A pdb=" N VAL J1176 " --> pdb=" O SER J1164 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.161A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Z' and resid 46 through 49 removed outlier: 4.392A pdb=" N VAL Z 47 " --> pdb=" O LEU Z 54 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU Z 54 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET Z 49 " --> pdb=" O SER Z 52 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER Z 52 " --> pdb=" O MET Z 49 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ 1065 hydrogen bonds defined for protein. 3027 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 13.50 Time building geometry restraints manager: 15.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5469 1.32 - 1.44: 8425 1.44 - 1.56: 18907 1.56 - 1.69: 230 1.69 - 1.81: 234 Bond restraints: 33265 Sorted by residual: bond pdb=" CA GLU G 229 " pdb=" C GLU G 229 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.35e-02 5.49e+03 1.90e+01 bond pdb=" CA THR H 38 " pdb=" C THR H 38 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.34e-02 5.57e+03 1.40e+01 bond pdb=" CA GLN G 227 " pdb=" C GLN G 227 " ideal model delta sigma weight residual 1.522 1.472 0.050 1.41e-02 5.03e+03 1.24e+01 bond pdb=" C THR H 38 " pdb=" O THR H 38 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.26e-02 6.30e+03 1.17e+01 bond pdb=" CA LEU H 9 " pdb=" C LEU H 9 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.23e-02 6.61e+03 1.11e+01 ... (remaining 33260 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.57: 1524 106.57 - 113.44: 18289 113.44 - 120.30: 12066 120.30 - 127.16: 13129 127.16 - 134.03: 429 Bond angle restraints: 45437 Sorted by residual: angle pdb=" C LEU G 228 " pdb=" N GLU G 229 " pdb=" CA GLU G 229 " ideal model delta sigma weight residual 120.38 110.49 9.89 1.37e+00 5.33e-01 5.22e+01 angle pdb=" N ASP I1004 " pdb=" CA ASP I1004 " pdb=" C ASP I1004 " ideal model delta sigma weight residual 113.37 103.50 9.87 1.38e+00 5.25e-01 5.12e+01 angle pdb=" N GLU I 50 " pdb=" CA GLU I 50 " pdb=" C GLU I 50 " ideal model delta sigma weight residual 111.28 103.79 7.49 1.09e+00 8.42e-01 4.72e+01 angle pdb=" N ASP I 234 " pdb=" CA ASP I 234 " pdb=" C ASP I 234 " ideal model delta sigma weight residual 110.24 100.60 9.64 1.41e+00 5.03e-01 4.67e+01 angle pdb=" N VAL G 232 " pdb=" CA VAL G 232 " pdb=" C VAL G 232 " ideal model delta sigma weight residual 110.09 100.49 9.60 1.50e+00 4.44e-01 4.10e+01 ... (remaining 45432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.86: 18663 26.86 - 53.72: 1475 53.72 - 80.57: 195 80.57 - 107.43: 16 107.43 - 134.29: 4 Dihedral angle restraints: 20353 sinusoidal: 9340 harmonic: 11013 Sorted by residual: dihedral pdb=" CA GLN H 93 " pdb=" C GLN H 93 " pdb=" N GLY H 94 " pdb=" CA GLY H 94 " ideal model delta harmonic sigma weight residual 180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLN G 93 " pdb=" C GLN G 93 " pdb=" N GLY G 94 " pdb=" CA GLY G 94 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C22 1N7 I1401 " pdb=" C23 1N7 I1401 " pdb=" C24 1N7 I1401 " pdb=" N1 1N7 I1401 " ideal model delta sinusoidal sigma weight residual 227.30 93.01 134.29 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 20350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4098 0.045 - 0.090: 808 0.090 - 0.134: 277 0.134 - 0.179: 9 0.179 - 0.224: 4 Chirality restraints: 5196 Sorted by residual: chirality pdb=" CG LEU I1000 " pdb=" CB LEU I1000 " pdb=" CD1 LEU I1000 " pdb=" CD2 LEU I1000 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA PRO H 30 " pdb=" N PRO H 30 " pdb=" C PRO H 30 " pdb=" CB PRO H 30 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA VAL G 232 " pdb=" N VAL G 232 " pdb=" C VAL G 232 " pdb=" CB VAL G 232 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.72e-01 ... (remaining 5193 not shown) Planarity restraints: 5512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 29 " -0.104 5.00e-02 4.00e+02 1.55e-01 3.82e+01 pdb=" N PRO H 30 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO H 30 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO H 30 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR G 27 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C THR G 27 " 0.060 2.00e-02 2.50e+03 pdb=" O THR G 27 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU G 28 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS H 176 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C CYS H 176 " -0.049 2.00e-02 2.50e+03 pdb=" O CYS H 176 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR H 177 " 0.016 2.00e-02 2.50e+03 ... (remaining 5509 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 764 2.68 - 3.24: 29702 3.24 - 3.79: 50187 3.79 - 4.35: 64580 4.35 - 4.90: 106653 Nonbonded interactions: 251886 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.126 2.170 nonbonded pdb=" N GLN G 194 " pdb=" OE1 GLN G 194 " model vdw 2.143 2.520 nonbonded pdb=" O ARG G 45 " pdb=" OG SER G 49 " model vdw 2.204 2.440 nonbonded pdb=" OG SER J1271 " pdb=" O VAL J1298 " model vdw 2.218 2.440 nonbonded pdb=" NH1 ARG I1223 " pdb=" OG SER J 721 " model vdw 2.231 2.520 ... (remaining 251881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and ((resid 5 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 158 or resid 171 through 233 or (resid 234 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 5 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 234)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 12.630 Check model and map are aligned: 0.500 Set scattering table: 0.330 Process input model: 102.690 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33265 Z= 0.224 Angle : 0.581 9.894 45437 Z= 0.348 Chirality : 0.040 0.224 5196 Planarity : 0.004 0.155 5512 Dihedral : 17.818 134.288 13249 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 2.88 % Allowed : 9.77 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3797 helix: 1.38 (0.14), residues: 1518 sheet: 0.13 (0.27), residues: 405 loop : -1.15 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 686 HIS 0.007 0.001 HIS G 23 PHE 0.011 0.001 PHE G 8 TYR 0.017 0.001 TYR G 177 ARG 0.004 0.000 ARG I 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 569 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.7148 (mtmm) cc_final: 0.6861 (ttpp) REVERT: G 120 ASP cc_start: 0.7522 (m-30) cc_final: 0.7204 (m-30) REVERT: G 226 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6662 (mm-30) REVERT: H 15 ASP cc_start: 0.6607 (OUTLIER) cc_final: 0.5479 (p0) REVERT: H 120 ASP cc_start: 0.6478 (m-30) cc_final: 0.5600 (p0) REVERT: H 197 ASP cc_start: 0.6711 (t0) cc_final: 0.6424 (p0) REVERT: H 218 ARG cc_start: 0.5479 (mtp-110) cc_final: 0.5192 (mtt90) REVERT: I 119 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7296 (tm-30) REVERT: I 414 ILE cc_start: 0.8419 (pt) cc_final: 0.7698 (mm) REVERT: I 441 GLU cc_start: 0.7199 (tp30) cc_final: 0.6940 (mp0) REVERT: I 583 GLU cc_start: 0.7382 (tt0) cc_final: 0.6949 (tt0) REVERT: I 658 GLN cc_start: 0.6223 (mt0) cc_final: 0.5973 (pt0) REVERT: I 687 ARG cc_start: 0.7265 (ptt90) cc_final: 0.6999 (mtm-85) REVERT: I 742 TYR cc_start: 0.6695 (m-10) cc_final: 0.6327 (m-10) REVERT: I 778 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6757 (mm-30) REVERT: I 919 ARG cc_start: 0.8049 (ptp-110) cc_final: 0.7725 (mtp85) REVERT: I 958 LYS cc_start: 0.6593 (tttt) cc_final: 0.6374 (tttm) REVERT: I 998 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6623 (pt) REVERT: I 1006 GLU cc_start: 0.3190 (OUTLIER) cc_final: 0.2637 (pm20) REVERT: I 1020 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6141 (tp30) REVERT: I 1080 ASN cc_start: 0.7426 (m110) cc_final: 0.7175 (m-40) REVERT: I 1119 MET cc_start: 0.5978 (tpt) cc_final: 0.5225 (ttt) REVERT: I 1137 GLU cc_start: 0.6347 (mp0) cc_final: 0.6032 (mp0) REVERT: I 1211 ARG cc_start: 0.7265 (ttm170) cc_final: 0.6461 (mmt180) REVERT: I 1321 GLU cc_start: 0.6250 (tp30) cc_final: 0.5786 (tp30) REVERT: J 81 ARG cc_start: 0.7862 (tmm-80) cc_final: 0.7232 (ptm160) REVERT: J 192 MET cc_start: 0.7124 (ttm) cc_final: 0.6919 (ptm) REVERT: J 314 ARG cc_start: 0.7856 (ptp-170) cc_final: 0.7004 (ptm-80) REVERT: J 322 ARG cc_start: 0.7037 (mtp85) cc_final: 0.5702 (mtp-110) REVERT: J 329 ASP cc_start: 0.6664 (m-30) cc_final: 0.5978 (m-30) REVERT: J 464 ASP cc_start: 0.8480 (m-30) cc_final: 0.8217 (m-30) REVERT: J 562 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6381 (tp30) REVERT: J 603 LYS cc_start: 0.6959 (mtmt) cc_final: 0.6741 (mmpt) REVERT: J 802 ASP cc_start: 0.7079 (t0) cc_final: 0.6454 (m-30) REVERT: J 874 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6980 (tt0) REVERT: J 1152 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6521 (pm20) REVERT: J 1278 GLU cc_start: 0.6453 (tt0) cc_final: 0.5932 (tp30) REVERT: K 11 GLU cc_start: 0.6696 (tm-30) cc_final: 0.6325 (mt-10) REVERT: K 43 ASN cc_start: 0.6996 (t0) cc_final: 0.6705 (t0) REVERT: K 55 GLU cc_start: 0.6525 (tt0) cc_final: 0.6245 (mt-10) REVERT: L 133 SER cc_start: 0.4121 (m) cc_final: 0.3759 (p) REVERT: L 244 THR cc_start: 0.3005 (OUTLIER) cc_final: 0.2784 (t) REVERT: L 259 PHE cc_start: 0.6654 (m-10) cc_final: 0.6374 (m-80) REVERT: L 278 ASP cc_start: 0.7262 (m-30) cc_final: 0.7062 (t70) REVERT: L 297 MET cc_start: 0.0897 (ppp) cc_final: 0.0634 (mtt) REVERT: L 322 MET cc_start: 0.2538 (ptt) cc_final: 0.1989 (ttp) REVERT: L 482 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7102 (mt-10) REVERT: L 485 GLU cc_start: 0.7247 (mp0) cc_final: 0.6986 (tt0) REVERT: L 561 MET cc_start: 0.5859 (mmt) cc_final: 0.5396 (ttm) REVERT: R 316 MET cc_start: 0.1620 (ppp) cc_final: 0.0888 (pmm) REVERT: Z 38 MET cc_start: 0.3921 (mmp) cc_final: 0.3569 (mmt) REVERT: Z 49 MET cc_start: 0.4216 (mmm) cc_final: 0.3520 (tmt) outliers start: 94 outliers final: 13 residues processed: 639 average time/residue: 1.5749 time to fit residues: 1176.0858 Evaluate side-chains 356 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 338 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 30 PRO Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 195 ARG Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1006 GLU Chi-restraints excluded: chain I residue 1020 GLU Chi-restraints excluded: chain I residue 1105 SER Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain Z residue 44 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 305 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 185 optimal weight: 0.3980 chunk 227 optimal weight: 3.9990 chunk 354 optimal weight: 0.6980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 37 HIS H 41 ASN I 60 GLN I 83 GLN I 238 GLN I 314 ASN I 339 ASN I 517 GLN I 955 GLN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 GLN J 335 GLN J 430 HIS J 504 GLN J 817 HIS J 875 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 33265 Z= 0.216 Angle : 0.570 11.804 45437 Z= 0.298 Chirality : 0.042 0.242 5196 Planarity : 0.005 0.138 5512 Dihedral : 16.156 132.030 5726 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 3.25 % Allowed : 15.49 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3797 helix: 1.78 (0.14), residues: 1501 sheet: 0.35 (0.27), residues: 361 loop : -1.07 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J1193 HIS 0.009 0.001 HIS G 23 PHE 0.016 0.002 PHE I 35 TYR 0.018 0.001 TYR J 631 ARG 0.007 0.001 ARG I1246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 366 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: G 117 HIS cc_start: 0.6680 (OUTLIER) cc_final: 0.5864 (p-80) REVERT: G 139 SER cc_start: 0.8070 (m) cc_final: 0.7752 (p) REVERT: H 15 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6326 (t0) REVERT: H 122 GLU cc_start: 0.7444 (tt0) cc_final: 0.7231 (tm-30) REVERT: H 204 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: H 214 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6550 (tp30) REVERT: H 219 ARG cc_start: 0.6087 (mtm-85) cc_final: 0.5801 (mtm-85) REVERT: I 119 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7247 (tm-30) REVERT: I 231 GLU cc_start: 0.6362 (mm-30) cc_final: 0.6010 (tp30) REVERT: I 583 GLU cc_start: 0.7316 (tt0) cc_final: 0.6965 (tt0) REVERT: I 658 GLN cc_start: 0.6697 (mt0) cc_final: 0.6402 (pt0) REVERT: I 681 MET cc_start: 0.7209 (mtp) cc_final: 0.6844 (mtt) REVERT: I 694 ARG cc_start: 0.5833 (mtt180) cc_final: 0.5472 (mtm180) REVERT: I 742 TYR cc_start: 0.6818 (m-80) cc_final: 0.6396 (m-10) REVERT: I 778 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6822 (mm-30) REVERT: I 854 ILE cc_start: 0.7612 (mm) cc_final: 0.7385 (mm) REVERT: I 908 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: I 955 GLN cc_start: 0.6497 (tp40) cc_final: 0.6202 (mm110) REVERT: I 1080 ASN cc_start: 0.8059 (m110) cc_final: 0.7844 (m-40) REVERT: I 1137 GLU cc_start: 0.6436 (mp0) cc_final: 0.6209 (mp0) REVERT: I 1211 ARG cc_start: 0.7288 (ttm170) cc_final: 0.6441 (mmt180) REVERT: I 1220 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: I 1321 GLU cc_start: 0.6279 (tp30) cc_final: 0.5840 (tp30) REVERT: J 81 ARG cc_start: 0.7929 (tmm-80) cc_final: 0.7306 (ptm160) REVERT: J 183 GLU cc_start: 0.6623 (tt0) cc_final: 0.6307 (mp0) REVERT: J 227 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.6500 (t80) REVERT: J 314 ARG cc_start: 0.7904 (ptp-170) cc_final: 0.6818 (ptm-80) REVERT: J 322 ARG cc_start: 0.6970 (mtp85) cc_final: 0.5827 (mtp-110) REVERT: J 340 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6585 (tp-100) REVERT: J 443 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7427 (mm-30) REVERT: J 562 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6282 (tp30) REVERT: J 603 LYS cc_start: 0.6767 (mtmt) cc_final: 0.6540 (mmpt) REVERT: J 648 GLU cc_start: 0.7852 (mp0) cc_final: 0.7533 (pt0) REVERT: J 663 GLU cc_start: 0.6544 (tm-30) cc_final: 0.6036 (tt0) REVERT: J 802 ASP cc_start: 0.7337 (t0) cc_final: 0.6720 (m-30) REVERT: J 820 ILE cc_start: 0.7542 (mm) cc_final: 0.7306 (tt) REVERT: J 1040 MET cc_start: 0.2990 (mtt) cc_final: 0.2410 (pmm) REVERT: J 1152 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6651 (pm20) REVERT: J 1169 THR cc_start: 0.4892 (OUTLIER) cc_final: 0.4472 (p) REVERT: J 1262 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6724 (mtm180) REVERT: J 1327 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: K 11 GLU cc_start: 0.6645 (tm-30) cc_final: 0.6324 (mt-10) REVERT: K 43 ASN cc_start: 0.7247 (t0) cc_final: 0.6760 (t0) REVERT: K 55 GLU cc_start: 0.6620 (tt0) cc_final: 0.6280 (mt-10) REVERT: K 56 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6141 (mp0) REVERT: L 244 THR cc_start: 0.2711 (OUTLIER) cc_final: 0.2497 (t) REVERT: L 259 PHE cc_start: 0.6657 (m-10) cc_final: 0.6434 (m-80) REVERT: L 260 ARG cc_start: 0.5639 (tpp-160) cc_final: 0.4991 (ttm110) REVERT: L 265 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7189 (mm-40) REVERT: L 284 GLU cc_start: 0.4620 (OUTLIER) cc_final: 0.4275 (pt0) REVERT: L 297 MET cc_start: 0.1401 (ppp) cc_final: 0.1004 (mtt) REVERT: L 322 MET cc_start: 0.2643 (ptt) cc_final: 0.2073 (ttp) REVERT: L 482 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7359 (mt-10) REVERT: L 485 GLU cc_start: 0.7397 (mp0) cc_final: 0.7119 (tt0) REVERT: L 524 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6676 (pp20) REVERT: L 525 ASP cc_start: 0.7405 (t0) cc_final: 0.7039 (t70) REVERT: L 561 MET cc_start: 0.5747 (mmt) cc_final: 0.5113 (ttm) REVERT: L 608 ARG cc_start: 0.6778 (tpp80) cc_final: 0.6091 (mtt90) REVERT: R 316 MET cc_start: 0.1546 (ppp) cc_final: 0.0764 (pmm) REVERT: Z 38 MET cc_start: 0.3961 (mmp) cc_final: 0.3544 (mmt) REVERT: Z 49 MET cc_start: 0.4192 (mmm) cc_final: 0.3634 (tmt) outliers start: 106 outliers final: 35 residues processed: 440 average time/residue: 1.6253 time to fit residues: 831.7510 Evaluate side-chains 355 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 305 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 1000 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1327 GLU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 294 optimal weight: 0.7980 chunk 241 optimal weight: 0.4980 chunk 97 optimal weight: 7.9990 chunk 354 optimal weight: 0.0770 chunk 383 optimal weight: 10.0000 chunk 315 optimal weight: 7.9990 chunk 351 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 284 optimal weight: 0.2980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 103 ASN I 83 GLN I 238 GLN I 339 ASN I 494 ASN I 517 GLN I 628 HIS ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1010 GLN I1038 GLN J 430 HIS J 817 HIS ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 33265 Z= 0.157 Angle : 0.495 13.628 45437 Z= 0.260 Chirality : 0.039 0.227 5196 Planarity : 0.004 0.133 5512 Dihedral : 15.985 131.088 5700 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.76 % Rotamer: Outliers : 2.91 % Allowed : 17.39 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3797 helix: 1.95 (0.14), residues: 1496 sheet: 0.29 (0.26), residues: 382 loop : -0.98 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J1193 HIS 0.007 0.001 HIS G 23 PHE 0.014 0.001 PHE I 337 TYR 0.018 0.001 TYR J 46 ARG 0.007 0.000 ARG Z 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 320 time to evaluate : 3.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 91 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.5527 (ttm170) REVERT: G 117 HIS cc_start: 0.6701 (OUTLIER) cc_final: 0.5888 (p-80) REVERT: H 12 ARG cc_start: 0.5348 (OUTLIER) cc_final: 0.5068 (ptp-170) REVERT: H 15 ASP cc_start: 0.6277 (OUTLIER) cc_final: 0.5923 (t0) REVERT: H 51 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8381 (mtp) REVERT: H 76 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: H 143 ARG cc_start: 0.7501 (mtp180) cc_final: 0.7255 (mtp180) REVERT: H 219 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5878 (mtm-85) REVERT: I 119 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7250 (mm-30) REVERT: I 583 GLU cc_start: 0.7330 (tt0) cc_final: 0.7030 (tt0) REVERT: I 641 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7371 (mm-30) REVERT: I 658 GLN cc_start: 0.6648 (mt0) cc_final: 0.6415 (pt0) REVERT: I 681 MET cc_start: 0.7258 (mtp) cc_final: 0.6941 (mtt) REVERT: I 694 ARG cc_start: 0.5559 (mtt180) cc_final: 0.5214 (mtm180) REVERT: I 742 TYR cc_start: 0.6869 (m-80) cc_final: 0.6420 (m-10) REVERT: I 778 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6897 (mm-30) REVERT: I 854 ILE cc_start: 0.7571 (mm) cc_final: 0.7311 (mp) REVERT: I 908 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: I 1137 GLU cc_start: 0.6313 (mp0) cc_final: 0.6073 (mp0) REVERT: I 1211 ARG cc_start: 0.7335 (ttm170) cc_final: 0.6452 (mmt180) REVERT: I 1220 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: I 1321 GLU cc_start: 0.6094 (tp30) cc_final: 0.5675 (tp30) REVERT: J 60 ARG cc_start: 0.7097 (ttt90) cc_final: 0.6678 (ttp80) REVERT: J 81 ARG cc_start: 0.7970 (tmm-80) cc_final: 0.7324 (ptm160) REVERT: J 183 GLU cc_start: 0.6487 (tt0) cc_final: 0.6100 (mp0) REVERT: J 227 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6370 (t80) REVERT: J 314 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.6769 (ptm-80) REVERT: J 322 ARG cc_start: 0.6917 (mtp85) cc_final: 0.5754 (mtp-110) REVERT: J 562 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6250 (tp30) REVERT: J 603 LYS cc_start: 0.6713 (mtmt) cc_final: 0.6496 (mmpt) REVERT: J 644 MET cc_start: 0.7976 (mpp) cc_final: 0.7532 (mtt) REVERT: J 648 GLU cc_start: 0.7740 (mp0) cc_final: 0.7502 (pt0) REVERT: J 664 ILE cc_start: 0.5878 (OUTLIER) cc_final: 0.5596 (mm) REVERT: J 802 ASP cc_start: 0.7140 (t0) cc_final: 0.6684 (m-30) REVERT: J 1040 MET cc_start: 0.2295 (mtt) cc_final: 0.1840 (pmm) REVERT: J 1152 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6602 (pm20) REVERT: J 1169 THR cc_start: 0.4991 (OUTLIER) cc_final: 0.4405 (p) REVERT: J 1177 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6507 (mp) REVERT: K 11 GLU cc_start: 0.6671 (tm-30) cc_final: 0.6365 (mt-10) REVERT: K 43 ASN cc_start: 0.7194 (t0) cc_final: 0.6707 (t0) REVERT: K 55 GLU cc_start: 0.6591 (tt0) cc_final: 0.6255 (mt-10) REVERT: K 56 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6109 (mp0) REVERT: L 244 THR cc_start: 0.2733 (OUTLIER) cc_final: 0.2522 (t) REVERT: L 259 PHE cc_start: 0.6662 (m-10) cc_final: 0.6423 (m-80) REVERT: L 260 ARG cc_start: 0.5665 (tpp-160) cc_final: 0.5030 (ttm110) REVERT: L 265 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7113 (mm-40) REVERT: L 266 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: L 277 MET cc_start: 0.6022 (tpp) cc_final: 0.5248 (tpp) REVERT: L 284 GLU cc_start: 0.4426 (OUTLIER) cc_final: 0.3754 (pt0) REVERT: L 297 MET cc_start: 0.1706 (ppp) cc_final: 0.1317 (mpt) REVERT: L 322 MET cc_start: 0.2732 (ptt) cc_final: 0.2092 (ttm) REVERT: L 425 TYR cc_start: 0.7979 (m-80) cc_final: 0.7733 (m-80) REVERT: L 482 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7443 (mt-10) REVERT: L 485 GLU cc_start: 0.7423 (mp0) cc_final: 0.7155 (tt0) REVERT: L 561 MET cc_start: 0.5659 (mmt) cc_final: 0.4933 (ttm) REVERT: L 608 ARG cc_start: 0.6861 (tpp80) cc_final: 0.6180 (mtt90) REVERT: R 316 MET cc_start: 0.1455 (ppp) cc_final: 0.0745 (pmm) REVERT: Z 38 MET cc_start: 0.4091 (mmp) cc_final: 0.2264 (ptt) REVERT: Z 44 VAL cc_start: 0.4734 (OUTLIER) cc_final: 0.4406 (t) REVERT: Z 49 MET cc_start: 0.4209 (mmm) cc_final: 0.3719 (tmt) outliers start: 95 outliers final: 30 residues processed: 390 average time/residue: 1.6080 time to fit residues: 731.4723 Evaluate side-chains 340 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 291 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 219 ARG Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1062 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 445 ASP Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 20 GLU Chi-restraints excluded: chain Z residue 44 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 5.9990 chunk 266 optimal weight: 0.0270 chunk 184 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 169 optimal weight: 1.9990 chunk 238 optimal weight: 0.2980 chunk 356 optimal weight: 6.9990 chunk 376 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 337 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 83 GLN I 799 ASN I 955 GLN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1038 GLN J 430 HIS J 875 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 11 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33265 Z= 0.141 Angle : 0.483 16.908 45437 Z= 0.250 Chirality : 0.039 0.283 5196 Planarity : 0.004 0.172 5512 Dihedral : 15.933 130.436 5697 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 3.12 % Allowed : 17.70 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3797 helix: 2.01 (0.14), residues: 1494 sheet: 0.26 (0.26), residues: 383 loop : -0.91 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J1193 HIS 0.004 0.001 HIS H 37 PHE 0.016 0.001 PHE I 337 TYR 0.017 0.001 TYR J 46 ARG 0.005 0.000 ARG J 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 313 time to evaluate : 3.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.6695 (OUTLIER) cc_final: 0.5860 (p-80) REVERT: G 235 ARG cc_start: 0.4508 (ppt170) cc_final: 0.4210 (ppt170) REVERT: H 15 ASP cc_start: 0.6423 (OUTLIER) cc_final: 0.6105 (t0) REVERT: H 51 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8354 (mtp) REVERT: H 218 ARG cc_start: 0.5729 (mtp-110) cc_final: 0.5365 (mtt180) REVERT: H 219 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.5899 (mtm-85) REVERT: I 119 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7089 (mm-30) REVERT: I 545 PHE cc_start: 0.6566 (t80) cc_final: 0.5815 (m-80) REVERT: I 583 GLU cc_start: 0.7359 (tt0) cc_final: 0.7043 (tt0) REVERT: I 681 MET cc_start: 0.7234 (mtp) cc_final: 0.6930 (mtt) REVERT: I 694 ARG cc_start: 0.5581 (mtt180) cc_final: 0.5249 (mtm180) REVERT: I 742 TYR cc_start: 0.6856 (m-80) cc_final: 0.6325 (m-10) REVERT: I 778 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6893 (mm-30) REVERT: I 854 ILE cc_start: 0.7565 (mm) cc_final: 0.7314 (mp) REVERT: I 908 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: I 1211 ARG cc_start: 0.7389 (ttm170) cc_final: 0.6452 (mmt180) REVERT: I 1321 GLU cc_start: 0.6018 (tp30) cc_final: 0.5611 (tp30) REVERT: J 81 ARG cc_start: 0.7959 (tmm-80) cc_final: 0.7353 (ptm160) REVERT: J 183 GLU cc_start: 0.6453 (tt0) cc_final: 0.6104 (mp0) REVERT: J 227 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.6311 (t80) REVERT: J 314 ARG cc_start: 0.7909 (ptp-170) cc_final: 0.6821 (ptm-80) REVERT: J 322 ARG cc_start: 0.6777 (mtp85) cc_final: 0.5669 (mtp-110) REVERT: J 340 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.6649 (tp-100) REVERT: J 562 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6245 (tp30) REVERT: J 664 ILE cc_start: 0.5857 (OUTLIER) cc_final: 0.5554 (mm) REVERT: J 707 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7759 (tp) REVERT: J 802 ASP cc_start: 0.7088 (t0) cc_final: 0.6610 (m-30) REVERT: J 867 GLN cc_start: 0.7116 (mp10) cc_final: 0.6873 (mm-40) REVERT: J 1040 MET cc_start: 0.2349 (mtt) cc_final: 0.1888 (pmm) REVERT: J 1152 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6598 (pm20) REVERT: J 1169 THR cc_start: 0.4971 (OUTLIER) cc_final: 0.4455 (p) REVERT: K 11 GLU cc_start: 0.6714 (tm-30) cc_final: 0.6378 (mt-10) REVERT: K 43 ASN cc_start: 0.7206 (t0) cc_final: 0.6630 (t0) REVERT: K 55 GLU cc_start: 0.6568 (tt0) cc_final: 0.6247 (mt-10) REVERT: K 56 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6033 (mp0) REVERT: L 259 PHE cc_start: 0.6651 (m-10) cc_final: 0.6414 (m-80) REVERT: L 260 ARG cc_start: 0.5649 (tpp-160) cc_final: 0.5008 (ttm110) REVERT: L 265 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7168 (mm-40) REVERT: L 266 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7170 (m-80) REVERT: L 297 MET cc_start: 0.1609 (ppp) cc_final: 0.1215 (mpt) REVERT: L 322 MET cc_start: 0.2863 (ptt) cc_final: 0.2183 (ttm) REVERT: L 425 TYR cc_start: 0.7973 (m-80) cc_final: 0.7756 (m-80) REVERT: L 477 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7907 (mm-30) REVERT: L 482 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7462 (mt-10) REVERT: L 485 GLU cc_start: 0.7530 (mp0) cc_final: 0.7119 (tt0) REVERT: L 561 MET cc_start: 0.5639 (mmt) cc_final: 0.4937 (ttm) REVERT: R 260 LEU cc_start: 0.3870 (mt) cc_final: 0.3395 (tp) REVERT: R 316 MET cc_start: 0.1451 (ppp) cc_final: 0.0793 (pmm) REVERT: Z 38 MET cc_start: 0.4254 (mmp) cc_final: 0.2469 (ptt) REVERT: Z 44 VAL cc_start: 0.4688 (OUTLIER) cc_final: 0.4185 (t) REVERT: Z 46 PHE cc_start: 0.4702 (OUTLIER) cc_final: 0.4283 (t80) REVERT: Z 49 MET cc_start: 0.4395 (mmm) cc_final: 0.3961 (tmt) outliers start: 102 outliers final: 40 residues processed: 387 average time/residue: 1.5710 time to fit residues: 712.3068 Evaluate side-chains 341 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 287 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 219 ARG Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1062 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 20 GLU Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 46 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 280 optimal weight: 40.0000 chunk 155 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 260 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 338 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN H 132 HIS I 83 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 517 GLN I 628 HIS I 955 GLN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1038 GLN I1312 ASN J 80 HIS J 430 HIS J 817 HIS J1195 GLN J1259 GLN L 362 ASN R 283 GLN Z 11 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 33265 Z= 0.404 Angle : 0.664 21.948 45437 Z= 0.345 Chirality : 0.045 0.245 5196 Planarity : 0.006 0.183 5512 Dihedral : 16.307 126.202 5696 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 3.64 % Allowed : 17.79 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.08 (0.13), residues: 3797 helix: 1.31 (0.14), residues: 1499 sheet: 0.30 (0.26), residues: 397 loop : -1.29 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J1193 HIS 0.011 0.001 HIS H 37 PHE 0.017 0.002 PHE K 17 TYR 0.035 0.002 TYR I 47 ARG 0.009 0.001 ARG I1246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 286 time to evaluate : 3.496 Fit side-chains revert: symmetry clash REVERT: G 33 ARG cc_start: 0.6851 (tpp-160) cc_final: 0.5859 (tpp-160) REVERT: G 117 HIS cc_start: 0.7120 (OUTLIER) cc_final: 0.6360 (p-80) REVERT: H 76 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: H 107 ILE cc_start: 0.7900 (tp) cc_final: 0.7634 (tp) REVERT: H 218 ARG cc_start: 0.5589 (mtp-110) cc_final: 0.5259 (mtt180) REVERT: I 386 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6388 (tm-30) REVERT: I 681 MET cc_start: 0.7336 (mtp) cc_final: 0.6957 (mtt) REVERT: I 790 ASP cc_start: 0.7153 (t70) cc_final: 0.6922 (t0) REVERT: I 854 ILE cc_start: 0.7652 (mm) cc_final: 0.7356 (mp) REVERT: I 908 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: I 1143 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: I 1211 ARG cc_start: 0.7512 (ttm170) cc_final: 0.6664 (mmt180) REVERT: I 1321 GLU cc_start: 0.6179 (tp30) cc_final: 0.5783 (tp30) REVERT: J 45 ASN cc_start: 0.7288 (t0) cc_final: 0.6859 (t0) REVERT: J 81 ARG cc_start: 0.7950 (tmm-80) cc_final: 0.7214 (ptm160) REVERT: J 183 GLU cc_start: 0.6754 (tt0) cc_final: 0.5998 (mp0) REVERT: J 227 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6231 (t80) REVERT: J 314 ARG cc_start: 0.7847 (ptp-170) cc_final: 0.6607 (ptm-80) REVERT: J 322 ARG cc_start: 0.7067 (mtp85) cc_final: 0.5760 (mtp-110) REVERT: J 340 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6898 (tt0) REVERT: J 562 GLU cc_start: 0.6676 (mm-30) cc_final: 0.6228 (tp30) REVERT: J 594 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7069 (pt0) REVERT: J 664 ILE cc_start: 0.6019 (OUTLIER) cc_final: 0.5729 (mm) REVERT: J 802 ASP cc_start: 0.7311 (t0) cc_final: 0.6811 (m-30) REVERT: J 1152 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6530 (pm20) REVERT: J 1169 THR cc_start: 0.4704 (OUTLIER) cc_final: 0.4207 (p) REVERT: J 1177 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6488 (mp) REVERT: K 11 GLU cc_start: 0.6778 (tm-30) cc_final: 0.6362 (mt-10) REVERT: K 55 GLU cc_start: 0.6653 (tt0) cc_final: 0.6367 (tt0) REVERT: L 259 PHE cc_start: 0.6730 (m-10) cc_final: 0.6432 (m-80) REVERT: L 265 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7106 (mm-40) REVERT: L 266 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7171 (m-80) REVERT: L 297 MET cc_start: 0.1917 (ppp) cc_final: 0.1434 (mpt) REVERT: L 322 MET cc_start: 0.3272 (ptt) cc_final: 0.2510 (ttp) REVERT: L 471 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6223 (tp) REVERT: L 524 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6774 (pp20) REVERT: L 561 MET cc_start: 0.5686 (mmt) cc_final: 0.5013 (ttm) REVERT: Z 38 MET cc_start: 0.4216 (mmp) cc_final: 0.2412 (ptt) REVERT: Z 44 VAL cc_start: 0.4891 (OUTLIER) cc_final: 0.4467 (t) REVERT: Z 49 MET cc_start: 0.4566 (mmm) cc_final: 0.4258 (tmt) outliers start: 119 outliers final: 52 residues processed: 379 average time/residue: 1.6809 time to fit residues: 740.1714 Evaluate side-chains 327 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 260 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 481 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 1062 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 60 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 0.7980 chunk 339 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 83 GLN I 120 GLN I 490 GLN I 628 HIS ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J1126 GLN K 43 ASN Z 11 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 33265 Z= 0.159 Angle : 0.509 12.993 45437 Z= 0.266 Chirality : 0.040 0.235 5196 Planarity : 0.004 0.148 5512 Dihedral : 16.100 130.118 5694 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 2.69 % Allowed : 19.20 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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 (0.14), residues: 3797 helix: 1.51 (0.14), residues: 1500 sheet: 0.39 (0.26), residues: 385 loop : -1.16 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J1193 HIS 0.005 0.001 HIS G 23 PHE 0.019 0.001 PHE I 337 TYR 0.019 0.001 TYR J 46 ARG 0.004 0.000 ARG L 608 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 287 time to evaluate : 3.539 Fit side-chains revert: symmetry clash REVERT: G 33 ARG cc_start: 0.6735 (tpp-160) cc_final: 0.5979 (tpp80) REVERT: G 117 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6049 (p-80) REVERT: H 15 ASP cc_start: 0.6020 (OUTLIER) cc_final: 0.5571 (t0) REVERT: H 76 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: H 218 ARG cc_start: 0.5603 (mtp-110) cc_final: 0.5309 (mtt180) REVERT: H 219 ARG cc_start: 0.6254 (mtm-85) cc_final: 0.6043 (mtt180) REVERT: I 681 MET cc_start: 0.7262 (mtp) cc_final: 0.6969 (mtt) REVERT: I 854 ILE cc_start: 0.7539 (mm) cc_final: 0.7323 (mp) REVERT: I 867 GLU cc_start: 0.7951 (pm20) cc_final: 0.7146 (pm20) REVERT: I 908 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: I 1211 ARG cc_start: 0.7392 (ttm170) cc_final: 0.6550 (mmt180) REVERT: I 1219 GLU cc_start: 0.7633 (pt0) cc_final: 0.7270 (mt-10) REVERT: J 81 ARG cc_start: 0.7913 (tmm-80) cc_final: 0.6820 (ttt-90) REVERT: J 183 GLU cc_start: 0.6358 (tt0) cc_final: 0.5777 (mp0) REVERT: J 227 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.6269 (t80) REVERT: J 314 ARG cc_start: 0.7860 (ptp-170) cc_final: 0.6685 (ptm-80) REVERT: J 322 ARG cc_start: 0.6787 (mtp85) cc_final: 0.5541 (mtp-110) REVERT: J 340 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6878 (tt0) REVERT: J 386 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6612 (mt-10) REVERT: J 460 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7280 (t0) REVERT: J 562 GLU cc_start: 0.6704 (mm-30) cc_final: 0.6299 (tp30) REVERT: J 664 ILE cc_start: 0.5931 (OUTLIER) cc_final: 0.5636 (mm) REVERT: J 802 ASP cc_start: 0.7028 (t0) cc_final: 0.6755 (m-30) REVERT: J 1062 LEU cc_start: 0.2841 (OUTLIER) cc_final: 0.2428 (tp) REVERT: J 1152 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6509 (pm20) REVERT: J 1169 THR cc_start: 0.4647 (OUTLIER) cc_final: 0.4171 (p) REVERT: J 1177 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6439 (mp) REVERT: J 1278 GLU cc_start: 0.6329 (tt0) cc_final: 0.6005 (tp30) REVERT: K 11 GLU cc_start: 0.6749 (tm-30) cc_final: 0.6394 (mt-10) REVERT: K 55 GLU cc_start: 0.6591 (tt0) cc_final: 0.6296 (tt0) REVERT: L 259 PHE cc_start: 0.6746 (m-10) cc_final: 0.6441 (m-80) REVERT: L 260 ARG cc_start: 0.5489 (tpp-160) cc_final: 0.4790 (ttm110) REVERT: L 265 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7110 (mm-40) REVERT: L 284 GLU cc_start: 0.4258 (OUTLIER) cc_final: 0.3931 (pt0) REVERT: L 297 MET cc_start: 0.1838 (ppp) cc_final: 0.1325 (mpt) REVERT: L 322 MET cc_start: 0.3051 (ptt) cc_final: 0.2268 (ttm) REVERT: L 524 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6837 (pp20) REVERT: L 561 MET cc_start: 0.5625 (mmt) cc_final: 0.5021 (ttm) REVERT: L 582 VAL cc_start: 0.4388 (t) cc_final: 0.4132 (m) REVERT: R 260 LEU cc_start: 0.4268 (mm) cc_final: 0.3851 (tp) REVERT: R 270 LEU cc_start: 0.4298 (mt) cc_final: 0.3946 (tm) REVERT: R 316 MET cc_start: 0.3022 (pp-130) cc_final: 0.1918 (pmm) REVERT: Z 38 MET cc_start: 0.4170 (mmp) cc_final: 0.2385 (ptt) REVERT: Z 44 VAL cc_start: 0.4744 (OUTLIER) cc_final: 0.4528 (t) REVERT: Z 49 MET cc_start: 0.4603 (mmm) cc_final: 0.4270 (tmt) outliers start: 88 outliers final: 38 residues processed: 355 average time/residue: 1.6562 time to fit residues: 683.0546 Evaluate side-chains 321 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 269 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1062 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 60 THR Chi-restraints excluded: chain Z residue 61 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 9.9990 chunk 42 optimal weight: 0.0570 chunk 214 optimal weight: 2.9990 chunk 275 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 317 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 375 optimal weight: 20.0000 chunk 235 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 955 GLN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J 817 HIS K 43 ASN Z 11 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33265 Z= 0.214 Angle : 0.541 13.669 45437 Z= 0.283 Chirality : 0.041 0.158 5196 Planarity : 0.004 0.068 5512 Dihedral : 16.109 130.347 5694 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.71 % Rotamer: Outliers : 3.15 % Allowed : 19.23 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: 0.08 (0.14), residues: 3797 helix: 1.47 (0.14), residues: 1505 sheet: 0.30 (0.26), residues: 390 loop : -1.21 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP J1193 HIS 0.007 0.001 HIS J 545 PHE 0.015 0.001 PHE I 337 TYR 0.017 0.001 TYR I 47 ARG 0.005 0.000 ARG J 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 271 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.6819 (tpp-160) cc_final: 0.6041 (tpp80) REVERT: G 117 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.6046 (p-80) REVERT: H 6 THR cc_start: 0.6740 (m) cc_final: 0.6368 (p) REVERT: H 15 ASP cc_start: 0.6015 (OUTLIER) cc_final: 0.5497 (t0) REVERT: H 65 LEU cc_start: 0.8279 (tt) cc_final: 0.8058 (mm) REVERT: H 76 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: H 218 ARG cc_start: 0.5605 (mtp-110) cc_final: 0.5287 (mtt180) REVERT: I 386 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6129 (tm-30) REVERT: I 681 MET cc_start: 0.7293 (mtp) cc_final: 0.6975 (mtt) REVERT: I 908 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: I 1143 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6794 (tt0) REVERT: I 1211 ARG cc_start: 0.7453 (ttm170) cc_final: 0.6625 (mmt180) REVERT: I 1321 GLU cc_start: 0.6097 (tp30) cc_final: 0.5714 (tp30) REVERT: J 45 ASN cc_start: 0.7204 (t0) cc_final: 0.6837 (t0) REVERT: J 81 ARG cc_start: 0.7940 (tmm-80) cc_final: 0.6839 (ttt-90) REVERT: J 183 GLU cc_start: 0.6494 (tt0) cc_final: 0.5872 (mp0) REVERT: J 192 MET cc_start: 0.7886 (ttp) cc_final: 0.7105 (ptm) REVERT: J 227 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6251 (t80) REVERT: J 314 ARG cc_start: 0.7848 (ptp-170) cc_final: 0.6634 (ptm-80) REVERT: J 322 ARG cc_start: 0.6820 (mtp85) cc_final: 0.5565 (mtp-110) REVERT: J 340 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6873 (tt0) REVERT: J 460 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7514 (t0) REVERT: J 562 GLU cc_start: 0.6645 (mm-30) cc_final: 0.6230 (tp30) REVERT: J 664 ILE cc_start: 0.5966 (OUTLIER) cc_final: 0.5673 (mm) REVERT: J 802 ASP cc_start: 0.7100 (t0) cc_final: 0.6780 (m-30) REVERT: J 1062 LEU cc_start: 0.2998 (OUTLIER) cc_final: 0.2558 (tp) REVERT: J 1152 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6502 (pm20) REVERT: J 1169 THR cc_start: 0.4676 (OUTLIER) cc_final: 0.4201 (p) REVERT: J 1177 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6494 (mp) REVERT: K 11 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6381 (mt-10) REVERT: K 12 LYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5785 (mptp) REVERT: L 259 PHE cc_start: 0.6755 (m-10) cc_final: 0.6439 (m-80) REVERT: L 260 ARG cc_start: 0.5505 (tpp-160) cc_final: 0.4779 (ttm110) REVERT: L 265 GLN cc_start: 0.7375 (mm-40) cc_final: 0.7079 (mm-40) REVERT: L 297 MET cc_start: 0.2003 (ppp) cc_final: 0.1461 (mpt) REVERT: L 322 MET cc_start: 0.3109 (ptt) cc_final: 0.2325 (ttp) REVERT: L 524 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6857 (pp20) REVERT: L 561 MET cc_start: 0.5622 (mmt) cc_final: 0.5031 (ttm) REVERT: L 582 VAL cc_start: 0.4471 (t) cc_final: 0.4223 (m) REVERT: L 608 ARG cc_start: 0.6864 (tpp80) cc_final: 0.6098 (mtt90) REVERT: R 260 LEU cc_start: 0.4301 (mm) cc_final: 0.3882 (tp) REVERT: R 316 MET cc_start: 0.3318 (pp-130) cc_final: 0.2178 (pmm) REVERT: Z 44 VAL cc_start: 0.4754 (OUTLIER) cc_final: 0.4464 (t) REVERT: Z 49 MET cc_start: 0.4587 (mmm) cc_final: 0.4275 (tmt) outliers start: 103 outliers final: 54 residues processed: 349 average time/residue: 1.6766 time to fit residues: 683.2763 Evaluate side-chains 332 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 262 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 1062 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 8 GLN Chi-restraints excluded: chain Z residue 37 TRP Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 60 THR Chi-restraints excluded: chain Z residue 61 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 0.2980 chunk 150 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 955 GLN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J 817 HIS K 43 ASN Z 11 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33265 Z= 0.325 Angle : 0.618 14.097 45437 Z= 0.322 Chirality : 0.043 0.164 5196 Planarity : 0.005 0.077 5512 Dihedral : 16.249 129.109 5694 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.90 % Favored : 94.07 % Rotamer: Outliers : 3.25 % Allowed : 19.53 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 1.31 % 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: -0.26 (0.13), residues: 3797 helix: 1.15 (0.13), residues: 1507 sheet: 0.04 (0.26), residues: 404 loop : -1.36 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J1193 HIS 0.010 0.001 HIS J 545 PHE 0.016 0.002 PHE I 337 TYR 0.021 0.002 TYR I 47 ARG 0.005 0.001 ARG I1246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 268 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.6918 (tpp-160) cc_final: 0.6571 (tpp80) REVERT: G 117 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6764 (p-80) REVERT: H 6 THR cc_start: 0.6870 (m) cc_final: 0.6499 (p) REVERT: H 51 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7812 (mmm) REVERT: H 76 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: I 386 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6368 (tm-30) REVERT: I 681 MET cc_start: 0.7349 (mtp) cc_final: 0.6995 (mtt) REVERT: I 790 ASP cc_start: 0.7282 (t70) cc_final: 0.7038 (t0) REVERT: I 908 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: I 1143 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: I 1211 ARG cc_start: 0.7545 (ttm170) cc_final: 0.6736 (mmt180) REVERT: I 1321 GLU cc_start: 0.6121 (tp30) cc_final: 0.5730 (tp30) REVERT: J 45 ASN cc_start: 0.7277 (t0) cc_final: 0.7024 (t0) REVERT: J 81 ARG cc_start: 0.7976 (tmm-80) cc_final: 0.6791 (ttt-90) REVERT: J 183 GLU cc_start: 0.6637 (tt0) cc_final: 0.5909 (mp0) REVERT: J 192 MET cc_start: 0.7883 (ttp) cc_final: 0.7122 (ptm) REVERT: J 227 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6186 (t80) REVERT: J 314 ARG cc_start: 0.7837 (ptp-170) cc_final: 0.6613 (ptm-80) REVERT: J 322 ARG cc_start: 0.6919 (mtp85) cc_final: 0.5675 (mtm-85) REVERT: J 340 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6833 (tt0) REVERT: J 460 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7584 (t0) REVERT: J 562 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6269 (tp30) REVERT: J 594 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7117 (pt0) REVERT: J 664 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5734 (mm) REVERT: J 708 ASN cc_start: 0.8654 (p0) cc_final: 0.8408 (p0) REVERT: J 802 ASP cc_start: 0.7267 (t0) cc_final: 0.6805 (m-30) REVERT: J 1152 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6663 (mm-30) REVERT: J 1169 THR cc_start: 0.4565 (OUTLIER) cc_final: 0.4098 (p) REVERT: J 1177 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6560 (mp) REVERT: J 1278 GLU cc_start: 0.6330 (tt0) cc_final: 0.6129 (tp30) REVERT: K 11 GLU cc_start: 0.6619 (tm-30) cc_final: 0.6235 (OUTLIER) REVERT: K 12 LYS cc_start: 0.6223 (OUTLIER) cc_final: 0.5559 (mptp) REVERT: L 259 PHE cc_start: 0.6775 (m-10) cc_final: 0.6481 (m-80) REVERT: L 277 MET cc_start: 0.5085 (tpp) cc_final: 0.4815 (tpp) REVERT: L 284 GLU cc_start: 0.4025 (OUTLIER) cc_final: 0.3774 (pt0) REVERT: L 288 MET cc_start: 0.3734 (pp-130) cc_final: 0.3490 (ppp) REVERT: L 297 MET cc_start: 0.2103 (ppp) cc_final: 0.1502 (mpt) REVERT: L 322 MET cc_start: 0.3266 (ptt) cc_final: 0.2358 (ttm) REVERT: L 524 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6808 (pp20) REVERT: L 561 MET cc_start: 0.5492 (mmt) cc_final: 0.4724 (ttt) REVERT: L 582 VAL cc_start: 0.4272 (t) cc_final: 0.4030 (m) REVERT: R 260 LEU cc_start: 0.4318 (mm) cc_final: 0.3889 (tp) REVERT: R 316 MET cc_start: 0.3413 (pp-130) cc_final: 0.2326 (pmm) REVERT: Z 20 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5082 (tp30) REVERT: Z 44 VAL cc_start: 0.5000 (OUTLIER) cc_final: 0.4695 (t) outliers start: 106 outliers final: 56 residues processed: 357 average time/residue: 1.7304 time to fit residues: 722.5188 Evaluate side-chains 331 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 258 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 1062 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 20 GLU Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 60 THR Chi-restraints excluded: chain Z residue 61 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 2.9990 chunk 360 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 350 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 275 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 316 optimal weight: 5.9990 chunk 331 optimal weight: 30.0000 chunk 349 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN I 955 GLN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J 817 HIS K 43 ASN Z 11 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 33265 Z= 0.350 Angle : 0.629 14.466 45437 Z= 0.328 Chirality : 0.044 0.179 5196 Planarity : 0.005 0.078 5512 Dihedral : 16.278 129.589 5694 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.16 % Favored : 93.81 % Rotamer: Outliers : 3.09 % Allowed : 19.99 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 1.31 % 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: -0.46 (0.13), residues: 3797 helix: 0.98 (0.13), residues: 1508 sheet: -0.08 (0.25), residues: 416 loop : -1.46 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP J1193 HIS 0.011 0.001 HIS H 37 PHE 0.018 0.002 PHE I 337 TYR 0.019 0.002 TYR I 47 ARG 0.006 0.001 ARG J 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 259 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.7037 (OUTLIER) cc_final: 0.6822 (p-80) REVERT: H 6 THR cc_start: 0.6921 (m) cc_final: 0.6592 (p) REVERT: H 51 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7778 (mmm) REVERT: H 76 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: H 104 LYS cc_start: 0.7575 (tptm) cc_final: 0.7326 (tttt) REVERT: I 386 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6375 (tm-30) REVERT: I 681 MET cc_start: 0.7339 (mtp) cc_final: 0.6978 (mtt) REVERT: I 790 ASP cc_start: 0.7293 (t70) cc_final: 0.7034 (t0) REVERT: I 908 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: I 1143 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: I 1211 ARG cc_start: 0.7533 (ttm170) cc_final: 0.6704 (mmt180) REVERT: I 1321 GLU cc_start: 0.6142 (tp30) cc_final: 0.5766 (tp30) REVERT: J 81 ARG cc_start: 0.7967 (tmm-80) cc_final: 0.6771 (ttt-90) REVERT: J 183 GLU cc_start: 0.6631 (tt0) cc_final: 0.5900 (mp0) REVERT: J 192 MET cc_start: 0.7984 (ttp) cc_final: 0.7331 (ptm) REVERT: J 227 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6149 (t80) REVERT: J 314 ARG cc_start: 0.7852 (ptp-170) cc_final: 0.6571 (ptm-80) REVERT: J 340 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: J 460 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7582 (t0) REVERT: J 562 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6261 (tp30) REVERT: J 594 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: J 664 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5723 (mm) REVERT: J 802 ASP cc_start: 0.7243 (t0) cc_final: 0.6772 (m-30) REVERT: J 1152 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6665 (mm-30) REVERT: J 1169 THR cc_start: 0.4479 (OUTLIER) cc_final: 0.4014 (p) REVERT: J 1177 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6563 (mp) REVERT: J 1345 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7438 (ttt90) REVERT: K 11 GLU cc_start: 0.6535 (tm-30) cc_final: 0.6135 (OUTLIER) REVERT: K 12 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5609 (mptp) REVERT: L 259 PHE cc_start: 0.6813 (m-10) cc_final: 0.6542 (m-80) REVERT: L 277 MET cc_start: 0.5130 (tpp) cc_final: 0.4752 (tpp) REVERT: L 284 GLU cc_start: 0.3912 (OUTLIER) cc_final: 0.3533 (pt0) REVERT: L 288 MET cc_start: 0.3738 (pp-130) cc_final: 0.3398 (mtm) REVERT: L 297 MET cc_start: 0.1990 (ppp) cc_final: 0.1446 (mpt) REVERT: L 322 MET cc_start: 0.3136 (ptt) cc_final: 0.2093 (ttp) REVERT: L 489 MET cc_start: 0.7870 (mmp) cc_final: 0.7635 (mmm) REVERT: L 524 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6818 (pp20) REVERT: L 561 MET cc_start: 0.5450 (mmt) cc_final: 0.4754 (ttt) REVERT: L 582 VAL cc_start: 0.4325 (t) cc_final: 0.4109 (m) REVERT: R 260 LEU cc_start: 0.4324 (mm) cc_final: 0.3879 (tp) REVERT: R 316 MET cc_start: 0.3409 (pp-130) cc_final: 0.2333 (pmm) REVERT: Z 44 VAL cc_start: 0.5085 (OUTLIER) cc_final: 0.4779 (t) outliers start: 101 outliers final: 61 residues processed: 341 average time/residue: 1.7419 time to fit residues: 689.1971 Evaluate side-chains 327 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 249 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 386 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1143 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1062 LEU Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1345 ARG Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 266 PHE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 379 MET Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 60 THR Chi-restraints excluded: chain Z residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 2.9990 chunk 370 optimal weight: 20.0000 chunk 226 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 357 optimal weight: 9.9990 chunk 309 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 238 optimal weight: 0.7980 chunk 189 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J 817 HIS K 43 ASN Z 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33265 Z= 0.145 Angle : 0.506 14.079 45437 Z= 0.264 Chirality : 0.040 0.208 5196 Planarity : 0.004 0.079 5512 Dihedral : 16.025 132.938 5694 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.13 % Rotamer: Outliers : 1.78 % Allowed : 21.25 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 1.31 % 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: -0.06 (0.14), residues: 3797 helix: 1.37 (0.14), residues: 1509 sheet: 0.07 (0.25), residues: 406 loop : -1.27 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J1193 HIS 0.004 0.001 HIS G 23 PHE 0.011 0.001 PHE I 337 TYR 0.022 0.001 TYR J 46 ARG 0.005 0.000 ARG L 608 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7594 Ramachandran restraints generated. 3797 Oldfield, 0 Emsley, 3797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 276 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.6797 (tpp-160) cc_final: 0.6561 (mmt-90) REVERT: H 6 THR cc_start: 0.6850 (m) cc_final: 0.6532 (p) REVERT: H 51 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7857 (mmm) REVERT: H 104 LYS cc_start: 0.7551 (tptm) cc_final: 0.7300 (tttt) REVERT: H 186 ASN cc_start: 0.6819 (p0) cc_final: 0.6533 (p0) REVERT: H 218 ARG cc_start: 0.5631 (mtp-110) cc_final: 0.5341 (mtt180) REVERT: I 583 GLU cc_start: 0.7561 (tt0) cc_final: 0.7321 (pt0) REVERT: I 641 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: I 681 MET cc_start: 0.7243 (mtp) cc_final: 0.6974 (mtt) REVERT: I 908 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: I 1026 GLU cc_start: 0.5716 (OUTLIER) cc_final: 0.5297 (tt0) REVERT: I 1211 ARG cc_start: 0.7404 (ttm170) cc_final: 0.6547 (mmt180) REVERT: I 1230 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8362 (ptp) REVERT: J 81 ARG cc_start: 0.7927 (tmm-80) cc_final: 0.6766 (ttt-90) REVERT: J 183 GLU cc_start: 0.6322 (tt0) cc_final: 0.5761 (mp0) REVERT: J 192 MET cc_start: 0.7885 (ttp) cc_final: 0.7301 (ptm) REVERT: J 227 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6155 (t80) REVERT: J 314 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.6594 (ptm-80) REVERT: J 322 ARG cc_start: 0.6766 (mtp85) cc_final: 0.5550 (mtp-110) REVERT: J 340 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6759 (tt0) REVERT: J 525 MET cc_start: 0.8232 (mtm) cc_final: 0.8001 (mtp) REVERT: J 562 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6346 (tp30) REVERT: J 664 ILE cc_start: 0.5909 (mm) cc_final: 0.5624 (mm) REVERT: J 802 ASP cc_start: 0.6842 (t0) cc_final: 0.6603 (m-30) REVERT: J 1040 MET cc_start: 0.3533 (ptp) cc_final: 0.2058 (mpt) REVERT: J 1152 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6545 (pm20) REVERT: J 1177 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6390 (mp) REVERT: J 1193 TRP cc_start: 0.6018 (p90) cc_final: 0.5533 (p90) REVERT: J 1345 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7421 (ttt90) REVERT: K 11 GLU cc_start: 0.6662 (tm-30) cc_final: 0.6338 (mt-10) REVERT: L 259 PHE cc_start: 0.6802 (m-10) cc_final: 0.6497 (m-80) REVERT: L 265 GLN cc_start: 0.7344 (mm-40) cc_final: 0.7069 (mm-40) REVERT: L 277 MET cc_start: 0.5101 (tpp) cc_final: 0.4717 (tpp) REVERT: L 284 GLU cc_start: 0.4156 (OUTLIER) cc_final: 0.3775 (pt0) REVERT: L 288 MET cc_start: 0.3723 (pp-130) cc_final: 0.3414 (mtm) REVERT: L 297 MET cc_start: 0.1913 (ppp) cc_final: 0.1315 (mpt) REVERT: L 322 MET cc_start: 0.3114 (ptt) cc_final: 0.2048 (ttp) REVERT: L 561 MET cc_start: 0.5481 (mmt) cc_final: 0.4712 (ttt) REVERT: L 582 VAL cc_start: 0.4214 (t) cc_final: 0.4007 (m) REVERT: L 608 ARG cc_start: 0.6818 (tpp80) cc_final: 0.6131 (mtt90) REVERT: R 260 LEU cc_start: 0.4341 (mm) cc_final: 0.3993 (tp) REVERT: R 270 LEU cc_start: 0.4306 (mt) cc_final: 0.3965 (tm) REVERT: R 316 MET cc_start: 0.3213 (pp-130) cc_final: 0.2094 (pmm) REVERT: Z 30 MET cc_start: 0.3247 (mmm) cc_final: 0.2893 (mmp) outliers start: 58 outliers final: 37 residues processed: 323 average time/residue: 1.7343 time to fit residues: 650.6950 Evaluate side-chains 310 residues out of total 3277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 264 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 1026 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 832 LYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 379 MET Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 587 ILE Chi-restraints excluded: chain L residue 606 VAL Chi-restraints excluded: chain Z residue 60 THR Chi-restraints excluded: chain Z residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 6.9990 chunk 329 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 285 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 309 optimal weight: 4.9990 chunk 129 optimal weight: 0.3980 chunk 318 optimal weight: 7.9990 chunk 39 optimal weight: 0.0040 chunk 57 optimal weight: 0.0570 overall best weight: 2.0914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 955 GLN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J 817 HIS K 43 ASN Z 11 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.173574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104800 restraints weight = 40668.353| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.09 r_work: 0.3056 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33265 Z= 0.239 Angle : 0.554 13.996 45437 Z= 0.288 Chirality : 0.041 0.187 5196 Planarity : 0.004 0.079 5512 Dihedral : 16.046 132.180 5693 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 2.05 % Allowed : 21.10 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 1.31 % 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: -0.09 (0.14), residues: 3797 helix: 1.31 (0.14), residues: 1507 sheet: 0.09 (0.26), residues: 398 loop : -1.27 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP J1193 HIS 0.007 0.001 HIS H 37 PHE 0.012 0.001 PHE I 337 TYR 0.017 0.001 TYR G 177 ARG 0.010 0.000 ARG J1206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13754.24 seconds wall clock time: 244 minutes 32.36 seconds (14672.36 seconds total)