Starting phenix.real_space_refine on Sat Aug 8 12:10:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gh6_0002/08_2026/6gh6_0002.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gh6_0002/08_2026/6gh6_0002.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/cci-nas-00/data/ceres_data/6gh6_0002/08_2026/6gh6_0002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gh6_0002/08_2026/6gh6_0002.map" model { file = "/net/cci-nas-00/data/ceres_data/6gh6_0002/08_2026/6gh6_0002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gh6_0002/08_2026/6gh6_0002.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 96 5.16 5 C 17252 2.51 5 N 4960 2.21 5 O 5647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28051 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1776 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1729 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'ASP:plan': 4, 'HIS:plan': 2, 'GLU:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 10068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10068 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'TYR:plan': 4, 'GLU:plan': 24, 'ARG:plan': 20, 'ASP:plan': 10, 'PHE:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 6, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 333 Chain: "D" Number of atoms: 10063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10063 Classifications: {'peptide': 1334} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 65} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 51, 'TRANS': 1279} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 398 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 11, 'ARG:plan': 14, 'TYR:plan': 4, 'HIS:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 206 Chain: "E" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 568 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 27 Chain: "M" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 958 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 3, 'TRANS': 139} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 9, 'ARG:plan': 7, 'GLN:plan1': 2, 'PHE:plan': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 144 Chain: "M" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 536 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'UNK:plan-1': 35, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 128 Chain: "M" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 381 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 61} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'UNK:plan-1': 16, 'ARG:plan': 5, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "N" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 988 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "T" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 984 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N ASP M 168 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP M 168 " occ=0.20 residue: pdb=" N GLU M 169 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU M 169 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 6.22, per 1000 atoms: 0.22 Number of scatterers: 28051 At special positions: 0 Unit cell: (137.16, 171.72, 165.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 96 15.00 O 5647 8.00 N 4960 7.00 C 17252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6558 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 36 sheets defined 38.4% alpha, 11.5% beta 38 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.970A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.657A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.600A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.829A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.961A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.609A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 28 through 39 removed outlier: 4.064A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.620A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 159 through 163 removed outlier: 4.014A pdb=" N GLY C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.060A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.753A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.532A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.700A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 4.083A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.705A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 388 removed outlier: 3.660A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 removed outlier: 4.112A pdb=" N ARG C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.522A pdb=" N GLY C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) 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 479 removed outlier: 3.548A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 4.435A pdb=" N ASP C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 487 through 492' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.899A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 607 through 613 removed outlier: 4.151A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.160A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.751A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.646A pdb=" N GLN C 686 " --> pdb=" O GLY C 682 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.623A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 removed outlier: 3.710A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 911 removed outlier: 4.575A pdb=" N ALA C 910 " --> pdb=" O GLY C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 979 removed outlier: 4.159A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.538A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1037 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.095A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.911A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1168 through 1177 Processing helix chain 'C' and resid 1191 through 1201 removed outlier: 3.785A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1310 removed outlier: 4.063A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1321 through 1333 removed outlier: 4.098A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.793A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.511A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.730A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.583A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.530A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.788A 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 331 removed outlier: 3.792A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 4.245A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 376 " --> pdb=" O MET D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 removed outlier: 3.878A pdb=" N GLY D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.022A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.653A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 483 removed outlier: 4.179A pdb=" N LEU D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.713A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 539 removed outlier: 4.328A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 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 588 through 592 removed outlier: 3.822A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.697A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.741A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 701 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.812A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 783 removed outlier: 4.365A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 805 removed outlier: 3.875A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR D 797 " --> pdb=" O SER D 793 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.103A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 916 through 925 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.815A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.397A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1291 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.977A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1353 Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 3.702A pdb=" N MET D1370 " --> pdb=" O HIS D1366 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D1372 " --> pdb=" O ASP D1368 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.909A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.561A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 120 through 131 removed outlier: 3.582A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 146 removed outlier: 3.805A pdb=" N ASP M 146 " --> pdb=" O THR M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 164 removed outlier: 3.675A pdb=" N ILE M 161 " --> pdb=" O GLN M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 3.787A pdb=" N ALA M 177 " --> pdb=" O GLU M 173 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 207 removed outlier: 4.747A pdb=" N ALA M 207 " --> pdb=" O LEU M 203 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.834A pdb=" N ALA M 216 " --> pdb=" O TRP M 212 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS M 223 " --> pdb=" O ILE M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 231 removed outlier: 4.592A pdb=" N HIS M 230 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP M 231 " --> pdb=" O LEU M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 255 removed outlier: 4.230A pdb=" N LYS M 247 " --> pdb=" O GLU M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 355 removed outlier: 3.716A pdb=" N SER M 344 " --> pdb=" O LEU M 340 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 374 removed outlier: 3.960A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 388 removed outlier: 3.958A pdb=" N GLN M 387 " --> pdb=" O ARG M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 428 Processing helix chain 'M' and resid 438 through 449 removed outlier: 3.642A pdb=" N GLN M 449 " --> pdb=" O MET M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 455 through 463 removed outlier: 3.608A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 5.153A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 105 removed outlier: 8.377A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 105 removed outlier: 3.568A pdb=" N LEU B 102 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA6, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.440A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.534A pdb=" N GLU C 67 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 103 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.534A pdb=" N GLU C 67 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 103 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 145 removed outlier: 3.689A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 454 removed outlier: 7.007A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 154 through 158 removed outlier: 4.177A pdb=" N ALA C 174 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 285 through 286 removed outlier: 4.001A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.796A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.606A pdb=" N VAL C 296 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 336 " --> pdb=" O VAL C 296 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.741A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.741A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.637A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.731A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 724 through 727 removed outlier: 4.896A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC3, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 5.093A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AC5, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.974A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.974A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 865 through 866 removed outlier: 3.503A pdb=" N ILE C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1335 through 1336 removed outlier: 3.965A pdb=" N ALA D 23 " --> pdb=" O ASN C1336 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 104 through 106 Processing sheet with id=AD1, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.488A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 435 through 437 removed outlier: 3.570A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 366 through 369 Processing sheet with id=AD4, first strand: chain 'D' and resid 527 through 528 removed outlier: 7.233A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD6, first strand: chain 'D' and resid 959 through 961 removed outlier: 4.311A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1160 through 1163 removed outlier: 4.418A pdb=" N ILE D1162 " --> pdb=" O GLU D1202 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU D1202 " --> pdb=" O ILE D1162 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AD9, first strand: chain 'M' and resid 279 through 281 964 hydrogen bonds defined for protein. 2736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 7.31 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 1 1.13 - 1.30: 4748 1.30 - 1.47: 11003 1.47 - 1.64: 12712 1.64 - 1.81: 170 Bond restraints: 28634 Sorted by residual: bond pdb=" C THR D 514 " pdb=" N ARG D 515 " ideal model delta sigma weight residual 1.329 0.964 0.365 1.36e-02 5.41e+03 7.22e+02 bond pdb=" C GLU M 356 " pdb=" N GLN M 357 " ideal model delta sigma weight residual 1.332 1.507 -0.175 1.40e-02 5.10e+03 1.56e+02 bond pdb=" C THR M 210 " pdb=" N PRO M 211 " ideal model delta sigma weight residual 1.334 1.511 -0.177 2.34e-02 1.83e+03 5.75e+01 bond pdb=" O3' DA T 1 " pdb=" P DG T 2 " ideal model delta sigma weight residual 1.607 1.686 -0.079 1.20e-02 6.94e+03 4.33e+01 bond pdb=" O3' DG T 2 " pdb=" P DG T 3 " ideal model delta sigma weight residual 1.607 1.670 -0.063 1.20e-02 6.94e+03 2.76e+01 ... (remaining 28629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.35: 39213 6.35 - 12.71: 65 12.71 - 19.06: 13 19.06 - 25.41: 4 25.41 - 31.76: 2 Bond angle restraints: 39297 Sorted by residual: angle pdb=" CA GLU M 356 " pdb=" C GLU M 356 " pdb=" N GLN M 357 " ideal model delta sigma weight residual 116.51 85.96 30.55 1.34e+00 5.57e-01 5.20e+02 angle pdb=" O GLU M 356 " pdb=" C GLU M 356 " pdb=" N GLN M 357 " ideal model delta sigma weight residual 123.12 146.82 -23.70 1.32e+00 5.74e-01 3.22e+02 angle pdb=" C GLU M 356 " pdb=" N GLN M 357 " pdb=" CA GLN M 357 " ideal model delta sigma weight residual 121.54 89.78 31.76 1.91e+00 2.74e-01 2.77e+02 angle pdb=" O5' DC N -6 " pdb=" C5' DC N -6 " pdb=" C4' DC N -6 " ideal model delta sigma weight residual 109.40 119.41 -10.01 8.00e-01 1.56e+00 1.57e+02 angle pdb=" O3' DC T 5 " pdb=" P DT T 6 " pdb=" O5' DT T 6 " ideal model delta sigma weight residual 104.00 125.91 -21.91 1.90e+00 2.77e-01 1.33e+02 ... (remaining 39292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 16615 35.29 - 70.58: 557 70.58 - 105.87: 24 105.87 - 141.17: 3 141.17 - 176.46: 4 Dihedral angle restraints: 17203 sinusoidal: 7047 harmonic: 10156 Sorted by residual: dihedral pdb=" CA ALA C1263 " pdb=" C ALA C1263 " pdb=" N GLN C1264 " pdb=" CA GLN C1264 " ideal model delta harmonic sigma weight residual -180.00 -139.71 -40.29 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" CA LEU D 343 " pdb=" C LEU D 343 " pdb=" N GLY D 344 " pdb=" CA GLY D 344 " ideal model delta harmonic sigma weight residual 180.00 -146.65 -33.35 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA PRO D1026 " pdb=" C PRO D1026 " pdb=" N VAL D1027 " pdb=" CA VAL D1027 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 17200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 4645 0.207 - 0.414: 22 0.414 - 0.621: 3 0.621 - 0.828: 0 0.828 - 1.035: 1 Chirality restraints: 4671 Sorted by residual: chirality pdb=" C4' DC T 5 " pdb=" C5' DC T 5 " pdb=" O4' DC T 5 " pdb=" C3' DC T 5 " both_signs ideal model delta sigma weight residual False -2.53 -1.50 -1.03 2.00e-01 2.50e+01 2.68e+01 chirality pdb=" C4' DT T 6 " pdb=" C5' DT T 6 " pdb=" O4' DT T 6 " pdb=" C3' DT T 6 " both_signs ideal model delta sigma weight residual False -2.53 -1.94 -0.59 2.00e-01 2.50e+01 8.74e+00 chirality pdb=" CA UNK M 270 " pdb=" N UNK M 270 " pdb=" C UNK M 270 " pdb=" CB UNK M 270 " both_signs ideal model delta sigma weight residual False 2.52 2.02 0.50 2.00e-01 2.50e+01 6.24e+00 ... (remaining 4668 not shown) Planarity restraints: 4826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU M 356 " 0.026 2.00e-02 2.50e+03 7.98e-02 6.37e+01 pdb=" C GLU M 356 " -0.136 2.00e-02 2.50e+03 pdb=" O GLU M 356 " 0.066 2.00e-02 2.50e+03 pdb=" N GLN M 357 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N -8 " -0.051 2.00e-02 2.50e+03 2.31e-02 1.60e+01 pdb=" N9 DG N -8 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG N -8 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG N -8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG N -8 " 0.014 2.00e-02 2.50e+03 pdb=" C6 DG N -8 " -0.020 2.00e-02 2.50e+03 pdb=" O6 DG N -8 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG N -8 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DG N -8 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG N -8 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG N -8 " 0.027 2.00e-02 2.50e+03 pdb=" C4 DG N -8 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N -7 " -0.050 2.00e-02 2.50e+03 2.31e-02 1.46e+01 pdb=" N9 DA N -7 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA N -7 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA N -7 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA N -7 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA N -7 " -0.014 2.00e-02 2.50e+03 pdb=" N6 DA N -7 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DA N -7 " -0.019 2.00e-02 2.50e+03 pdb=" C2 DA N -7 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA N -7 " 0.023 2.00e-02 2.50e+03 pdb=" C4 DA N -7 " 0.028 2.00e-02 2.50e+03 ... (remaining 4823 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 172 2.53 - 3.12: 22138 3.12 - 3.71: 41188 3.71 - 4.31: 55642 4.31 - 4.90: 90379 Nonbonded interactions: 209519 Sorted by model distance: nonbonded pdb=" OE1 GLU D 523 " pdb=" N GLY D 524 " model vdw 1.934 3.120 nonbonded pdb=" C1' DC N -11 " pdb=" OP1 DT N -10 " model vdw 2.124 3.470 nonbonded pdb=" C GLU M 356 " pdb=" C GLN M 357 " model vdw 2.209 2.800 nonbonded pdb=" OG SER C1322 " pdb=" NZ LYS D 332 " model vdw 2.215 3.120 nonbonded pdb=" C4' DA N -12 " pdb=" OP1 DC N -11 " model vdw 2.220 3.470 ... (remaining 209514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 65 or (resid 66 through 68 and (nam \ e N or name CA or name C or name O or name CB )) or resid 69 through 70 or (resi \ d 71 through 72 and (name N or name CA or name C or name O or name CB )) or resi \ d 73 through 79 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 134 or (resid 135 through 138 and (name N or name CA o \ r name C or name O or name CB )) or resid 139 through 142 or (resid 143 and (nam \ e N or name CA or name C or name O or name CB )) or resid 144 through 159 or (re \ sid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 or \ (resid 162 through 166 and (name N or name CA or name C or name O or name CB )) \ or resid 167 through 169 or (resid 170 and (name N or name CA or name C or name \ O or name CB )) or resid 171 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 232 or (resid 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 through 237)) selection = (chain 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 71 or (resid 72 and (name N or name CA or name C or name O \ or name CB )) or resid 73 through 92 or (resid 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 or (resid 95 and (name N or name CA or na \ me C or name O or name CB )) or resid 96 through 190 or (resid 191 and (name N o \ r name CA or name C or name O or name CB )) or resid 192 or (resid 193 and (name \ N or name CA or name C or name O or name CB )) or resid 194 through 236 or (res \ id 237 and (name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 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: 1.060 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.220 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 : 0.004 0.365 28634 Z= 0.324 Angle : 0.921 31.765 39297 Z= 0.572 Chirality : 0.052 1.035 4671 Planarity : 0.004 0.080 4826 Dihedral : 14.496 176.458 10645 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.75 % Favored : 89.33 % Rotamer: Outliers : 0.38 % Allowed : 1.49 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.11), residues: 3458 helix: -2.82 (0.11), residues: 1112 sheet: -1.21 (0.26), residues: 285 loop : -2.40 (0.11), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 407 TYR 0.013 0.001 TYR C1229 PHE 0.015 0.001 PHE C 828 TRP 0.008 0.001 TRP D1193 HIS 0.006 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.32 (28634) covalent geometry : angle 0.92061 / 0.57 (39297) hydrogen bonds : bond 0.16556 / 10.88 ( 1054) hydrogen bonds : angle 10.22205 / 6.98 ( 2914) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 570 time to evaluate : 1.015 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8252 (mt) cc_final: 0.7511 (mt) REVERT: A 51 MET cc_start: 0.8819 (mmm) cc_final: 0.8549 (mmm) REVERT: A 80 GLU cc_start: 0.9072 (tt0) cc_final: 0.8842 (tt0) REVERT: A 97 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8477 (tm-30) REVERT: A 115 ILE cc_start: 0.9595 (mt) cc_final: 0.9225 (tp) REVERT: A 173 VAL cc_start: 0.9058 (m) cc_final: 0.8430 (p) REVERT: B 29 GLU cc_start: 0.9433 (tt0) cc_final: 0.9152 (tt0) REVERT: B 77 ASP cc_start: 0.9687 (t0) cc_final: 0.9447 (t70) REVERT: B 147 GLN cc_start: 0.9538 (pt0) cc_final: 0.9204 (pp30) REVERT: B 199 ASP cc_start: 0.8543 (m-30) cc_final: 0.8026 (m-30) REVERT: B 212 ASP cc_start: 0.8891 (t0) cc_final: 0.8458 (t0) REVERT: C 124 MET cc_start: 0.9053 (ptp) cc_final: 0.8776 (ptp) REVERT: C 562 GLU cc_start: 0.9315 (mt-10) cc_final: 0.9079 (mt-10) REVERT: C 741 MET cc_start: 0.9205 (ttm) cc_final: 0.8654 (ttm) REVERT: C 816 ILE cc_start: 0.8893 (mt) cc_final: 0.8534 (tt) REVERT: C 876 GLU cc_start: 0.9423 (tt0) cc_final: 0.9172 (mp0) REVERT: C 1046 VAL cc_start: 0.8958 (p) cc_final: 0.8736 (m) REVERT: C 1199 LEU cc_start: 0.9070 (tt) cc_final: 0.8596 (tp) REVERT: C 1226 THR cc_start: 0.9053 (p) cc_final: 0.8738 (t) REVERT: C 1297 ASP cc_start: 0.7788 (t0) cc_final: 0.6983 (t70) REVERT: C 1319 MET cc_start: 0.7962 (ptp) cc_final: 0.7713 (mtm) REVERT: C 1323 PHE cc_start: 0.8682 (t80) cc_final: 0.8439 (t80) REVERT: D 337 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7528 (mpp-170) REVERT: D 461 PHE cc_start: 0.8295 (m-10) cc_final: 0.7681 (m-80) REVERT: D 641 ILE cc_start: 0.9257 (pt) cc_final: 0.8833 (tp) REVERT: D 686 TRP cc_start: 0.7582 (m100) cc_final: 0.7366 (m100) REVERT: D 701 LEU cc_start: 0.5972 (mt) cc_final: 0.5651 (tt) REVERT: D 786 THR cc_start: 0.8602 (m) cc_final: 0.7780 (p) REVERT: D 901 ARG cc_start: 0.7375 (tpt90) cc_final: 0.6911 (tpm170) REVERT: D 917 VAL cc_start: 0.9105 (m) cc_final: 0.8030 (t) REVERT: D 918 ILE cc_start: 0.8322 (pt) cc_final: 0.7884 (mt) REVERT: D 1040 MET cc_start: 0.5240 (mtm) cc_final: 0.4824 (mtt) REVERT: E 5 THR cc_start: 0.9146 (m) cc_final: 0.8824 (t) REVERT: E 53 GLU cc_start: 0.9611 (mt-10) cc_final: 0.9324 (mt-10) REVERT: E 59 ILE cc_start: 0.8815 (mm) cc_final: 0.8580 (mt) REVERT: M 133 PHE cc_start: 0.1967 (m-10) cc_final: 0.1620 (m-10) REVERT: M 205 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8163 (mp10) outliers start: 10 outliers final: 3 residues processed: 580 average time/residue: 0.1913 time to fit residues: 175.5274 Evaluate side-chains 295 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 292 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 0.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 132 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 526 HIS C 582 ASN C 604 HIS C 686 GLN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN C1038 GLN C1072 ASN C1111 GLN C1256 GLN C1264 GLN D 94 GLN D 104 HIS D 209 ASN D 341 ASN D 465 GLN D 519 ASN D 665 GLN D 702 GLN D 897 HIS D 910 ASN D1244 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.124589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.093335 restraints weight = 98055.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.090882 restraints weight = 70381.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091454 restraints weight = 65182.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.091722 restraints weight = 50643.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091933 restraints weight = 47252.801| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1237 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1238 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 28634 Z= 0.148 Angle : 0.710 11.759 39297 Z= 0.371 Chirality : 0.047 0.437 4671 Planarity : 0.005 0.065 4826 Dihedral : 17.764 176.976 4819 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.14 % Favored : 92.22 % Rotamer: Outliers : 0.27 % Allowed : 2.02 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.12), residues: 3458 helix: -1.16 (0.13), residues: 1154 sheet: -0.68 (0.29), residues: 283 loop : -2.21 (0.12), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1034 TYR 0.027 0.001 TYR C1229 PHE 0.013 0.001 PHE C 545 TRP 0.017 0.002 TRP D1193 HIS 0.007 0.001 HIS D 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (28634) covalent geometry : angle 0.70969 / 0.37 (39297) hydrogen bonds : bond 0.05288 / 3.60 ( 1054) hydrogen bonds : angle 6.21648 / 4.21 ( 2914) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 349 time to evaluate : 1.231 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8191 (mt) cc_final: 0.7813 (mt) REVERT: A 58 GLU cc_start: 0.7923 (mp0) cc_final: 0.7714 (mp0) REVERT: A 67 GLU cc_start: 0.8373 (pm20) cc_final: 0.8061 (pm20) REVERT: A 76 GLU cc_start: 0.7875 (mp0) cc_final: 0.7195 (mp0) REVERT: A 79 LEU cc_start: 0.8426 (mp) cc_final: 0.8012 (mt) REVERT: A 226 GLU cc_start: 0.7865 (tp30) cc_final: 0.7609 (tp30) REVERT: B 147 GLN cc_start: 0.8969 (pt0) cc_final: 0.8744 (pp30) REVERT: C 369 MET cc_start: 0.9084 (tmm) cc_final: 0.8528 (tmm) REVERT: C 955 GLN cc_start: 0.8444 (mt0) cc_final: 0.8230 (tm-30) REVERT: C 959 ASP cc_start: 0.8441 (m-30) cc_final: 0.7135 (m-30) REVERT: C 960 LEU cc_start: 0.8970 (pp) cc_final: 0.8543 (tp) REVERT: C 967 LEU cc_start: 0.9537 (mm) cc_final: 0.9296 (pp) REVERT: C 1088 ASP cc_start: 0.8545 (p0) cc_final: 0.8335 (p0) REVERT: C 1170 MET cc_start: 0.7695 (pmm) cc_final: 0.7315 (pmm) REVERT: C 1304 MET cc_start: 0.8299 (tpp) cc_final: 0.8093 (tpp) REVERT: C 1315 MET cc_start: 0.8209 (tpp) cc_final: 0.7927 (tpp) REVERT: D 29 MET cc_start: 0.9231 (mtp) cc_final: 0.8989 (mtp) REVERT: D 35 PHE cc_start: 0.6444 (t80) cc_final: 0.6169 (t80) REVERT: D 151 MET cc_start: 0.7435 (pmm) cc_final: 0.6536 (pmm) REVERT: D 337 ARG cc_start: 0.6727 (mtt90) cc_final: 0.6524 (mpp-170) REVERT: D 339 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7741 (mmt90) REVERT: D 466 MET cc_start: 0.8995 (tpp) cc_final: 0.8622 (ttm) REVERT: D 744 ARG cc_start: 0.8598 (ttt180) cc_final: 0.8251 (mmm-85) REVERT: D 1040 MET cc_start: 0.0058 (mtm) cc_final: -0.0691 (mtt) REVERT: D 1156 LEU cc_start: 0.7510 (mt) cc_final: 0.7267 (mt) REVERT: E 53 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8147 (mt-10) REVERT: M 126 TRP cc_start: 0.9225 (t60) cc_final: 0.8960 (t60) REVERT: M 205 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7886 (mp10) outliers start: 7 outliers final: 3 residues processed: 356 average time/residue: 0.1828 time to fit residues: 105.7539 Evaluate side-chains 247 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 244 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 247 optimal weight: 50.0000 chunk 23 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 339 optimal weight: 50.0000 chunk 27 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C 799 ASN C1288 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 700 ASN D 907 HIS D1218 HIS ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.119227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088361 restraints weight = 97634.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085097 restraints weight = 81582.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086297 restraints weight = 79437.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.085869 restraints weight = 60237.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.086590 restraints weight = 53651.673| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1238 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1238 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 28634 Z= 0.233 Angle : 0.728 10.428 39297 Z= 0.383 Chirality : 0.047 0.394 4671 Planarity : 0.005 0.063 4826 Dihedral : 17.785 176.461 4819 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.53 % Favored : 90.86 % Rotamer: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.13), residues: 3458 helix: -0.33 (0.14), residues: 1158 sheet: -0.54 (0.28), residues: 291 loop : -2.08 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1269 TYR 0.050 0.002 TYR C 810 PHE 0.022 0.002 PHE D 437 TRP 0.023 0.002 TRP C1276 HIS 0.007 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.23 (28634) covalent geometry : angle 0.72815 / 0.38 (39297) hydrogen bonds : bond 0.05443 / 3.72 ( 1054) hydrogen bonds : angle 5.43644 / 3.70 ( 2914) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 280 time to evaluate : 1.069 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8615 (pm20) cc_final: 0.8148 (pm20) REVERT: B 147 GLN cc_start: 0.9045 (pt0) cc_final: 0.8837 (pt0) REVERT: C 805 MET cc_start: 0.9103 (ptm) cc_final: 0.8827 (ptm) REVERT: C 930 ASP cc_start: 0.8298 (t0) cc_final: 0.7931 (t0) REVERT: C 955 GLN cc_start: 0.8428 (mt0) cc_final: 0.8163 (tm-30) REVERT: C 959 ASP cc_start: 0.8467 (m-30) cc_final: 0.7046 (m-30) REVERT: C 1032 LYS cc_start: 0.9451 (tptp) cc_final: 0.9209 (tptp) REVERT: C 1088 ASP cc_start: 0.8861 (p0) cc_final: 0.8562 (p0) REVERT: C 1170 MET cc_start: 0.7812 (pmm) cc_final: 0.7585 (pmm) REVERT: D 29 MET cc_start: 0.9205 (mtp) cc_final: 0.8966 (mtp) REVERT: D 151 MET cc_start: 0.7901 (pmm) cc_final: 0.7174 (pmm) REVERT: D 239 LEU cc_start: 0.8485 (pt) cc_final: 0.8281 (pt) REVERT: D 743 MET cc_start: 0.8145 (mtp) cc_final: 0.7677 (mmm) REVERT: D 1040 MET cc_start: -0.0036 (mtm) cc_final: -0.0967 (mmm) REVERT: E 30 MET cc_start: 0.8425 (mmm) cc_final: 0.8060 (mmm) REVERT: E 53 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8169 (mt-10) REVERT: M 205 GLN cc_start: 0.8508 (mm-40) cc_final: 0.7890 (mp10) outliers start: 5 outliers final: 2 residues processed: 284 average time/residue: 0.1768 time to fit residues: 83.3792 Evaluate side-chains 220 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 81 optimal weight: 30.0000 chunk 258 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 222 optimal weight: 0.5980 chunk 338 optimal weight: 40.0000 chunk 164 optimal weight: 2.9990 chunk 276 optimal weight: 50.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 23 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS C 148 GLN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1264 GLN D 186 GLN D 519 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.119324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.088700 restraints weight = 96377.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.085622 restraints weight = 80326.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.086863 restraints weight = 76145.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086338 restraints weight = 57813.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.086858 restraints weight = 53414.944| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1238 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1238 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 28634 Z= 0.153 Angle : 0.653 10.905 39297 Z= 0.342 Chirality : 0.045 0.400 4671 Planarity : 0.004 0.062 4826 Dihedral : 17.718 177.667 4819 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.81 % Favored : 91.56 % Rotamer: Outliers : 0.04 % Allowed : 2.48 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3458 helix: 0.15 (0.15), residues: 1182 sheet: -0.31 (0.30), residues: 275 loop : -1.99 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 158 TYR 0.029 0.002 TYR C1229 PHE 0.014 0.001 PHE C 828 TRP 0.015 0.002 TRP M 126 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (28634) covalent geometry : angle 0.65303 / 0.34 (39297) hydrogen bonds : bond 0.04771 / 3.23 ( 1054) hydrogen bonds : angle 5.05590 / 3.43 ( 2914) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 1.018 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8064 (mp0) cc_final: 0.7625 (mp0) REVERT: B 15 ASP cc_start: 0.8706 (t0) cc_final: 0.8295 (t0) REVERT: B 147 GLN cc_start: 0.8949 (pt0) cc_final: 0.8729 (pt0) REVERT: B 196 THR cc_start: 0.8342 (p) cc_final: 0.7757 (t) REVERT: B 236 ASP cc_start: 0.5790 (t70) cc_final: 0.5475 (p0) REVERT: C 805 MET cc_start: 0.8991 (ptm) cc_final: 0.8675 (ptm) REVERT: C 930 ASP cc_start: 0.8229 (t0) cc_final: 0.7814 (t0) REVERT: C 955 GLN cc_start: 0.8383 (mt0) cc_final: 0.8176 (tm-30) REVERT: C 959 ASP cc_start: 0.8456 (m-30) cc_final: 0.7113 (m-30) REVERT: C 1023 HIS cc_start: 0.8914 (m90) cc_final: 0.8617 (m-70) REVERT: C 1088 ASP cc_start: 0.8882 (p0) cc_final: 0.8537 (p0) REVERT: C 1304 MET cc_start: 0.8322 (tpp) cc_final: 0.8026 (ttm) REVERT: D 29 MET cc_start: 0.9156 (mtp) cc_final: 0.8943 (mtp) REVERT: D 35 PHE cc_start: 0.6582 (t80) cc_final: 0.6292 (t80) REVERT: D 151 MET cc_start: 0.7873 (pmm) cc_final: 0.7146 (pmm) REVERT: D 725 MET cc_start: 0.8139 (mtm) cc_final: 0.7910 (mtm) REVERT: D 743 MET cc_start: 0.8067 (mtp) cc_final: 0.7702 (mmm) REVERT: D 1040 MET cc_start: -0.0215 (mtm) cc_final: -0.1145 (mmm) REVERT: E 6 VAL cc_start: 0.8609 (t) cc_final: 0.8385 (t) REVERT: E 53 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8039 (mt-10) REVERT: M 205 GLN cc_start: 0.8560 (mm-40) cc_final: 0.7854 (mp10) outliers start: 1 outliers final: 1 residues processed: 276 average time/residue: 0.1674 time to fit residues: 77.8628 Evaluate side-chains 213 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 302 optimal weight: 20.0000 chunk 116 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 257 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 87 optimal weight: 30.0000 chunk 337 optimal weight: 50.0000 chunk 141 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN C1313 HIS D 186 GLN D 419 HIS D 477 GLN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.116571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.076871 restraints weight = 96543.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.076211 restraints weight = 67281.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075902 restraints weight = 59393.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.075978 restraints weight = 58927.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.076236 restraints weight = 51532.340| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1238 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28634 Z= 0.212 Angle : 0.714 10.533 39297 Z= 0.369 Chirality : 0.047 0.388 4671 Planarity : 0.005 0.063 4826 Dihedral : 17.723 179.156 4819 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.79 % Favored : 90.57 % Rotamer: Outliers : 0.04 % Allowed : 2.59 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.14), residues: 3458 helix: 0.39 (0.15), residues: 1197 sheet: -0.71 (0.29), residues: 302 loop : -2.01 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 67 TYR 0.038 0.002 TYR C1229 PHE 0.019 0.002 PHE D 437 TRP 0.016 0.002 TRP C 807 HIS 0.013 0.001 HIS D1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (28634) covalent geometry : angle 0.71438 / 0.37 (39297) hydrogen bonds : bond 0.04992 / 3.42 ( 1054) hydrogen bonds : angle 4.91751 / 3.35 ( 2914) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASP cc_start: 0.8872 (t0) cc_final: 0.8508 (t0) REVERT: B 77 ASP cc_start: 0.9071 (t0) cc_final: 0.8772 (t0) REVERT: B 196 THR cc_start: 0.8864 (p) cc_final: 0.8402 (t) REVERT: B 236 ASP cc_start: 0.6205 (t70) cc_final: 0.5804 (p0) REVERT: C 930 ASP cc_start: 0.8324 (t0) cc_final: 0.7856 (t0) REVERT: C 955 GLN cc_start: 0.8565 (mt0) cc_final: 0.8222 (tm-30) REVERT: C 959 ASP cc_start: 0.8692 (m-30) cc_final: 0.7263 (m-30) REVERT: C 968 GLU cc_start: 0.9558 (tt0) cc_final: 0.9129 (tp30) REVERT: C 1023 HIS cc_start: 0.9265 (m90) cc_final: 0.8921 (m-70) REVERT: D 29 MET cc_start: 0.9339 (mtp) cc_final: 0.9111 (mtt) REVERT: D 102 MET cc_start: 0.8835 (pmm) cc_final: 0.8626 (pmm) REVERT: D 151 MET cc_start: 0.8108 (pmm) cc_final: 0.7631 (pmm) REVERT: D 298 MET cc_start: 0.9431 (mtp) cc_final: 0.9191 (mtp) REVERT: D 339 ARG cc_start: 0.8549 (ttp80) cc_final: 0.7807 (mpt-90) REVERT: D 479 GLU cc_start: 0.8631 (tt0) cc_final: 0.8302 (tt0) REVERT: D 725 MET cc_start: 0.8262 (mtm) cc_final: 0.7945 (mtm) REVERT: D 743 MET cc_start: 0.8198 (mtp) cc_final: 0.7534 (mmm) REVERT: D 837 ASP cc_start: 0.9247 (m-30) cc_final: 0.9033 (m-30) REVERT: D 1040 MET cc_start: 0.0210 (mtm) cc_final: -0.0752 (mmm) REVERT: D 1305 ASP cc_start: 0.8736 (m-30) cc_final: 0.8476 (t0) REVERT: E 6 VAL cc_start: 0.8494 (t) cc_final: 0.8272 (t) REVERT: E 53 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8573 (tt0) REVERT: E 58 LEU cc_start: 0.8988 (tt) cc_final: 0.8757 (tt) REVERT: M 205 GLN cc_start: 0.8699 (mm-40) cc_final: 0.7997 (mp10) outliers start: 1 outliers final: 1 residues processed: 262 average time/residue: 0.1723 time to fit residues: 75.0662 Evaluate side-chains 201 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 11 optimal weight: 9.9990 chunk 293 optimal weight: 20.0000 chunk 219 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 245 optimal weight: 50.0000 chunk 275 optimal weight: 50.0000 chunk 230 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 435 GLN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1259 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.115435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076276 restraints weight = 95969.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.075515 restraints weight = 64547.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.075051 restraints weight = 60702.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.075438 restraints weight = 59272.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.075857 restraints weight = 49653.629| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28634 Z= 0.228 Angle : 0.701 10.170 39297 Z= 0.365 Chirality : 0.047 0.372 4671 Planarity : 0.004 0.058 4826 Dihedral : 17.740 177.344 4819 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.76 % Favored : 90.57 % Rotamer: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.14), residues: 3458 helix: 0.56 (0.15), residues: 1195 sheet: -0.80 (0.30), residues: 278 loop : -2.01 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1355 TYR 0.038 0.002 TYR C1229 PHE 0.014 0.002 PHE D 437 TRP 0.021 0.002 TRP M 126 HIS 0.008 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (28634) covalent geometry : angle 0.70128 / 0.37 (39297) hydrogen bonds : bond 0.04883 / 3.34 ( 1054) hydrogen bonds : angle 4.81515 / 3.29 ( 2914) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 257 time to evaluate : 1.058 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASP cc_start: 0.8909 (t0) cc_final: 0.8495 (t0) REVERT: B 77 ASP cc_start: 0.9086 (t0) cc_final: 0.8774 (t0) REVERT: B 196 THR cc_start: 0.9003 (p) cc_final: 0.8589 (t) REVERT: B 236 ASP cc_start: 0.6234 (t70) cc_final: 0.5886 (p0) REVERT: C 195 PHE cc_start: 0.8964 (m-80) cc_final: 0.8481 (m-10) REVERT: C 805 MET cc_start: 0.8727 (ptm) cc_final: 0.8513 (ptm) REVERT: C 930 ASP cc_start: 0.8434 (t0) cc_final: 0.7968 (t0) REVERT: C 955 GLN cc_start: 0.8563 (mt0) cc_final: 0.8235 (tm-30) REVERT: C 959 ASP cc_start: 0.8640 (m-30) cc_final: 0.7207 (m-30) REVERT: C 967 LEU cc_start: 0.9621 (mm) cc_final: 0.9365 (pp) REVERT: C 1023 HIS cc_start: 0.9171 (m90) cc_final: 0.8837 (m-70) REVERT: C 1170 MET cc_start: 0.7980 (pmm) cc_final: 0.7727 (pmm) REVERT: D 29 MET cc_start: 0.9324 (mtp) cc_final: 0.9090 (mtp) REVERT: D 102 MET cc_start: 0.8919 (pmm) cc_final: 0.8707 (pmm) REVERT: D 151 MET cc_start: 0.8188 (pmm) cc_final: 0.7736 (pmm) REVERT: D 237 MET cc_start: 0.9009 (tpp) cc_final: 0.8695 (tpp) REVERT: D 298 MET cc_start: 0.9395 (mtp) cc_final: 0.9127 (mtp) REVERT: D 339 ARG cc_start: 0.8588 (ttp80) cc_final: 0.7865 (mpt-90) REVERT: D 466 MET cc_start: 0.8827 (mmm) cc_final: 0.8574 (tpp) REVERT: D 641 ILE cc_start: 0.9341 (pt) cc_final: 0.9065 (tp) REVERT: D 725 MET cc_start: 0.8293 (mtm) cc_final: 0.8016 (mtm) REVERT: D 1040 MET cc_start: 0.0071 (mtm) cc_final: -0.0888 (mmm) REVERT: E 6 VAL cc_start: 0.8545 (t) cc_final: 0.8300 (t) REVERT: E 15 ASN cc_start: 0.8152 (t0) cc_final: 0.7461 (t0) REVERT: E 53 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8553 (tt0) REVERT: E 65 ASP cc_start: 0.9030 (m-30) cc_final: 0.8588 (m-30) REVERT: E 67 ARG cc_start: 0.9210 (tpp80) cc_final: 0.9006 (mmm160) REVERT: E 69 ARG cc_start: 0.9373 (mmt90) cc_final: 0.9062 (mmp80) REVERT: M 205 GLN cc_start: 0.8702 (mm-40) cc_final: 0.7987 (mp10) outliers start: 3 outliers final: 2 residues processed: 260 average time/residue: 0.1728 time to fit residues: 74.6900 Evaluate side-chains 198 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 163 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 243 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 57 optimal weight: 50.0000 chunk 320 optimal weight: 6.9990 chunk 336 optimal weight: 40.0000 chunk 8 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C1111 GLN D 435 GLN D 469 HIS D 504 GLN D 702 GLN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.115301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.076698 restraints weight = 95470.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.075567 restraints weight = 69968.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075540 restraints weight = 57407.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.075853 restraints weight = 52116.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076016 restraints weight = 47866.893| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28634 Z= 0.197 Angle : 0.685 11.051 39297 Z= 0.356 Chirality : 0.046 0.365 4671 Planarity : 0.004 0.063 4826 Dihedral : 17.699 176.103 4819 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.79 % Favored : 90.54 % Rotamer: Outliers : 0.04 % Allowed : 1.60 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.14), residues: 3458 helix: 0.65 (0.15), residues: 1198 sheet: -0.84 (0.28), residues: 317 loop : -2.00 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1069 TYR 0.031 0.002 TYR C1229 PHE 0.013 0.001 PHE C 828 TRP 0.009 0.001 TRP M 126 HIS 0.006 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (28634) covalent geometry : angle 0.68500 / 0.36 (39297) hydrogen bonds : bond 0.04706 / 3.22 ( 1054) hydrogen bonds : angle 4.74119 / 3.24 ( 2914) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 1.005 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 15 ASP cc_start: 0.8972 (t0) cc_final: 0.8511 (t0) REVERT: B 77 ASP cc_start: 0.9124 (t0) cc_final: 0.8815 (t0) REVERT: B 196 THR cc_start: 0.9023 (p) cc_final: 0.8704 (t) REVERT: B 236 ASP cc_start: 0.6473 (t70) cc_final: 0.6021 (p0) REVERT: C 195 PHE cc_start: 0.8966 (m-80) cc_final: 0.8632 (m-10) REVERT: C 805 MET cc_start: 0.8617 (ptm) cc_final: 0.8391 (ptm) REVERT: C 930 ASP cc_start: 0.8423 (t0) cc_final: 0.7917 (t0) REVERT: C 955 GLN cc_start: 0.8584 (mt0) cc_final: 0.8237 (tm-30) REVERT: C 959 ASP cc_start: 0.8666 (m-30) cc_final: 0.7256 (m-30) REVERT: C 967 LEU cc_start: 0.9626 (mm) cc_final: 0.9381 (pp) REVERT: C 1023 HIS cc_start: 0.9152 (m90) cc_final: 0.8843 (m-70) REVERT: C 1170 MET cc_start: 0.7948 (pmm) cc_final: 0.7732 (pmm) REVERT: D 29 MET cc_start: 0.9370 (mtp) cc_final: 0.9122 (mtp) REVERT: D 151 MET cc_start: 0.8208 (pmm) cc_final: 0.7785 (pmm) REVERT: D 298 MET cc_start: 0.9446 (mtp) cc_final: 0.9157 (mtp) REVERT: D 479 GLU cc_start: 0.8559 (tt0) cc_final: 0.8254 (tt0) REVERT: D 725 MET cc_start: 0.8418 (mtm) cc_final: 0.8111 (mtm) REVERT: D 1040 MET cc_start: 0.0068 (mtm) cc_final: -0.0884 (mmm) REVERT: E 6 VAL cc_start: 0.8530 (t) cc_final: 0.8285 (t) REVERT: E 15 ASN cc_start: 0.8100 (t0) cc_final: 0.7381 (t0) REVERT: E 53 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8565 (tt0) REVERT: E 61 ASN cc_start: 0.9258 (t0) cc_final: 0.9026 (t0) REVERT: E 65 ASP cc_start: 0.9035 (m-30) cc_final: 0.8495 (m-30) REVERT: E 69 ARG cc_start: 0.9376 (mmt90) cc_final: 0.9084 (mmp80) REVERT: M 205 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8054 (mp10) outliers start: 1 outliers final: 1 residues processed: 252 average time/residue: 0.1739 time to fit residues: 72.5821 Evaluate side-chains 196 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 135 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 279 optimal weight: 20.0000 chunk 293 optimal weight: 0.3980 chunk 145 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 81 optimal weight: 0.4980 chunk 173 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.116812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.077246 restraints weight = 96051.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.076751 restraints weight = 68310.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.076393 restraints weight = 60924.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.076518 restraints weight = 61151.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.076729 restraints weight = 53322.539| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28634 Z= 0.123 Angle : 0.653 11.051 39297 Z= 0.338 Chirality : 0.045 0.373 4671 Planarity : 0.004 0.074 4826 Dihedral : 17.604 176.780 4819 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.13 % Favored : 91.18 % Rotamer: Outliers : 0.04 % Allowed : 0.95 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3458 helix: 0.83 (0.15), residues: 1194 sheet: -0.68 (0.28), residues: 317 loop : -1.94 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 158 TYR 0.030 0.001 TYR C1229 PHE 0.015 0.001 PHE C 828 TRP 0.017 0.001 TRP M 126 HIS 0.005 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (28634) covalent geometry : angle 0.65270 / 0.34 (39297) hydrogen bonds : bond 0.04346 / 2.95 ( 1054) hydrogen bonds : angle 4.62040 / 3.13 ( 2914) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 0.903 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7661 (mp0) cc_final: 0.7088 (mp0) REVERT: B 15 ASP cc_start: 0.8913 (t0) cc_final: 0.8389 (t0) REVERT: B 29 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 77 ASP cc_start: 0.9171 (t0) cc_final: 0.8832 (t0) REVERT: B 196 THR cc_start: 0.8976 (p) cc_final: 0.8668 (t) REVERT: B 236 ASP cc_start: 0.6380 (t70) cc_final: 0.5928 (p0) REVERT: C 195 PHE cc_start: 0.8952 (m-80) cc_final: 0.8417 (m-10) REVERT: C 723 VAL cc_start: 0.9342 (t) cc_final: 0.9070 (p) REVERT: C 805 MET cc_start: 0.8618 (ptm) cc_final: 0.8409 (ptm) REVERT: C 930 ASP cc_start: 0.8326 (t0) cc_final: 0.7732 (t0) REVERT: C 955 GLN cc_start: 0.8629 (mt0) cc_final: 0.8321 (tm-30) REVERT: C 959 ASP cc_start: 0.8779 (m-30) cc_final: 0.7466 (m-30) REVERT: C 967 LEU cc_start: 0.9655 (mm) cc_final: 0.9412 (pp) REVERT: C 1023 HIS cc_start: 0.9194 (m90) cc_final: 0.8860 (m-70) REVERT: D 29 MET cc_start: 0.9395 (mtp) cc_final: 0.9046 (mtp) REVERT: D 102 MET cc_start: 0.8873 (pmm) cc_final: 0.8647 (pmm) REVERT: D 151 MET cc_start: 0.8286 (pmm) cc_final: 0.7830 (pmm) REVERT: D 237 MET cc_start: 0.8987 (tpp) cc_final: 0.8779 (tpp) REVERT: D 466 MET cc_start: 0.8941 (mmm) cc_final: 0.8409 (tpp) REVERT: D 479 GLU cc_start: 0.8607 (tt0) cc_final: 0.8194 (tt0) REVERT: D 641 ILE cc_start: 0.9315 (pt) cc_final: 0.9022 (tp) REVERT: D 725 MET cc_start: 0.8354 (mtm) cc_final: 0.8092 (mtm) REVERT: D 743 MET cc_start: 0.7916 (tpp) cc_final: 0.7624 (tpp) REVERT: D 1040 MET cc_start: 0.0131 (mtm) cc_final: -0.0790 (mmm) REVERT: E 6 VAL cc_start: 0.8536 (t) cc_final: 0.8278 (t) REVERT: E 11 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8482 (pp20) REVERT: E 15 ASN cc_start: 0.8123 (t0) cc_final: 0.7338 (t0) REVERT: E 41 GLU cc_start: 0.8721 (tt0) cc_final: 0.8401 (pp20) REVERT: E 53 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8569 (tt0) REVERT: E 58 LEU cc_start: 0.9110 (tt) cc_final: 0.8858 (tt) REVERT: E 61 ASN cc_start: 0.9259 (t0) cc_final: 0.9049 (t0) REVERT: E 65 ASP cc_start: 0.9071 (m-30) cc_final: 0.8778 (m-30) REVERT: M 205 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8056 (mp10) outliers start: 1 outliers final: 1 residues processed: 259 average time/residue: 0.1681 time to fit residues: 71.2980 Evaluate side-chains 202 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 117 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 326 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 203 optimal weight: 20.0000 chunk 109 optimal weight: 0.0670 chunk 279 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN B 23 HIS B 132 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 ASN C1111 GLN C1264 GLN ** D 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.115906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.075678 restraints weight = 96463.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075334 restraints weight = 70699.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.075134 restraints weight = 59681.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.075410 restraints weight = 57307.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075493 restraints weight = 52319.297| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28634 Z= 0.156 Angle : 0.660 10.694 39297 Z= 0.341 Chirality : 0.045 0.374 4671 Planarity : 0.004 0.061 4826 Dihedral : 17.552 178.175 4819 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.94 % Favored : 90.40 % Rotamer: Outliers : 0.04 % Allowed : 0.38 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3458 helix: 0.87 (0.15), residues: 1202 sheet: -0.63 (0.30), residues: 303 loop : -1.97 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1106 TYR 0.029 0.001 TYR C1229 PHE 0.012 0.001 PHE C 828 TRP 0.017 0.001 TRP M 126 HIS 0.006 0.001 HIS D 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (28634) covalent geometry : angle 0.65995 / 0.34 (39297) hydrogen bonds : bond 0.04437 / 3.03 ( 1054) hydrogen bonds : angle 4.54892 / 3.09 ( 2914) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7649 (mp0) cc_final: 0.7107 (mp0) REVERT: A 103 ASN cc_start: 0.8550 (m-40) cc_final: 0.8317 (m-40) REVERT: B 15 ASP cc_start: 0.8933 (t0) cc_final: 0.8446 (t0) REVERT: B 77 ASP cc_start: 0.9170 (t0) cc_final: 0.8845 (t0) REVERT: B 196 THR cc_start: 0.8984 (p) cc_final: 0.8746 (t) REVERT: B 236 ASP cc_start: 0.6371 (t70) cc_final: 0.5972 (p0) REVERT: C 195 PHE cc_start: 0.8911 (m-80) cc_final: 0.8519 (m-10) REVERT: C 723 VAL cc_start: 0.9323 (t) cc_final: 0.9051 (p) REVERT: C 805 MET cc_start: 0.8612 (ptm) cc_final: 0.8401 (ptm) REVERT: C 930 ASP cc_start: 0.8368 (t0) cc_final: 0.7771 (t0) REVERT: C 1023 HIS cc_start: 0.9192 (m90) cc_final: 0.8872 (m-70) REVERT: D 29 MET cc_start: 0.9365 (mtp) cc_final: 0.9040 (mtp) REVERT: D 102 MET cc_start: 0.8877 (pmm) cc_final: 0.8641 (pmm) REVERT: D 151 MET cc_start: 0.8389 (pmm) cc_final: 0.7943 (pmm) REVERT: D 237 MET cc_start: 0.8927 (tpp) cc_final: 0.8707 (tpp) REVERT: D 466 MET cc_start: 0.8868 (mmm) cc_final: 0.8357 (tpp) REVERT: D 479 GLU cc_start: 0.8595 (tt0) cc_final: 0.8259 (tt0) REVERT: D 641 ILE cc_start: 0.9289 (pt) cc_final: 0.8997 (tp) REVERT: D 725 MET cc_start: 0.8384 (mtm) cc_final: 0.8131 (mtm) REVERT: D 743 MET cc_start: 0.7804 (tpp) cc_final: 0.7478 (tpp) REVERT: D 1040 MET cc_start: 0.0114 (mtm) cc_final: -0.0704 (mtt) REVERT: D 1260 MET cc_start: 0.8961 (tpp) cc_final: 0.8537 (mmm) REVERT: E 6 VAL cc_start: 0.8570 (t) cc_final: 0.8323 (t) REVERT: E 15 ASN cc_start: 0.8159 (t0) cc_final: 0.7423 (t0) REVERT: E 41 GLU cc_start: 0.8695 (tt0) cc_final: 0.8373 (pp20) REVERT: E 43 ASN cc_start: 0.7983 (m-40) cc_final: 0.7730 (m-40) REVERT: E 53 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8589 (tt0) REVERT: E 58 LEU cc_start: 0.9120 (tt) cc_final: 0.8869 (tt) REVERT: E 59 ILE cc_start: 0.7522 (tp) cc_final: 0.7134 (tp) REVERT: M 205 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8061 (mp10) outliers start: 1 outliers final: 1 residues processed: 242 average time/residue: 0.1656 time to fit residues: 66.4564 Evaluate side-chains 192 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 208 optimal weight: 20.0000 chunk 78 optimal weight: 50.0000 chunk 240 optimal weight: 4.9990 chunk 243 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 308 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS D 435 GLN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.114350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.073121 restraints weight = 96518.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.072743 restraints weight = 75247.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.072898 restraints weight = 65791.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.072926 restraints weight = 55182.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073093 restraints weight = 53591.201| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 28634 Z= 0.240 Angle : 0.732 14.298 39297 Z= 0.379 Chirality : 0.047 0.406 4671 Planarity : 0.005 0.058 4826 Dihedral : 17.640 179.499 4819 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.67 % Allowed : 9.37 % Favored : 89.97 % Rotamer: Outliers : 0.04 % Allowed : 0.15 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3458 helix: 0.82 (0.15), residues: 1192 sheet: -0.83 (0.29), residues: 315 loop : -2.04 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1355 TYR 0.039 0.002 TYR C1229 PHE 0.015 0.002 PHE D 437 TRP 0.009 0.001 TRP D 236 HIS 0.008 0.001 HIS D 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (28634) covalent geometry : angle 0.73199 / 0.38 (39297) hydrogen bonds : bond 0.04971 / 3.41 ( 1054) hydrogen bonds : angle 4.69710 / 3.21 ( 2914) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.944 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 TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASP cc_start: 0.8925 (t0) cc_final: 0.8463 (t0) REVERT: B 77 ASP cc_start: 0.9201 (t0) cc_final: 0.8883 (t0) REVERT: B 196 THR cc_start: 0.8966 (p) cc_final: 0.8724 (t) REVERT: B 236 ASP cc_start: 0.6372 (t70) cc_final: 0.6002 (p0) REVERT: C 195 PHE cc_start: 0.8951 (m-80) cc_final: 0.8570 (m-10) REVERT: C 723 VAL cc_start: 0.9354 (t) cc_final: 0.9069 (p) REVERT: C 805 MET cc_start: 0.8611 (ptm) cc_final: 0.8380 (ptm) REVERT: C 930 ASP cc_start: 0.8506 (t0) cc_final: 0.8007 (t0) REVERT: C 959 ASP cc_start: 0.8709 (m-30) cc_final: 0.8309 (m-30) REVERT: C 967 LEU cc_start: 0.9659 (mm) cc_final: 0.9386 (pp) REVERT: C 1023 HIS cc_start: 0.9226 (m90) cc_final: 0.8902 (m-70) REVERT: D 29 MET cc_start: 0.9354 (mtp) cc_final: 0.9062 (mtp) REVERT: D 102 MET cc_start: 0.8885 (pmm) cc_final: 0.8624 (pmm) REVERT: D 151 MET cc_start: 0.8473 (pmm) cc_final: 0.8028 (pmm) REVERT: D 237 MET cc_start: 0.8910 (tpp) cc_final: 0.8680 (tpp) REVERT: D 466 MET cc_start: 0.8834 (mmm) cc_final: 0.8428 (tpp) REVERT: D 479 GLU cc_start: 0.8507 (tt0) cc_final: 0.8232 (tt0) REVERT: D 641 ILE cc_start: 0.9293 (pt) cc_final: 0.8985 (tp) REVERT: D 725 MET cc_start: 0.8425 (mtm) cc_final: 0.8187 (mtm) REVERT: D 1040 MET cc_start: 0.0078 (mtm) cc_final: -0.0722 (mtt) REVERT: D 1260 MET cc_start: 0.9040 (tpp) cc_final: 0.8479 (mmm) REVERT: E 6 VAL cc_start: 0.8616 (t) cc_final: 0.8348 (t) REVERT: E 15 ASN cc_start: 0.8220 (t0) cc_final: 0.7380 (t0) REVERT: E 41 GLU cc_start: 0.8682 (tt0) cc_final: 0.8312 (pp20) REVERT: E 43 ASN cc_start: 0.8146 (m-40) cc_final: 0.7783 (m-40) REVERT: E 53 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8512 (tt0) REVERT: E 58 LEU cc_start: 0.9237 (tt) cc_final: 0.9001 (tt) REVERT: E 59 ILE cc_start: 0.7508 (tp) cc_final: 0.7128 (tp) REVERT: E 65 ASP cc_start: 0.9129 (m-30) cc_final: 0.8925 (m-30) REVERT: M 205 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8132 (mp10) outliers start: 1 outliers final: 1 residues processed: 226 average time/residue: 0.1636 time to fit residues: 61.4812 Evaluate side-chains 188 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 40 optimal weight: 6.9990 chunk 279 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 64 optimal weight: 0.4980 chunk 75 optimal weight: 50.0000 chunk 36 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 228 optimal weight: 0.0980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 ASN ** D 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.114298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.074054 restraints weight = 96612.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.073281 restraints weight = 74061.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.073220 restraints weight = 62708.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.073459 restraints weight = 58457.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.073537 restraints weight = 53151.823| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28634 Z= 0.206 Angle : 0.698 11.024 39297 Z= 0.363 Chirality : 0.046 0.372 4671 Planarity : 0.004 0.058 4826 Dihedral : 17.659 179.684 4819 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.96 % Favored : 90.37 % Rotamer: Outliers : 0.04 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.14), residues: 3458 helix: 0.84 (0.15), residues: 1200 sheet: -0.88 (0.30), residues: 302 loop : -2.06 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 158 TYR 0.036 0.002 TYR C1229 PHE 0.014 0.001 PHE D 172 TRP 0.019 0.002 TRP M 126 HIS 0.008 0.001 HIS D 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (28634) covalent geometry : angle 0.69833 / 0.36 (39297) hydrogen bonds : bond 0.04700 / 3.21 ( 1054) hydrogen bonds : angle 4.64659 / 3.18 ( 2914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4544.97 seconds wall clock time: 79 minutes 15.73 seconds (4755.73 seconds total)