Starting phenix.real_space_refine on Wed Mar 20 05:42:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flp_4274/03_2024/6flp_4274_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flp_4274/03_2024/6flp_4274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flp_4274/03_2024/6flp_4274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flp_4274/03_2024/6flp_4274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flp_4274/03_2024/6flp_4274_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6flp_4274/03_2024/6flp_4274_neut.pdb" } resolution = 4.1 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= 0.005 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 80 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 16357 2.51 5 N 4696 2.21 5 O 5271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 860": "NH1" <-> "NH2" Residue "D ARG 905": "NH1" <-> "NH2" Residue "D ARG 1123": "NH1" <-> "NH2" Residue "D ARG 1194": "NH1" <-> "NH2" Residue "D ARG 1284": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26512 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1767 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 10363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1314, 10363 Classifications: {'peptide': 1314} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 54, 'TRANS': 1258} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 10357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10357 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 55, 'TRANS': 1278} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "N" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 647 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 785 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14260 SG CYS D 72 111.636 59.038 75.832 1.00211.78 S ATOM 20080 SG CYS D 814 88.557 126.912 76.974 1.00152.41 S ATOM 20645 SG CYS D 888 87.250 123.598 76.448 1.00144.53 S ATOM 20696 SG CYS D 895 88.413 124.558 79.651 1.00144.06 S Time building chain proxies: 13.53, per 1000 atoms: 0.51 Number of scatterers: 26512 At special positions: 0 Unit cell: (155.1, 163.9, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 105 16.00 P 80 15.00 Mg 1 11.99 O 5271 8.00 N 4696 7.00 C 16357 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: 10.36 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 43 sheets defined 38.0% alpha, 13.1% beta 36 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 7.84 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.666A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.630A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.739A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.718A pdb=" N ILE A 159 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 3.521A pdb=" N ALA A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.876A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.738A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 removed outlier: 4.075A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR B 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 49 through 57 removed outlier: 4.331A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.003A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.893A pdb=" N GLU C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 4.607A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 4.127A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.774A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 removed outlier: 3.598A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.934A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.836A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.632A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 612' Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.937A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.987A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 4.332A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 710 removed outlier: 4.592A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 705 through 710' Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.783A pdb=" N SER C 863 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 860 through 864' Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.696A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1000 Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.561A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 4.175A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C1114 " --> pdb=" O GLY C1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1149 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.515A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C1164 " --> pdb=" O LEU C1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1164' Processing helix chain 'C' and resid 1166 through 1176 removed outlier: 3.689A pdb=" N MET C1170 " --> pdb=" O ASP C1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1262 through 1266 removed outlier: 4.002A pdb=" N PHE C1265 " --> pdb=" O LYS C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.729A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1299 through 1309 removed outlier: 3.973A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1334 removed outlier: 3.614A pdb=" N GLY C1334 " --> pdb=" O ILE C1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.549A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 263 through 285 removed outlier: 4.296A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 406 through 417 removed outlier: 3.869A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.734A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.849A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.598A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.806A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.680A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 669 removed outlier: 4.491A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.830A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.528A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.539A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 1138 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.708A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1243 Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 4.200A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1327 through 1337 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.658A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 4.344A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 16 through 32 removed outlier: 4.326A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 91 removed outlier: 3.505A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 19 removed outlier: 5.254A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU A 17 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 205 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 188 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 104 removed outlier: 3.522A pdb=" N LEU A 102 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 149 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.604A pdb=" N ARG A 91 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.702A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.706A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 18 removed outlier: 3.624A pdb=" N LEU B 201 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 200 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 184 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 206 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.592A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.900A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 67 through 75 removed outlier: 3.688A pdb=" N GLU C 67 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 71 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB2, first strand: chain 'C' and resid 154 through 159 removed outlier: 3.612A pdb=" N PHE C 156 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C 175 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 238 through 239 removed outlier: 4.159A pdb=" N GLN C 238 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 231 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.910A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.868A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 558 through 559 removed outlier: 4.648A pdb=" N SER C 574 " --> pdb=" O CYS C 559 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.532A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 591 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AC1, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC2, first strand: chain 'C' and resid 748 through 752 removed outlier: 7.105A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1097 through 1098 removed outlier: 7.338A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.717A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.535A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C1058 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY C 926 " --> pdb=" O VAL C 877 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 885 removed outlier: 7.275A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.796A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.796A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD3, first strand: chain 'C' and resid 1336 through 1339 Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AD5, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD6, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.581A pdb=" N THR D 572 " --> pdb=" O VAL D 548 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD9, first strand: chain 'D' and resid 951 through 952 Processing sheet with id=AE1, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.602A pdb=" N LYS D 959 " --> pdb=" O LYS D 983 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.626A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 6.524A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1079 through 1081 removed outlier: 3.970A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.619A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1187 through 1190 removed outlier: 3.863A pdb=" N GLU D1188 " --> pdb=" O LEU D1175 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D1173 " --> pdb=" O ILE D1190 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 6.466A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2667 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 11.94 Time building geometry restraints manager: 11.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8510 1.34 - 1.46: 3657 1.46 - 1.57: 14565 1.57 - 1.69: 156 1.69 - 1.81: 182 Bond restraints: 27070 Sorted by residual: bond pdb=" C ASP D1184 " pdb=" N PRO D1185 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.41e+00 bond pdb=" CA THR D 514 " pdb=" CB THR D 514 " ideal model delta sigma weight residual 1.528 1.564 -0.036 2.61e-02 1.47e+03 1.92e+00 bond pdb=" CA VAL D 83 " pdb=" CB VAL D 83 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.05e-02 9.07e+03 1.44e+00 bond pdb=" N ILE C 445 " pdb=" CA ILE C 445 " ideal model delta sigma weight residual 1.474 1.456 0.018 1.57e-02 4.06e+03 1.39e+00 bond pdb=" CA ASP D1184 " pdb=" C ASP D1184 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.26e-02 6.30e+03 1.06e+00 ... (remaining 27065 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.61: 725 104.61 - 111.95: 13311 111.95 - 119.28: 9064 119.28 - 126.61: 13354 126.61 - 133.94: 456 Bond angle restraints: 36910 Sorted by residual: angle pdb=" N VAL C 630 " pdb=" CA VAL C 630 " pdb=" C VAL C 630 " ideal model delta sigma weight residual 111.91 106.82 5.09 8.90e-01 1.26e+00 3.27e+01 angle pdb=" N ILE D1210 " pdb=" CA ILE D1210 " pdb=" C ILE D1210 " ideal model delta sigma weight residual 111.48 107.36 4.12 9.40e-01 1.13e+00 1.92e+01 angle pdb=" N ILE D1253 " pdb=" CA ILE D1253 " pdb=" C ILE D1253 " ideal model delta sigma weight residual 111.81 108.46 3.35 8.60e-01 1.35e+00 1.52e+01 angle pdb=" C VAL C 727 " pdb=" N ASP C 728 " pdb=" CA ASP C 728 " ideal model delta sigma weight residual 122.44 117.90 4.54 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C TYR D 46 " pdb=" N ARG D 47 " pdb=" CA ARG D 47 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 ... (remaining 36905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 15911 30.32 - 60.63: 522 60.63 - 90.95: 40 90.95 - 121.27: 3 121.27 - 151.59: 3 Dihedral angle restraints: 16479 sinusoidal: 7339 harmonic: 9140 Sorted by residual: dihedral pdb=" CA PHE C 57 " pdb=" C PHE C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta harmonic sigma weight residual -180.00 -118.71 -61.29 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA SER A 20 " pdb=" C SER A 20 " pdb=" N SER A 21 " pdb=" CA SER A 21 " ideal model delta harmonic sigma weight residual 180.00 156.14 23.86 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA VAL B 19 " pdb=" C VAL B 19 " pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta harmonic sigma weight residual -180.00 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 16476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2938 0.035 - 0.071: 890 0.071 - 0.106: 292 0.106 - 0.141: 95 0.141 - 0.176: 9 Chirality restraints: 4224 Sorted by residual: chirality pdb=" C3' G R 20 " pdb=" C4' G R 20 " pdb=" O3' G R 20 " pdb=" C2' G R 20 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CA ILE C 59 " pdb=" N ILE C 59 " pdb=" C ILE C 59 " pdb=" CB ILE C 59 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ASP D1184 " pdb=" N ASP D1184 " pdb=" C ASP D1184 " pdb=" CB ASP D1184 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 4221 not shown) Planarity restraints: 4556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 57 " -0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO C 58 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 58 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 58 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 109 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO C 110 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 559 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO C 560 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 560 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 560 " -0.023 5.00e-02 4.00e+02 ... (remaining 4553 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 287 2.63 - 3.20: 23404 3.20 - 3.76: 38985 3.76 - 4.33: 51882 4.33 - 4.90: 83587 Nonbonded interactions: 198145 Sorted by model distance: nonbonded pdb=" N2 DG N 29 " pdb=" O2 DC T 11 " model vdw 2.062 2.496 nonbonded pdb=" NH2 ARG C 200 " pdb=" OP2 DC N 24 " model vdw 2.108 2.520 nonbonded pdb=" OE1 GLU C 562 " pdb=" OG SER C 662 " model vdw 2.195 2.440 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1502 " model vdw 2.233 2.310 nonbonded pdb=" OD2 ASP D 129 " pdb=" NH1 ARG D 220 " model vdw 2.235 2.520 ... (remaining 198140 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 'A' and (resid 6 through 158 or resid 171 through 234)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.760 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 79.080 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27070 Z= 0.144 Angle : 0.571 8.550 36910 Z= 0.340 Chirality : 0.041 0.176 4224 Planarity : 0.004 0.082 4556 Dihedral : 13.142 151.585 10599 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 0.04 % Allowed : 1.74 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % 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: -3.10 (0.13), residues: 3166 helix: -0.56 (0.14), residues: 1085 sheet: -2.53 (0.24), residues: 355 loop : -3.08 (0.13), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C1276 HIS 0.004 0.001 HIS D 817 PHE 0.022 0.001 PHE D 49 TYR 0.018 0.001 TYR D1241 ARG 0.005 0.000 ARG C1301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 507 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ILE cc_start: 0.9395 (mt) cc_final: 0.9094 (mm) REVERT: B 28 LEU cc_start: 0.9461 (tp) cc_final: 0.9253 (tt) REVERT: C 96 LEU cc_start: 0.9084 (tp) cc_final: 0.8832 (tp) REVERT: C 336 LEU cc_start: 0.9143 (mt) cc_final: 0.8842 (mp) REVERT: C 484 LEU cc_start: 0.8928 (mt) cc_final: 0.8353 (tp) REVERT: C 515 MET cc_start: 0.6482 (ptm) cc_final: 0.4818 (ptm) REVERT: C 519 ASN cc_start: 0.8595 (t0) cc_final: 0.8015 (t0) REVERT: C 653 MET cc_start: 0.8367 (ttp) cc_final: 0.8038 (ttp) REVERT: C 696 ASP cc_start: 0.8887 (t70) cc_final: 0.8525 (t0) REVERT: C 930 ASP cc_start: 0.8490 (t70) cc_final: 0.8197 (t0) REVERT: C 1094 VAL cc_start: 0.9475 (t) cc_final: 0.9271 (p) REVERT: C 1107 MET cc_start: 0.8899 (mtp) cc_final: 0.8649 (mtt) REVERT: C 1292 THR cc_start: 0.9201 (m) cc_final: 0.8909 (m) REVERT: D 183 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8846 (pm20) REVERT: D 189 LEU cc_start: 0.9637 (mp) cc_final: 0.9352 (mt) REVERT: D 375 GLU cc_start: 0.9161 (tp30) cc_final: 0.8741 (tm-30) REVERT: D 466 MET cc_start: 0.8575 (mtp) cc_final: 0.8280 (mtp) REVERT: D 513 MET cc_start: 0.9104 (ttp) cc_final: 0.8527 (tmm) REVERT: D 654 ILE cc_start: 0.8991 (mt) cc_final: 0.8620 (pt) REVERT: D 724 MET cc_start: 0.9311 (mtm) cc_final: 0.8830 (mtt) REVERT: D 756 GLU cc_start: 0.8849 (pt0) cc_final: 0.8490 (pp20) REVERT: D 1236 GLU cc_start: 0.8955 (tp30) cc_final: 0.8699 (tp30) REVERT: D 1254 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8351 (mt-10) REVERT: E 38 LEU cc_start: 0.9432 (mp) cc_final: 0.8298 (tt) REVERT: E 52 ARG cc_start: 0.9428 (mtp85) cc_final: 0.9207 (ttm110) outliers start: 1 outliers final: 0 residues processed: 507 average time/residue: 0.4243 time to fit residues: 323.2638 Evaluate side-chains 234 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 20.0000 chunk 244 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 253 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS A 132 HIS B 66 HIS B 84 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 551 HIS C 628 HIS C 686 GLN C1080 ASN C1134 GLN C1136 GLN C1146 GLN C1209 GLN ** C1237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 157 GLN D 232 ASN D 341 ASN D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 665 GLN D1218 HIS D1326 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27070 Z= 0.270 Angle : 0.607 7.685 36910 Z= 0.319 Chirality : 0.042 0.173 4224 Planarity : 0.004 0.077 4556 Dihedral : 16.255 154.923 4407 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.46 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % 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: -2.22 (0.14), residues: 3166 helix: 0.39 (0.16), residues: 1108 sheet: -2.25 (0.24), residues: 391 loop : -2.69 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 409 HIS 0.004 0.001 HIS C 150 PHE 0.028 0.002 PHE D 892 TYR 0.019 0.001 TYR D1241 ARG 0.008 0.001 ARG D1149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8779 (tm-30) REVERT: B 8 PHE cc_start: 0.8027 (p90) cc_final: 0.6996 (p90) REVERT: B 25 LYS cc_start: 0.9322 (ptmm) cc_final: 0.8997 (ptmm) REVERT: C 124 MET cc_start: 0.8761 (pmm) cc_final: 0.8442 (pmm) REVERT: C 239 MET cc_start: 0.9031 (ppp) cc_final: 0.8661 (tpt) REVERT: C 484 LEU cc_start: 0.8846 (mt) cc_final: 0.8234 (tp) REVERT: C 519 ASN cc_start: 0.8769 (t0) cc_final: 0.8370 (t0) REVERT: C 696 ASP cc_start: 0.8997 (t70) cc_final: 0.8624 (t0) REVERT: C 1094 VAL cc_start: 0.9510 (t) cc_final: 0.9276 (p) REVERT: C 1243 MET cc_start: 0.8999 (tmm) cc_final: 0.8716 (tmm) REVERT: D 29 MET cc_start: 0.8977 (ttm) cc_final: 0.8713 (ttp) REVERT: D 183 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8966 (pm20) REVERT: D 321 LYS cc_start: 0.8523 (mptt) cc_final: 0.8040 (mmtt) REVERT: D 375 GLU cc_start: 0.9120 (tp30) cc_final: 0.8740 (tm-30) REVERT: D 466 MET cc_start: 0.8699 (mtp) cc_final: 0.8454 (mtp) REVERT: D 479 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8139 (mt-10) REVERT: D 513 MET cc_start: 0.9080 (ttp) cc_final: 0.8718 (tmm) REVERT: D 644 MET cc_start: 0.9207 (mpp) cc_final: 0.8890 (mpp) REVERT: D 698 MET cc_start: 0.9406 (mmt) cc_final: 0.9155 (tpp) REVERT: D 724 MET cc_start: 0.9307 (mtm) cc_final: 0.8936 (mtt) REVERT: D 725 MET cc_start: 0.8900 (mtp) cc_final: 0.8627 (tmm) REVERT: D 1186 TYR cc_start: 0.8661 (m-10) cc_final: 0.8378 (m-10) REVERT: D 1189 MET cc_start: 0.8691 (ppp) cc_final: 0.8371 (ppp) REVERT: D 1236 GLU cc_start: 0.8986 (tp30) cc_final: 0.8659 (tp30) REVERT: D 1254 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8426 (mt-10) REVERT: E 26 ARG cc_start: 0.9386 (tpm170) cc_final: 0.9000 (tpm170) REVERT: E 38 LEU cc_start: 0.9456 (mp) cc_final: 0.8390 (tt) REVERT: E 62 GLN cc_start: 0.9585 (mp10) cc_final: 0.9319 (mp10) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.3864 time to fit residues: 158.8192 Evaluate side-chains 178 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 293 optimal weight: 6.9990 chunk 317 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 291 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 84 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1307 ASN D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27070 Z= 0.248 Angle : 0.582 8.287 36910 Z= 0.305 Chirality : 0.042 0.171 4224 Planarity : 0.004 0.079 4556 Dihedral : 16.373 159.107 4407 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.96 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.15), residues: 3166 helix: 0.72 (0.16), residues: 1112 sheet: -1.96 (0.26), residues: 375 loop : -2.47 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 807 HIS 0.004 0.001 HIS D 104 PHE 0.020 0.002 PHE C 57 TYR 0.015 0.001 TYR D1241 ARG 0.004 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 PHE cc_start: 0.8063 (p90) cc_final: 0.7121 (p90) REVERT: B 25 LYS cc_start: 0.9353 (ptmm) cc_final: 0.9017 (ptmm) REVERT: B 86 LYS cc_start: 0.9093 (tptm) cc_final: 0.8653 (tppt) REVERT: C 124 MET cc_start: 0.8858 (pmm) cc_final: 0.8611 (pmm) REVERT: C 239 MET cc_start: 0.8946 (ppp) cc_final: 0.8536 (tpt) REVERT: C 429 MET cc_start: 0.9381 (mmt) cc_final: 0.9101 (mmm) REVERT: C 484 LEU cc_start: 0.8889 (mt) cc_final: 0.8180 (tp) REVERT: C 488 MET cc_start: 0.8758 (ttp) cc_final: 0.8458 (tpp) REVERT: C 519 ASN cc_start: 0.8764 (t0) cc_final: 0.8407 (t0) REVERT: C 696 ASP cc_start: 0.8998 (t70) cc_final: 0.8602 (t0) REVERT: C 800 MET cc_start: 0.9163 (pmm) cc_final: 0.8797 (pmm) REVERT: C 930 ASP cc_start: 0.8517 (t70) cc_final: 0.8108 (t0) REVERT: C 1064 ASP cc_start: 0.8072 (m-30) cc_final: 0.7555 (m-30) REVERT: C 1098 LEU cc_start: 0.9525 (mp) cc_final: 0.9284 (mp) REVERT: C 1131 MET cc_start: 0.8972 (mtt) cc_final: 0.8698 (mmm) REVERT: C 1170 MET cc_start: 0.8931 (tmm) cc_final: 0.8681 (tmm) REVERT: C 1304 MET cc_start: 0.9102 (tpp) cc_final: 0.8821 (tpp) REVERT: D 29 MET cc_start: 0.9015 (ttm) cc_final: 0.8722 (ttp) REVERT: D 183 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8944 (pm20) REVERT: D 321 LYS cc_start: 0.8585 (mptt) cc_final: 0.8104 (mmtt) REVERT: D 372 MET cc_start: 0.8871 (mtm) cc_final: 0.8617 (ptp) REVERT: D 375 GLU cc_start: 0.9136 (tp30) cc_final: 0.8785 (tm-30) REVERT: D 466 MET cc_start: 0.8674 (mtp) cc_final: 0.8428 (mtp) REVERT: D 513 MET cc_start: 0.9097 (ttp) cc_final: 0.8713 (tmm) REVERT: D 644 MET cc_start: 0.9267 (mpp) cc_final: 0.8895 (mpp) REVERT: D 698 MET cc_start: 0.9412 (mmt) cc_final: 0.9190 (tpp) REVERT: D 724 MET cc_start: 0.9305 (mtm) cc_final: 0.9072 (mtt) REVERT: D 725 MET cc_start: 0.8968 (mtp) cc_final: 0.8627 (tmm) REVERT: D 822 MET cc_start: 0.8921 (tpt) cc_final: 0.7980 (tpp) REVERT: D 1186 TYR cc_start: 0.8621 (m-10) cc_final: 0.8295 (m-10) REVERT: D 1189 MET cc_start: 0.8715 (ppp) cc_final: 0.8408 (ppp) REVERT: D 1236 GLU cc_start: 0.8943 (tp30) cc_final: 0.8571 (tp30) REVERT: D 1254 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8410 (mt-10) REVERT: E 7 GLN cc_start: 0.9415 (mm110) cc_final: 0.9070 (pp30) REVERT: E 62 GLN cc_start: 0.9589 (mp10) cc_final: 0.9348 (mp10) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3743 time to fit residues: 139.2591 Evaluate side-chains 171 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 0.0040 chunk 220 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 312 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 chunk 279 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 84 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27070 Z= 0.163 Angle : 0.539 7.563 36910 Z= 0.280 Chirality : 0.041 0.169 4224 Planarity : 0.004 0.075 4556 Dihedral : 16.353 159.029 4407 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.26 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 3166 helix: 1.04 (0.16), residues: 1094 sheet: -1.85 (0.25), residues: 391 loop : -2.29 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1276 HIS 0.003 0.001 HIS D 865 PHE 0.016 0.001 PHE C 57 TYR 0.011 0.001 TYR C 3 ARG 0.004 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8807 (tm-30) REVERT: B 8 PHE cc_start: 0.7970 (p90) cc_final: 0.7020 (p90) REVERT: B 86 LYS cc_start: 0.9084 (tptm) cc_final: 0.8782 (tppt) REVERT: B 227 GLN cc_start: 0.8906 (tt0) cc_final: 0.8687 (tt0) REVERT: C 124 MET cc_start: 0.8813 (pmm) cc_final: 0.8506 (pmm) REVERT: C 239 MET cc_start: 0.8907 (ppp) cc_final: 0.8540 (tpt) REVERT: C 319 LEU cc_start: 0.9094 (mt) cc_final: 0.8857 (tp) REVERT: C 484 LEU cc_start: 0.8823 (mt) cc_final: 0.8139 (tp) REVERT: C 519 ASN cc_start: 0.8713 (t0) cc_final: 0.8397 (t0) REVERT: C 565 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8595 (tm-30) REVERT: C 696 ASP cc_start: 0.8928 (t70) cc_final: 0.8532 (t0) REVERT: C 800 MET cc_start: 0.9131 (pmm) cc_final: 0.8746 (pmm) REVERT: C 930 ASP cc_start: 0.8591 (t70) cc_final: 0.8161 (t0) REVERT: C 1064 ASP cc_start: 0.7994 (m-30) cc_final: 0.7514 (m-30) REVERT: C 1094 VAL cc_start: 0.9537 (t) cc_final: 0.9297 (p) REVERT: C 1098 LEU cc_start: 0.9511 (mp) cc_final: 0.9299 (mp) REVERT: C 1131 MET cc_start: 0.8994 (mtt) cc_final: 0.8734 (mmm) REVERT: C 1170 MET cc_start: 0.8962 (tmm) cc_final: 0.8715 (tmm) REVERT: C 1279 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8857 (mm-30) REVERT: C 1329 GLU cc_start: 0.9118 (tt0) cc_final: 0.8895 (tt0) REVERT: D 29 MET cc_start: 0.9002 (ttm) cc_final: 0.8682 (ttp) REVERT: D 151 MET cc_start: 0.5004 (mmp) cc_final: 0.3565 (mmp) REVERT: D 321 LYS cc_start: 0.8639 (mptt) cc_final: 0.8098 (mmtt) REVERT: D 375 GLU cc_start: 0.9081 (tp30) cc_final: 0.8713 (tm-30) REVERT: D 466 MET cc_start: 0.8703 (mtp) cc_final: 0.8428 (mtp) REVERT: D 479 GLU cc_start: 0.8614 (tt0) cc_final: 0.8356 (tt0) REVERT: D 513 MET cc_start: 0.9136 (ttp) cc_final: 0.8706 (tmm) REVERT: D 644 MET cc_start: 0.9240 (mpp) cc_final: 0.8827 (mpp) REVERT: D 724 MET cc_start: 0.9278 (mtm) cc_final: 0.8947 (mtt) REVERT: D 725 MET cc_start: 0.8938 (mtp) cc_final: 0.8575 (tmm) REVERT: D 1186 TYR cc_start: 0.8487 (m-10) cc_final: 0.8248 (m-10) REVERT: D 1189 MET cc_start: 0.8741 (ppp) cc_final: 0.8413 (ppp) REVERT: D 1236 GLU cc_start: 0.8922 (tp30) cc_final: 0.8525 (tp30) REVERT: D 1254 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8360 (mt-10) REVERT: E 62 GLN cc_start: 0.9590 (mp10) cc_final: 0.9328 (mp10) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3602 time to fit residues: 136.2834 Evaluate side-chains 175 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 7.9990 chunk 177 optimal weight: 0.0050 chunk 4 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 266 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 0.0470 chunk 280 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 overall best weight: 4.0098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 84 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 628 HIS C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 811 ASN C1268 GLN D 365 GLN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 : 0.004 0.039 27070 Z= 0.287 Angle : 0.617 7.679 36910 Z= 0.320 Chirality : 0.042 0.198 4224 Planarity : 0.004 0.075 4556 Dihedral : 16.524 158.213 4407 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.44 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 3166 helix: 0.91 (0.16), residues: 1119 sheet: -1.75 (0.27), residues: 378 loop : -2.26 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C1276 HIS 0.005 0.001 HIS D 104 PHE 0.017 0.002 PHE C 57 TYR 0.016 0.001 TYR C 367 ARG 0.005 0.001 ARG C 706 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 PHE cc_start: 0.8038 (p90) cc_final: 0.7104 (p90) REVERT: C 124 MET cc_start: 0.8876 (pmm) cc_final: 0.8599 (pmm) REVERT: C 319 LEU cc_start: 0.9148 (mt) cc_final: 0.8867 (tp) REVERT: C 696 ASP cc_start: 0.8969 (t70) cc_final: 0.8600 (t0) REVERT: C 800 MET cc_start: 0.9172 (pmm) cc_final: 0.8860 (pmm) REVERT: C 930 ASP cc_start: 0.8653 (t70) cc_final: 0.8239 (t0) REVERT: C 1119 MET cc_start: 0.9340 (tpp) cc_final: 0.8873 (tpp) REVERT: C 1131 MET cc_start: 0.9033 (mtt) cc_final: 0.8799 (mmm) REVERT: C 1170 MET cc_start: 0.8996 (tmm) cc_final: 0.8789 (tmm) REVERT: C 1232 MET cc_start: 0.8768 (mmm) cc_final: 0.8544 (mmm) REVERT: C 1274 GLU cc_start: 0.9178 (mp0) cc_final: 0.8727 (mp0) REVERT: C 1290 MET cc_start: 0.9503 (ttm) cc_final: 0.9198 (ttm) REVERT: D 29 MET cc_start: 0.9103 (ttm) cc_final: 0.8823 (ttp) REVERT: D 192 MET cc_start: 0.8071 (ppp) cc_final: 0.7870 (ppp) REVERT: D 321 LYS cc_start: 0.8721 (mptt) cc_final: 0.8135 (mmtt) REVERT: D 372 MET cc_start: 0.8711 (mtp) cc_final: 0.8219 (mtm) REVERT: D 375 GLU cc_start: 0.9136 (tp30) cc_final: 0.8704 (tm-30) REVERT: D 513 MET cc_start: 0.9135 (ttp) cc_final: 0.8695 (tmm) REVERT: D 644 MET cc_start: 0.9223 (mpp) cc_final: 0.8792 (mpp) REVERT: D 724 MET cc_start: 0.9297 (mtm) cc_final: 0.8759 (mtm) REVERT: D 725 MET cc_start: 0.9006 (mtp) cc_final: 0.8648 (tmm) REVERT: D 1156 LEU cc_start: 0.9172 (mp) cc_final: 0.8961 (mp) REVERT: D 1186 TYR cc_start: 0.8635 (m-10) cc_final: 0.8361 (m-10) REVERT: D 1189 MET cc_start: 0.8764 (ppp) cc_final: 0.8430 (ppp) REVERT: D 1236 GLU cc_start: 0.8908 (tp30) cc_final: 0.8482 (tp30) REVERT: D 1254 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8405 (mt-10) REVERT: E 7 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9054 (mm-40) REVERT: E 43 ASN cc_start: 0.9627 (t0) cc_final: 0.9412 (t0) REVERT: E 62 GLN cc_start: 0.9604 (mp10) cc_final: 0.9400 (mp10) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.3623 time to fit residues: 126.4375 Evaluate side-chains 155 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 312 optimal weight: 0.0980 chunk 259 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27070 Z= 0.341 Angle : 0.665 7.984 36910 Z= 0.345 Chirality : 0.043 0.225 4224 Planarity : 0.004 0.080 4556 Dihedral : 16.729 161.124 4407 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.38 % Favored : 90.56 % Rotamer: Outliers : 0.04 % Allowed : 2.19 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.15), residues: 3166 helix: 0.70 (0.16), residues: 1122 sheet: -1.77 (0.26), residues: 385 loop : -2.19 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C1276 HIS 0.006 0.001 HIS D 450 PHE 0.026 0.002 PHE C 812 TYR 0.021 0.002 TYR C 367 ARG 0.006 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 PHE cc_start: 0.8178 (p90) cc_final: 0.7253 (p90) REVERT: C 124 MET cc_start: 0.8925 (pmm) cc_final: 0.8660 (pmm) REVERT: C 369 MET cc_start: 0.9417 (tmm) cc_final: 0.9188 (tmm) REVERT: C 488 MET cc_start: 0.8289 (tpt) cc_final: 0.8053 (tpp) REVERT: C 696 ASP cc_start: 0.9059 (t70) cc_final: 0.8713 (t0) REVERT: C 800 MET cc_start: 0.9196 (pmm) cc_final: 0.8953 (pmm) REVERT: C 930 ASP cc_start: 0.8696 (t70) cc_final: 0.8274 (t0) REVERT: C 1107 MET cc_start: 0.8918 (mtp) cc_final: 0.8683 (mtt) REVERT: C 1119 MET cc_start: 0.9387 (tpp) cc_final: 0.9026 (tpp) REVERT: C 1131 MET cc_start: 0.8984 (mtt) cc_final: 0.8548 (mmp) REVERT: C 1170 MET cc_start: 0.9037 (tmm) cc_final: 0.8828 (tmm) REVERT: C 1274 GLU cc_start: 0.9161 (mp0) cc_final: 0.8661 (mp0) REVERT: C 1290 MET cc_start: 0.9401 (ttm) cc_final: 0.9072 (ttm) REVERT: D 29 MET cc_start: 0.9063 (ttm) cc_final: 0.8727 (ttp) REVERT: D 102 MET cc_start: 0.8625 (pmm) cc_final: 0.8294 (pmm) REVERT: D 192 MET cc_start: 0.8140 (ppp) cc_final: 0.7930 (ppp) REVERT: D 321 LYS cc_start: 0.8808 (mptt) cc_final: 0.8444 (mmtm) REVERT: D 348 ASP cc_start: 0.8775 (p0) cc_final: 0.8523 (p0) REVERT: D 375 GLU cc_start: 0.9141 (tp30) cc_final: 0.8723 (tm-30) REVERT: D 466 MET cc_start: 0.8529 (mtp) cc_final: 0.8307 (mtp) REVERT: D 644 MET cc_start: 0.9223 (mpp) cc_final: 0.8718 (mpp) REVERT: D 724 MET cc_start: 0.9307 (mtm) cc_final: 0.8761 (mtm) REVERT: D 725 MET cc_start: 0.8998 (mtp) cc_final: 0.8635 (tmm) REVERT: D 822 MET cc_start: 0.8638 (tpp) cc_final: 0.8423 (tpp) REVERT: D 1186 TYR cc_start: 0.8644 (m-10) cc_final: 0.8291 (m-10) REVERT: D 1189 MET cc_start: 0.8778 (ppp) cc_final: 0.8463 (ppp) REVERT: D 1236 GLU cc_start: 0.8869 (tp30) cc_final: 0.8423 (tp30) REVERT: D 1254 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8366 (mt-10) REVERT: E 7 GLN cc_start: 0.9330 (mm-40) cc_final: 0.8977 (mm-40) REVERT: E 43 ASN cc_start: 0.9642 (t0) cc_final: 0.9421 (t0) REVERT: E 62 GLN cc_start: 0.9592 (mp10) cc_final: 0.9313 (mp10) REVERT: E 67 ARG cc_start: 0.9551 (ttm110) cc_final: 0.9332 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.3753 time to fit residues: 123.8168 Evaluate side-chains 156 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 176 optimal weight: 0.0070 chunk 263 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 311 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27070 Z= 0.176 Angle : 0.573 8.776 36910 Z= 0.297 Chirality : 0.042 0.221 4224 Planarity : 0.004 0.076 4556 Dihedral : 16.621 162.293 4407 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.68 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3166 helix: 1.01 (0.16), residues: 1114 sheet: -1.54 (0.26), residues: 395 loop : -2.09 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1276 HIS 0.005 0.001 HIS D 450 PHE 0.033 0.001 PHE C 253 TYR 0.013 0.001 TYR C1229 ARG 0.005 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8121 (t80) cc_final: 0.7907 (t80) REVERT: B 8 PHE cc_start: 0.7985 (p90) cc_final: 0.7249 (p90) REVERT: C 124 MET cc_start: 0.8792 (pmm) cc_final: 0.8549 (pmm) REVERT: C 369 MET cc_start: 0.9376 (tmm) cc_final: 0.9111 (tmm) REVERT: C 565 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8711 (tm-30) REVERT: C 696 ASP cc_start: 0.8966 (t70) cc_final: 0.8596 (t0) REVERT: C 930 ASP cc_start: 0.8681 (t70) cc_final: 0.8253 (t0) REVERT: C 1107 MET cc_start: 0.8935 (mtp) cc_final: 0.8659 (mtt) REVERT: C 1119 MET cc_start: 0.9356 (tpp) cc_final: 0.8942 (tpp) REVERT: C 1131 MET cc_start: 0.9019 (mtt) cc_final: 0.8555 (mmp) REVERT: C 1170 MET cc_start: 0.9007 (tmm) cc_final: 0.8777 (tmm) REVERT: C 1290 MET cc_start: 0.9285 (ttm) cc_final: 0.8994 (ttm) REVERT: C 1329 GLU cc_start: 0.9130 (tt0) cc_final: 0.8826 (tt0) REVERT: D 29 MET cc_start: 0.9054 (ttm) cc_final: 0.8702 (ttp) REVERT: D 102 MET cc_start: 0.8585 (pmm) cc_final: 0.8284 (pmm) REVERT: D 321 LYS cc_start: 0.8767 (mptt) cc_final: 0.8416 (mmtm) REVERT: D 348 ASP cc_start: 0.8750 (p0) cc_final: 0.8499 (p0) REVERT: D 375 GLU cc_start: 0.9073 (tp30) cc_final: 0.8695 (tm-30) REVERT: D 466 MET cc_start: 0.8471 (mtp) cc_final: 0.8266 (mtp) REVERT: D 513 MET cc_start: 0.9143 (ttp) cc_final: 0.8863 (ttp) REVERT: D 644 MET cc_start: 0.9249 (mpp) cc_final: 0.8966 (mpp) REVERT: D 725 MET cc_start: 0.8969 (mtp) cc_final: 0.8620 (tmm) REVERT: D 1040 MET cc_start: 0.2983 (ttt) cc_final: 0.2037 (ppp) REVERT: D 1186 TYR cc_start: 0.8515 (m-10) cc_final: 0.8233 (m-10) REVERT: D 1189 MET cc_start: 0.8725 (ppp) cc_final: 0.8438 (ppp) REVERT: D 1236 GLU cc_start: 0.8853 (tp30) cc_final: 0.8387 (tp30) REVERT: D 1254 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8308 (mt-10) REVERT: E 7 GLN cc_start: 0.9324 (mm-40) cc_final: 0.8952 (mm-40) REVERT: E 43 ASN cc_start: 0.9665 (t0) cc_final: 0.9420 (t0) REVERT: E 62 GLN cc_start: 0.9587 (mp10) cc_final: 0.9327 (mp10) REVERT: E 67 ARG cc_start: 0.9549 (ttm110) cc_final: 0.9311 (tpp80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3748 time to fit residues: 128.4017 Evaluate side-chains 159 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 3.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 27070 Z= 0.378 Angle : 0.705 9.369 36910 Z= 0.365 Chirality : 0.044 0.247 4224 Planarity : 0.005 0.076 4556 Dihedral : 16.825 162.178 4407 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.30 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 3166 helix: 0.65 (0.16), residues: 1122 sheet: -1.65 (0.27), residues: 376 loop : -2.14 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C1276 HIS 0.006 0.001 HIS D1227 PHE 0.025 0.002 PHE C 57 TYR 0.026 0.002 TYR C1281 ARG 0.014 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 PHE cc_start: 0.8169 (p90) cc_final: 0.7259 (p90) REVERT: C 124 MET cc_start: 0.8956 (pmm) cc_final: 0.8648 (pmm) REVERT: C 369 MET cc_start: 0.9440 (tmm) cc_final: 0.9219 (tmm) REVERT: C 800 MET cc_start: 0.9238 (pmm) cc_final: 0.8910 (pmm) REVERT: C 996 ARG cc_start: 0.8846 (tmt-80) cc_final: 0.8568 (tpt90) REVERT: C 1107 MET cc_start: 0.8870 (mtp) cc_final: 0.8579 (mtt) REVERT: C 1131 MET cc_start: 0.8993 (mtt) cc_final: 0.8572 (mmp) REVERT: C 1170 MET cc_start: 0.9083 (tmm) cc_final: 0.8859 (tmm) REVERT: C 1290 MET cc_start: 0.9513 (ttm) cc_final: 0.9029 (ttm) REVERT: D 29 MET cc_start: 0.9056 (ttm) cc_final: 0.8733 (ttp) REVERT: D 102 MET cc_start: 0.8597 (pmm) cc_final: 0.8150 (pmm) REVERT: D 192 MET cc_start: 0.8075 (ppp) cc_final: 0.7851 (ppp) REVERT: D 242 LEU cc_start: 0.9169 (tp) cc_final: 0.8967 (tp) REVERT: D 321 LYS cc_start: 0.8809 (mptt) cc_final: 0.8461 (mmtm) REVERT: D 348 ASP cc_start: 0.8821 (p0) cc_final: 0.8504 (p0) REVERT: D 375 GLU cc_start: 0.9154 (tp30) cc_final: 0.8719 (tm-30) REVERT: D 513 MET cc_start: 0.9206 (ttp) cc_final: 0.8905 (ttp) REVERT: D 644 MET cc_start: 0.9127 (mpp) cc_final: 0.8589 (mpp) REVERT: D 724 MET cc_start: 0.9335 (mtt) cc_final: 0.8889 (mtt) REVERT: D 725 MET cc_start: 0.8978 (mtp) cc_final: 0.8498 (tmm) REVERT: D 1040 MET cc_start: 0.2592 (ttt) cc_final: 0.1660 (ppp) REVERT: D 1186 TYR cc_start: 0.8661 (m-10) cc_final: 0.8324 (m-10) REVERT: D 1189 MET cc_start: 0.8822 (ppp) cc_final: 0.8512 (ppp) REVERT: D 1236 GLU cc_start: 0.8873 (tp30) cc_final: 0.8469 (tp30) REVERT: D 1254 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8324 (mt-10) REVERT: E 7 GLN cc_start: 0.9319 (mm-40) cc_final: 0.8942 (mm110) REVERT: E 43 ASN cc_start: 0.9628 (t0) cc_final: 0.9396 (t0) REVERT: E 62 GLN cc_start: 0.9567 (mp10) cc_final: 0.9301 (mp10) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.3665 time to fit residues: 112.2552 Evaluate side-chains 148 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 chunk 272 optimal weight: 20.0000 chunk 290 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 262 optimal weight: 9.9990 chunk 274 optimal weight: 7.9990 chunk 289 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27070 Z= 0.176 Angle : 0.587 8.518 36910 Z= 0.302 Chirality : 0.042 0.200 4224 Planarity : 0.004 0.078 4556 Dihedral : 16.719 165.145 4407 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.15), residues: 3166 helix: 1.03 (0.16), residues: 1113 sheet: -1.46 (0.26), residues: 389 loop : -2.02 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1276 HIS 0.005 0.001 HIS D 450 PHE 0.024 0.001 PHE C 812 TYR 0.020 0.001 TYR C1281 ARG 0.004 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 PHE cc_start: 0.7958 (p90) cc_final: 0.7283 (p90) REVERT: C 124 MET cc_start: 0.8792 (pmm) cc_final: 0.8489 (pmm) REVERT: C 369 MET cc_start: 0.9429 (tmm) cc_final: 0.9134 (tmm) REVERT: C 561 ILE cc_start: 0.9628 (mp) cc_final: 0.9282 (tp) REVERT: C 696 ASP cc_start: 0.8980 (t70) cc_final: 0.8603 (t0) REVERT: C 800 MET cc_start: 0.9269 (pmm) cc_final: 0.8841 (pmm) REVERT: C 930 ASP cc_start: 0.8703 (t70) cc_final: 0.8283 (t0) REVERT: C 996 ARG cc_start: 0.8805 (tmt-80) cc_final: 0.8484 (tpt90) REVERT: C 1107 MET cc_start: 0.8859 (mtp) cc_final: 0.8504 (mtt) REVERT: C 1119 MET cc_start: 0.9508 (tpp) cc_final: 0.8808 (tpp) REVERT: C 1131 MET cc_start: 0.9005 (mtt) cc_final: 0.8551 (mmp) REVERT: C 1170 MET cc_start: 0.9047 (tmm) cc_final: 0.8799 (tmm) REVERT: C 1290 MET cc_start: 0.9453 (ttm) cc_final: 0.8936 (ttm) REVERT: C 1329 GLU cc_start: 0.9060 (tt0) cc_final: 0.8744 (tt0) REVERT: D 29 MET cc_start: 0.9056 (ttm) cc_final: 0.8724 (ttp) REVERT: D 102 MET cc_start: 0.8630 (pmm) cc_final: 0.8258 (pmm) REVERT: D 192 MET cc_start: 0.8057 (ppp) cc_final: 0.7831 (ppp) REVERT: D 321 LYS cc_start: 0.8756 (mptt) cc_final: 0.8398 (mmtm) REVERT: D 348 ASP cc_start: 0.8766 (p0) cc_final: 0.8453 (p0) REVERT: D 375 GLU cc_start: 0.9110 (tp30) cc_final: 0.8682 (tm-30) REVERT: D 505 ASP cc_start: 0.8456 (t70) cc_final: 0.8227 (t70) REVERT: D 513 MET cc_start: 0.9225 (ttp) cc_final: 0.8905 (ttp) REVERT: D 644 MET cc_start: 0.9096 (mpp) cc_final: 0.8580 (mpp) REVERT: D 724 MET cc_start: 0.9288 (mtt) cc_final: 0.8843 (mtt) REVERT: D 1040 MET cc_start: 0.2615 (ttt) cc_final: 0.1725 (ppp) REVERT: D 1186 TYR cc_start: 0.8460 (m-10) cc_final: 0.8173 (m-10) REVERT: D 1189 MET cc_start: 0.8735 (ppp) cc_final: 0.8459 (ppp) REVERT: D 1236 GLU cc_start: 0.8852 (tp30) cc_final: 0.8384 (tp30) REVERT: D 1254 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8303 (mt-10) REVERT: E 7 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8920 (mm110) REVERT: E 62 GLN cc_start: 0.9555 (mp10) cc_final: 0.9317 (mp10) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.3775 time to fit residues: 123.7125 Evaluate side-chains 152 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 197 optimal weight: 0.0980 chunk 157 optimal weight: 0.6980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27070 Z= 0.258 Angle : 0.628 9.207 36910 Z= 0.324 Chirality : 0.043 0.217 4224 Planarity : 0.004 0.076 4556 Dihedral : 16.758 163.853 4407 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.78 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 3166 helix: 0.99 (0.16), residues: 1114 sheet: -1.62 (0.25), residues: 401 loop : -2.01 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1276 HIS 0.005 0.001 HIS D 450 PHE 0.024 0.002 PHE C 57 TYR 0.023 0.001 TYR C1281 ARG 0.007 0.000 ARG E 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6332 Ramachandran restraints generated. 3166 Oldfield, 0 Emsley, 3166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 PHE cc_start: 0.8061 (p90) cc_final: 0.7266 (p90) REVERT: C 124 MET cc_start: 0.8828 (pmm) cc_final: 0.8538 (pmm) REVERT: C 369 MET cc_start: 0.9471 (tmm) cc_final: 0.9218 (tmm) REVERT: C 653 MET cc_start: 0.8324 (tpt) cc_final: 0.8051 (tpp) REVERT: C 696 ASP cc_start: 0.8998 (t70) cc_final: 0.8648 (t0) REVERT: C 800 MET cc_start: 0.9291 (pmm) cc_final: 0.8876 (pmm) REVERT: C 930 ASP cc_start: 0.8754 (t70) cc_final: 0.8357 (t0) REVERT: C 1107 MET cc_start: 0.8845 (mtp) cc_final: 0.8547 (mtt) REVERT: C 1119 MET cc_start: 0.9507 (tpp) cc_final: 0.8791 (tpp) REVERT: C 1131 MET cc_start: 0.9044 (mtt) cc_final: 0.8615 (mmp) REVERT: C 1170 MET cc_start: 0.9071 (tmm) cc_final: 0.8834 (tmm) REVERT: C 1290 MET cc_start: 0.9459 (ttm) cc_final: 0.8992 (ttm) REVERT: C 1329 GLU cc_start: 0.9038 (tt0) cc_final: 0.8717 (tt0) REVERT: D 29 MET cc_start: 0.9066 (ttm) cc_final: 0.8702 (ttp) REVERT: D 102 MET cc_start: 0.8579 (pmm) cc_final: 0.8113 (pmm) REVERT: D 192 MET cc_start: 0.8085 (ppp) cc_final: 0.7865 (ppp) REVERT: D 321 LYS cc_start: 0.8791 (mptt) cc_final: 0.8416 (mmtm) REVERT: D 375 GLU cc_start: 0.9139 (tp30) cc_final: 0.8683 (tm-30) REVERT: D 505 ASP cc_start: 0.8555 (t70) cc_final: 0.8337 (t70) REVERT: D 644 MET cc_start: 0.9130 (mpp) cc_final: 0.8643 (mpp) REVERT: D 724 MET cc_start: 0.9262 (mtt) cc_final: 0.8841 (mtt) REVERT: D 1040 MET cc_start: 0.2600 (ttt) cc_final: 0.1702 (ppp) REVERT: D 1186 TYR cc_start: 0.8475 (m-10) cc_final: 0.8238 (m-10) REVERT: D 1189 MET cc_start: 0.8740 (ppp) cc_final: 0.8460 (ppp) REVERT: D 1236 GLU cc_start: 0.8844 (tp30) cc_final: 0.8431 (tp30) REVERT: D 1254 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8262 (mt-10) REVERT: E 7 GLN cc_start: 0.9262 (mm-40) cc_final: 0.8925 (mm110) REVERT: E 43 ASN cc_start: 0.9601 (t0) cc_final: 0.9385 (t0) REVERT: E 62 GLN cc_start: 0.9559 (mp10) cc_final: 0.9311 (mp10) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3801 time to fit residues: 115.6456 Evaluate side-chains 152 residues out of total 2708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 658 GLN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.041313 restraints weight = 153787.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.042556 restraints weight = 87661.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.043409 restraints weight = 60090.493| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 27070 Z= 0.477 Angle : 0.810 11.813 36910 Z= 0.419 Chirality : 0.046 0.265 4224 Planarity : 0.005 0.074 4556 Dihedral : 17.111 166.549 4407 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.40 % Favored : 88.53 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.15), residues: 3166 helix: 0.27 (0.15), residues: 1122 sheet: -1.64 (0.26), residues: 383 loop : -2.21 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C1276 HIS 0.008 0.002 HIS D1227 PHE 0.029 0.003 PHE C 57 TYR 0.028 0.002 TYR D1241 ARG 0.007 0.001 ARG E 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4571.59 seconds wall clock time: 84 minutes 4.81 seconds (5044.81 seconds total)