Starting phenix.real_space_refine on Sun Sep 13 19:35:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5nsr_3695/09_2026/5nsr_3695_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5nsr_3695/09_2026/5nsr_3695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5nsr_3695/09_2026/5nsr_3695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5nsr_3695/09_2026/5nsr_3695.map" model { file = "/net/cci-nas-00/data/ceres_data/5nsr_3695/09_2026/5nsr_3695_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5nsr_3695/09_2026/5nsr_3695_neut.cif" } resolution = 3.8 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= 0.000 sd= 0.003 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 54 5.49 5 S 83 5.16 5 C 15673 2.51 5 N 4552 2.21 5 O 5001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25363 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1694 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 102 Chain: "B" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1606 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 3, 'GLU:plan': 6, 'ASP:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 9472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 9472 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 264} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1138 Unresolved non-hydrogen angles: 1396 Unresolved non-hydrogen dihedrals: 965 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'TYR:plan': 13, 'GLU:plan': 48, 'GLN:plan1': 17, 'ASP:plan': 32, 'PHE:plan': 13, 'ASN:plan1': 10, 'ARG:plan': 37, 'HIS:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 779 Chain: "D" Number of atoms: 8969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 8969 Classifications: {'peptide': 1320} Incomplete info: {'truncation_to_alanine': 348} Link IDs: {'PTRANS': 53, 'TRANS': 1266} Chain breaks: 6 Unresolved non-hydrogen bonds: 1364 Unresolved non-hydrogen angles: 1689 Unresolved non-hydrogen dihedrals: 1131 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLU:plan': 52, 'PHE:plan': 19, 'ASP:plan': 34, 'ARG:plan': 40, 'TYR:plan': 8, 'HIS:plan': 8, 'GLN:plan1': 20, 'ASN:plan1': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 857 Chain: "E" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 50 Chain: "M" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 916 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 3, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'UNK:plan-1': 34, 'GLN:plan1': 7, 'ASP:plan': 15, 'TYR:plan': 2, 'TRP:plan': 2, 'GLU:plan': 12, 'PHE:plan': 4, 'ARG:plan': 8, 'HIS:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 267 Chain: "M" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 692 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 372 Unresolved non-hydrogen angles: 492 Unresolved non-hydrogen dihedrals: 276 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'UNK:plan-1': 46, 'ASN:plan1': 4, 'ARG:plan': 8, 'ASP:plan': 4, 'GLN:plan1': 8, 'PHE:plan': 3, 'GLU:plan': 8, 'TRP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 225 Chain: "M" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 375 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 64} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 17 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: "F" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 511 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "G" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 596 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Residues with excluded nonbonded symmetry interactions: 7 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 167 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP M 167 " 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 ILE M 170 " occ=0.20 ... (3 atoms not shown) pdb=" CB ILE M 170 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 residue: pdb=" N ARG M 311 " occ=0.00 ... (3 atoms not shown) pdb=" CB ARG M 311 " occ=0.00 Time building chain proxies: 5.02, per 1000 atoms: 0.20 Number of scatterers: 25363 At special positions: 0 Unit cell: (150.52, 169.6, 164.3, 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 83 16.00 P 54 15.00 O 5001 8.00 N 4552 7.00 C 15673 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: 1.89 Conformation dependent library (CDL) restraints added in 874.1 milliseconds 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6652 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 41 sheets defined 39.2% alpha, 8.6% beta 20 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.652A pdb=" N GLY A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.757A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.493A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.538A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.767A pdb=" N GLN C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 removed outlier: 4.113A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 380 through 389 Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 438 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 482 removed outlier: 3.759A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.516A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.645A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.512A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 4.081A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.960A pdb=" N GLN C 659 " --> pdb=" O SER C 656 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.285A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 865 removed outlier: 4.156A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 907 removed outlier: 3.742A pdb=" N GLU C 899 " --> pdb=" O LEU C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 979 removed outlier: 3.802A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 4.467A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1039 removed outlier: 3.548A pdb=" N LYS C1035 " --> pdb=" O ALA C1031 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY C1039 " --> pdb=" O LYS C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 Processing helix chain 'C' and resid 1109 through 1135 removed outlier: 4.124A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.794A pdb=" N PHE C1144 " --> pdb=" O LYS C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1176 removed outlier: 4.045A pdb=" N GLU C1174 " --> pdb=" O MET C1170 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 3.709A pdb=" N ARG C1301 " --> pdb=" O ASP C1297 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.738A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.571A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 182 through 192 removed outlier: 4.047A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.853A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.754A 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 265 through 286 removed outlier: 3.648A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.518A pdb=" N LYS D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 419 removed outlier: 4.153A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.907A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.941A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.924A pdb=" N ALA D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 530 through 538 removed outlier: 4.151A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.955A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.839A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 613 removed outlier: 3.745A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET D 604 " --> pdb=" O ALA D 600 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 605 " --> pdb=" O ILE D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.778A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 671 removed outlier: 4.391A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.129A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 807 No H-bonds generated for 'chain 'D' and resid 805 through 807' Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.212A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 874 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.948A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 914 through 919 removed outlier: 3.781A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 936 removed outlier: 3.751A pdb=" N THR D 934 " --> pdb=" O THR D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 1139 through 1147 removed outlier: 3.670A pdb=" N GLU D1146 " --> pdb=" O ALA D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1223 Processing helix chain 'D' and resid 1225 through 1245 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.166A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.607A pdb=" N VAL D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1362 through 1371 Processing helix chain 'D' and resid 1372 through 1375 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 18 through 33 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 17 through 22 Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 121 through 130 Processing helix chain 'M' and resid 135 through 146 removed outlier: 3.925A pdb=" N ASP M 146 " --> pdb=" O THR M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 166 removed outlier: 3.993A pdb=" N GLY M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 184 removed outlier: 4.180A pdb=" N ARG M 181 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 205 removed outlier: 3.528A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 223 Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 242 through 245 Processing helix chain 'M' and resid 246 through 254 Processing helix chain 'M' and resid 303 through 304 No H-bonds generated for 'chain 'M' and resid 303 through 304' Processing helix chain 'M' and resid 306 through 309 removed outlier: 3.673A pdb=" N SER M 309 " --> pdb=" O MET M 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 306 through 309' Processing helix chain 'M' and resid 318 through 355 removed outlier: 3.683A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 375 removed outlier: 3.670A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 386 removed outlier: 3.809A pdb=" N THR M 386 " --> pdb=" O SER M 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 428 Processing helix chain 'M' and resid 438 through 449 Processing helix chain 'M' and resid 457 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 3.905A pdb=" N LEU A 198 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.554A pdb=" N GLY A 53 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.469A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 17 removed outlier: 5.316A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 61 removed outlier: 5.459A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.018A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.642A pdb=" N GLY C 154 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 177 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 175 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 174 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.487A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.496A pdb=" N VAL C 296 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.203A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC3, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 Processing sheet with id=AC5, first strand: chain 'C' and resid 722 through 724 removed outlier: 3.803A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.634A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1073 through 1074 removed outlier: 4.654A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1073 through 1074 removed outlier: 3.915A pdb=" N VAL C1225 " --> pdb=" O ILE C1210 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 838 removed outlier: 4.215A pdb=" N VAL C1050 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.693A pdb=" N GLU C 849 " --> pdb=" O VAL C 887 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1337 Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 147 removed outlier: 4.523A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 435 through 437 removed outlier: 3.527A pdb=" N LEU D 422 " --> pdb=" O HIS D 469 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 551 through 556 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 822 removed outlier: 4.350A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 960 through 961 Processing sheet with id=AE1, first strand: chain 'D' and resid 966 through 967 Processing sheet with id=AE2, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE3, first strand: chain 'D' and resid 1059 through 1060 Processing sheet with id=AE4, first strand: chain 'D' and resid 1165 through 1166 removed outlier: 3.638A pdb=" N GLY D1166 " --> pdb=" O VAL D1176 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL D1176 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 279 through 280 removed outlier: 4.168A pdb=" N UNK M 287 " --> pdb=" O UNK M 280 " (cutoff:3.500A) 1003 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.53: 22505 1.53 - 1.84: 3271 1.84 - 2.15: 0 2.15 - 2.46: 0 2.46 - 2.76: 1 Bond restraints: 25777 Sorted by residual: bond pdb=" C UNK M 304 " pdb=" N MET M 306 " ideal model delta sigma weight residual 1.329 2.765 -1.436 1.40e-02 5.10e+03 1.05e+04 bond pdb=" O3' DG G -10 " pdb=" P DA G -9 " ideal model delta sigma weight residual 1.607 1.317 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" O3' DA G -11 " pdb=" P DG G -10 " ideal model delta sigma weight residual 1.607 1.461 0.146 1.20e-02 6.94e+03 1.49e+02 bond pdb=" O3' DA G -9 " pdb=" P DT G -8 " ideal model delta sigma weight residual 1.607 1.464 0.143 1.20e-02 6.94e+03 1.42e+02 bond pdb=" O3' DC G -7 " pdb=" P DA G -6 " ideal model delta sigma weight residual 1.607 1.472 0.135 1.20e-02 6.94e+03 1.26e+02 ... (remaining 25772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.56: 35413 9.56 - 19.12: 23 19.12 - 28.68: 2 28.68 - 38.24: 1 38.24 - 47.80: 2 Bond angle restraints: 35441 Sorted by residual: angle pdb=" C3' DT F 71 " pdb=" O3' DT F 71 " pdb=" P DC F 72 " ideal model delta sigma weight residual 119.70 159.44 -39.74 1.20e+00 6.94e-01 1.10e+03 angle pdb=" O UNK M 304 " pdb=" C UNK M 304 " pdb=" N MET M 306 " ideal model delta sigma weight residual 123.00 75.20 47.80 1.60e+00 3.91e-01 8.93e+02 angle pdb=" O3' DT F 71 " pdb=" P DC F 72 " pdb=" OP1 DC F 72 " ideal model delta sigma weight residual 108.00 141.52 -33.52 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C3' DA G -11 " pdb=" O3' DA G -11 " pdb=" P DG G -10 " ideal model delta sigma weight residual 119.70 107.10 12.60 1.20e+00 6.94e-01 1.10e+02 angle pdb=" C3' DG G -10 " pdb=" O3' DG G -10 " pdb=" P DA G -9 " ideal model delta sigma weight residual 119.70 131.75 -12.05 1.20e+00 6.94e-01 1.01e+02 ... (remaining 35436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.69: 15068 31.69 - 63.39: 378 63.39 - 95.08: 16 95.08 - 126.78: 2 126.78 - 158.47: 2 Dihedral angle restraints: 15466 sinusoidal: 5193 harmonic: 10273 Sorted by residual: dihedral pdb=" CA UNK M 304 " pdb=" C UNK M 304 " pdb=" N MET M 306 " pdb=" CA MET M 306 " ideal model delta harmonic sigma weight residual -180.00 -68.20 -111.80 0 5.00e+00 4.00e-02 5.00e+02 dihedral pdb=" CA PHE M 133 " pdb=" C PHE M 133 " pdb=" N THR M 134 " pdb=" CA THR M 134 " ideal model delta harmonic sigma weight residual 180.00 149.52 30.48 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA THR D 473 " pdb=" C THR D 473 " pdb=" N LEU D 474 " pdb=" CA LEU D 474 " ideal model delta harmonic sigma weight residual 180.00 -152.30 -27.70 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 15463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4331 0.128 - 0.256: 58 0.256 - 0.383: 6 0.383 - 0.511: 2 0.511 - 0.639: 1 Chirality restraints: 4398 Sorted by residual: chirality pdb=" C1' DC G -7 " pdb=" O4' DC G -7 " pdb=" C2' DC G -7 " pdb=" N1 DC G -7 " both_signs ideal model delta sigma weight residual False 2.43 3.07 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C3' DC G -12 " pdb=" C4' DC G -12 " pdb=" O3' DC G -12 " pdb=" C2' DC G -12 " both_signs ideal model delta sigma weight residual False -2.73 -2.25 -0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" C4' DA G -6 " pdb=" C5' DA G -6 " pdb=" O4' DA G -6 " pdb=" C3' DA G -6 " both_signs ideal model delta sigma weight residual False -2.53 -2.13 -0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 4395 not shown) Planarity restraints: 4505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK M 304 " 0.177 2.00e-02 2.50e+03 2.27e-01 5.16e+02 pdb=" C UNK M 304 " -0.386 2.00e-02 2.50e+03 pdb=" O UNK M 304 " 0.153 2.00e-02 2.50e+03 pdb=" N MET M 306 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER M 221 " 0.026 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C SER M 221 " -0.092 2.00e-02 2.50e+03 pdb=" O SER M 221 " 0.035 2.00e-02 2.50e+03 pdb=" N ASP M 222 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT F 82 " 0.067 2.00e-02 2.50e+03 2.98e-02 2.22e+01 pdb=" N1 DT F 82 " -0.020 2.00e-02 2.50e+03 pdb=" C2 DT F 82 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DT F 82 " -0.025 2.00e-02 2.50e+03 pdb=" N3 DT F 82 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT F 82 " 0.011 2.00e-02 2.50e+03 pdb=" O4 DT F 82 " 0.038 2.00e-02 2.50e+03 pdb=" C5 DT F 82 " -0.013 2.00e-02 2.50e+03 pdb=" C7 DT F 82 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DT F 82 " -0.035 2.00e-02 2.50e+03 ... (remaining 4502 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 6 2.02 - 2.74: 2295 2.74 - 3.46: 35591 3.46 - 4.18: 54389 4.18 - 4.90: 94215 Nonbonded interactions: 186496 Sorted by model distance: nonbonded pdb=" O UNK M 289 " pdb=" N UNK M 291 " model vdw 1.302 3.120 nonbonded pdb=" C UNK M 289 " pdb=" N UNK M 291 " model vdw 1.446 3.350 nonbonded pdb=" O UNK M 303 " pdb=" N GLY M 307 " model vdw 1.559 3.120 nonbonded pdb=" O2 DC F 83 " pdb=" N2 DG G -21 " model vdw 1.832 3.120 nonbonded pdb=" O VAL A 192 " pdb=" N GLN A 194 " model vdw 1.985 3.120 ... (remaining 186491 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 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O or name CB )) or resid 25 through 64 or (resi \ d 65 through 67 and (name N or name CA or name C or name O or name CB )) or resi \ d 68 through 70 or (resid 71 through 72 and (name N or name CA or name C or name \ O or name CB )) or resid 73 or (resid 74 and (name N or name CA or name C or na \ me O or name CB )) or resid 75 through 79 or (resid 80 and (name N or name CA or \ name C or name O or name CB )) or resid 81 through 95 or (resid 96 and (name N \ or name CA or name C or name O or name CB )) or resid 97 through 102 or (resid 1 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 104 through \ 127 or (resid 128 and (name N or name CA or name C or name O or name CB )) or r \ esid 129 through 141 or (resid 142 and (name N or name CA or name C or name O or \ name CB )) or resid 143 through 157 or (resid 158 and (name N or name CA or nam \ e C or name O or name CB )) or resid 159 or resid 172 through 193 or (resid 194 \ through 195 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 6 or (resid 197 and (name N or name CA or name C or name O or name CB )) or resi \ d 198 through 226 or (resid 227 and (name N or name CA or name C or name O or na \ me CB )) or resid 228 through 230 or (resid 231 and (name N or name CA or name C \ or name O or name CB )) or resid 232 or (resid 233 through 235 and (name N or n \ ame CA or name C or name O or name CB )) or resid 236 through 237)) selection = (chain 'B' and (resid 5 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 32 or (resid 33 and (name N or name CA \ or name C or name O or name CB )) or resid 34 through 40 or (resid 41 through 4 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 43 through 7 \ 6 or (resid 77 and (name N or name CA or name C or name O or name CB )) or resid \ 78 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 184 or (resid 185 and (name N or name CA or name C o \ r name O or name CB )) or resid 186 through 190 or (resid 191 and (name N or nam \ e CA or name C or name O or name CB )) or resid 192 through 194 or (resid 195 an \ d (name N or name CA or name C or name O or name CB )) or resid 196 through 203 \ or (resid 204 and (name N or name CA or name C or name O or name CB )) or resid \ 205 through 211 or (resid 212 and (name N or name CA or name C or name O or name \ CB )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C o \ r name O or name CB )) or resid 218 through 225 or (resid 226 through 227 and (n \ ame N or name CA or name C or name O or name CB )) or resid 228 or (resid 229 th \ rough 231 and (name N or name CA or name C or name O or name CB )) or resid 232 \ through 237)) } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 22.930 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 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 : 0.010 1.436 25777 Z= 0.737 Angle : 0.907 47.804 35441 Z= 0.568 Chirality : 0.049 0.639 4398 Planarity : 0.005 0.227 4505 Dihedral : 12.710 158.471 8814 Min Nonbonded Distance : 1.302 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.78 % Favored : 90.26 % Rotamer: Outliers : 0.19 % Allowed : 1.35 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % 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: -3.59 (0.11), residues: 3451 helix: -2.95 (0.10), residues: 1161 sheet: -1.12 (0.28), residues: 258 loop : -2.25 (0.11), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 610 TYR 0.030 0.001 TYR D 140 PHE 0.023 0.001 PHE D 620 TRP 0.013 0.002 TRP D 686 HIS 0.003 0.000 HIS D 419 Details of bonding type rmsd/Z covalent geometry : bond 0.01016 / 0.74 (25777) covalent geometry : angle 0.90661 / 0.57 (35441) hydrogen bonds : bond 0.12506 / 8.88 ( 1047) hydrogen bonds : angle 11.09088 / 7.77 ( 2933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 718 time to evaluate : 0.812 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: A 60 GLU cc_start: 0.8622 (tt0) cc_final: 0.8227 (pm20) REVERT: A 65 LEU cc_start: 0.8967 (tp) cc_final: 0.8764 (tp) REVERT: A 133 LEU cc_start: 0.7995 (mt) cc_final: 0.7776 (mm) REVERT: A 139 SER cc_start: 0.7804 (p) cc_final: 0.7342 (m) REVERT: A 143 ARG cc_start: 0.8757 (mtm-85) cc_final: 0.8493 (mtm-85) REVERT: A 174 ASP cc_start: 0.7878 (m-30) cc_final: 0.6285 (p0) REVERT: A 197 ASP cc_start: 0.7864 (p0) cc_final: 0.6923 (p0) REVERT: A 231 PHE cc_start: 0.8314 (m-10) cc_final: 0.7994 (m-10) REVERT: B 57 THR cc_start: 0.4906 (t) cc_final: 0.4227 (m) REVERT: B 137 ASN cc_start: 0.8450 (m-40) cc_final: 0.8171 (p0) REVERT: B 212 ASP cc_start: 0.6979 (t0) cc_final: 0.6553 (t70) REVERT: C 79 VAL cc_start: 0.8358 (m) cc_final: 0.7551 (p) REVERT: C 183 TRP cc_start: 0.6609 (m-10) cc_final: 0.5978 (m-10) REVERT: C 195 PHE cc_start: 0.7406 (m-10) cc_final: 0.7182 (m-80) REVERT: C 201 ARG cc_start: 0.8719 (mmt-90) cc_final: 0.8476 (mmt90) REVERT: C 357 ASN cc_start: 0.8728 (t0) cc_final: 0.8361 (p0) REVERT: C 419 ILE cc_start: 0.9141 (pt) cc_final: 0.8750 (mp) REVERT: C 445 ILE cc_start: 0.8432 (mt) cc_final: 0.8008 (pt) REVERT: C 450 ASN cc_start: 0.7684 (m-40) cc_final: 0.7438 (p0) REVERT: C 575 LEU cc_start: 0.8867 (mt) cc_final: 0.8662 (mp) REVERT: C 629 PHE cc_start: 0.8508 (m-10) cc_final: 0.7836 (m-80) REVERT: C 660 VAL cc_start: 0.8572 (m) cc_final: 0.8362 (t) REVERT: C 726 TYR cc_start: 0.9138 (t80) cc_final: 0.8459 (t80) REVERT: C 752 ASN cc_start: 0.8965 (m-40) cc_final: 0.8724 (t0) REVERT: C 950 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9036 (pp20) REVERT: C 952 GLN cc_start: 0.9239 (mm110) cc_final: 0.8999 (tp-100) REVERT: C 954 LYS cc_start: 0.9503 (mmtp) cc_final: 0.9190 (mtmm) REVERT: C 1019 ASP cc_start: 0.9538 (m-30) cc_final: 0.9116 (t0) REVERT: C 1033 ARG cc_start: 0.8865 (ttt-90) cc_final: 0.8605 (ttp80) REVERT: C 1036 ILE cc_start: 0.9417 (mm) cc_final: 0.9132 (mm) REVERT: C 1076 ILE cc_start: 0.8349 (mp) cc_final: 0.7890 (mt) REVERT: C 1106 ARG cc_start: 0.8465 (mtt180) cc_final: 0.8082 (mpt180) REVERT: C 1109 ILE cc_start: 0.8533 (mm) cc_final: 0.8272 (mm) REVERT: C 1194 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7543 (mm-30) REVERT: C 1214 ASP cc_start: 0.9281 (t0) cc_final: 0.8990 (t0) REVERT: C 1219 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8461 (pp20) REVERT: C 1254 VAL cc_start: 0.7005 (t) cc_final: 0.6239 (m) REVERT: D 53 ARG cc_start: 0.7402 (ttt180) cc_final: 0.7038 (tpm170) REVERT: D 298 MET cc_start: 0.6799 (mmt) cc_final: 0.6165 (mmp) REVERT: D 353 SER cc_start: 0.9026 (p) cc_final: 0.8820 (p) REVERT: D 485 MET cc_start: 0.8601 (mmm) cc_final: 0.8122 (mmm) REVERT: D 568 SER cc_start: 0.7028 (t) cc_final: 0.6747 (m) REVERT: D 603 LYS cc_start: 0.8450 (pttt) cc_final: 0.8198 (tptp) REVERT: D 827 GLU cc_start: 0.8953 (tp30) cc_final: 0.8649 (pt0) REVERT: D 886 VAL cc_start: 0.8598 (p) cc_final: 0.8373 (p) REVERT: D 1040 MET cc_start: 0.3078 (mtp) cc_final: 0.1715 (mmt) REVERT: D 1256 ILE cc_start: 0.8680 (mt) cc_final: 0.8374 (pt) REVERT: D 1361 THR cc_start: 0.8858 (p) cc_final: 0.8416 (t) REVERT: D 1363 TYR cc_start: 0.8358 (t80) cc_final: 0.8039 (t80) REVERT: E 41 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7286 (mp0) REVERT: E 51 LEU cc_start: 0.6328 (mp) cc_final: 0.5901 (tt) outliers start: 4 outliers final: 2 residues processed: 719 average time/residue: 0.1627 time to fit residues: 181.7890 Evaluate side-chains 368 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 366 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain D residue 366 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 132 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 86 GLN C 139 ASN C 518 ASN C 604 HIS C 808 ASN C1146 GLN D 519 ASN D 861 ASN D 865 HIS D 867 GLN D 897 HIS D1218 HIS D1252 HIS D1367 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN M 121 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.143268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.117755 restraints weight = 70719.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.117229 restraints weight = 46620.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.118096 restraints weight = 35349.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.118448 restraints weight = 30269.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.118514 restraints weight = 25806.580| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25777 Z= 0.201 Angle : 0.771 14.058 35441 Z= 0.397 Chirality : 0.048 0.292 4398 Planarity : 0.005 0.052 4505 Dihedral : 14.115 160.933 4345 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.61 % Favored : 92.84 % Rotamer: Outliers : 4.25 % Allowed : 13.10 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % 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: -2.56 (0.12), residues: 3451 helix: -1.36 (0.13), residues: 1197 sheet: -0.95 (0.28), residues: 285 loop : -2.08 (0.12), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 838 TYR 0.024 0.002 TYR D 626 PHE 0.024 0.002 PHE C 812 TRP 0.024 0.002 TRP D 115 HIS 0.007 0.001 HIS D1227 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (25777) covalent geometry : angle 0.77088 / 0.40 (35441) hydrogen bonds : bond 0.04972 / 3.41 ( 1047) hydrogen bonds : angle 6.91405 / 4.85 ( 2933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 370 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7942 (mm) REVERT: B 85 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8362 (mt) REVERT: B 147 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6545 (mp10) REVERT: B 212 ASP cc_start: 0.5341 (t0) cc_final: 0.5034 (t0) REVERT: C 445 ILE cc_start: 0.8702 (mt) cc_final: 0.7904 (pt) REVERT: C 653 MET cc_start: 0.6124 (tpt) cc_final: 0.5905 (mtt) REVERT: C 872 TYR cc_start: 0.6276 (m-80) cc_final: 0.5860 (m-80) REVERT: C 1023 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8241 (m-70) REVERT: C 1036 ILE cc_start: 0.9265 (mm) cc_final: 0.9061 (mm) REVERT: C 1259 LEU cc_start: 0.7041 (mp) cc_final: 0.6719 (tt) REVERT: D 102 MET cc_start: 0.5855 (ttm) cc_final: 0.5631 (ttm) REVERT: D 564 VAL cc_start: 0.8795 (t) cc_final: 0.8593 (m) REVERT: D 743 MET cc_start: 0.7376 (mtm) cc_final: 0.7096 (mtm) outliers start: 88 outliers final: 59 residues processed: 430 average time/residue: 0.1371 time to fit residues: 97.7794 Evaluate side-chains 342 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 279 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 797 THR Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 867 GLN Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 286 optimal weight: 40.0000 chunk 307 optimal weight: 10.0000 chunk 319 optimal weight: 30.0000 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN B 147 GLN C 808 ASN C 832 HIS C1070 HIS C1313 HIS ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** 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 = 0.4240 r_free = 0.4240 target = 0.136219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.109705 restraints weight = 68942.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.108975 restraints weight = 47167.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.109784 restraints weight = 35114.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.110016 restraints weight = 32455.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.110160 restraints weight = 26801.586| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 25777 Z= 0.230 Angle : 0.779 11.357 35441 Z= 0.405 Chirality : 0.049 0.316 4398 Planarity : 0.005 0.073 4505 Dihedral : 13.927 161.066 4342 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.29 % Favored : 91.19 % Rotamer: Outliers : 5.51 % Allowed : 15.51 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % 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: -2.04 (0.13), residues: 3451 helix: -0.60 (0.14), residues: 1205 sheet: -0.81 (0.29), residues: 280 loop : -1.99 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 148 TYR 0.021 0.002 TYR C 92 PHE 0.021 0.002 PHE C1221 TRP 0.017 0.002 TRP D 868 HIS 0.043 0.003 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (25777) covalent geometry : angle 0.77857 / 0.40 (35441) hydrogen bonds : bond 0.05154 / 3.66 ( 1047) hydrogen bonds : angle 6.03099 / 4.24 ( 2933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 293 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: A 83 LEU cc_start: 0.8764 (mm) cc_final: 0.8487 (mp) REVERT: A 132 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.6942 (m-70) REVERT: B 81 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8311 (mm) REVERT: B 212 ASP cc_start: 0.5294 (t0) cc_final: 0.4894 (t0) REVERT: C 445 ILE cc_start: 0.8536 (mt) cc_final: 0.8150 (pt) REVERT: C 775 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: C 872 TYR cc_start: 0.6697 (m-80) cc_final: 0.6431 (m-80) REVERT: C 964 LEU cc_start: 0.9290 (tp) cc_final: 0.9008 (tp) REVERT: C 1023 HIS cc_start: 0.8701 (OUTLIER) cc_final: 0.8290 (m-70) REVERT: C 1066 MET cc_start: 0.8092 (mmm) cc_final: 0.7480 (mtp) REVERT: C 1085 MET cc_start: 0.8131 (mmt) cc_final: 0.7894 (mmp) REVERT: D 115 TRP cc_start: 0.2979 (m100) cc_final: 0.0930 (m100) REVERT: D 564 VAL cc_start: 0.8841 (t) cc_final: 0.8607 (m) REVERT: D 629 PHE cc_start: 0.8450 (m-80) cc_final: 0.8181 (m-80) REVERT: D 743 MET cc_start: 0.7472 (mtm) cc_final: 0.7237 (mtm) REVERT: E 30 MET cc_start: 0.7491 (mtp) cc_final: 0.7290 (mtt) outliers start: 114 outliers final: 64 residues processed: 374 average time/residue: 0.1318 time to fit residues: 84.1227 Evaluate side-chains 321 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 252 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 406 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 551 ARG Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 237 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 328 optimal weight: 0.0170 chunk 96 optimal weight: 3.9990 chunk 332 optimal weight: 0.0000 chunk 333 optimal weight: 0.0470 chunk 270 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 overall best weight: 0.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 808 ASN C1244 HIS D 186 GLN D 702 GLN D 716 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.139331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.113838 restraints weight = 68060.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.112456 restraints weight = 46811.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.113400 restraints weight = 36291.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.113707 restraints weight = 31332.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.113821 restraints weight = 25837.593| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25777 Z= 0.127 Angle : 0.671 11.414 35441 Z= 0.341 Chirality : 0.045 0.259 4398 Planarity : 0.004 0.055 4505 Dihedral : 13.828 163.900 4341 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.98 % Favored : 92.52 % Rotamer: Outliers : 4.30 % Allowed : 17.64 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % 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: -1.58 (0.13), residues: 3451 helix: -0.01 (0.15), residues: 1198 sheet: -0.82 (0.30), residues: 290 loop : -1.82 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 551 TYR 0.017 0.001 TYR D 679 PHE 0.019 0.001 PHE C 629 TRP 0.014 0.001 TRP D 580 HIS 0.008 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (25777) covalent geometry : angle 0.67094 / 0.34 (35441) hydrogen bonds : bond 0.04405 / 3.18 ( 1047) hydrogen bonds : angle 5.56655 / 3.92 ( 2933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 308 time to evaluate : 0.946 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: A 67 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: A 83 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8302 (mp) REVERT: A 132 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.7136 (m-70) REVERT: B 212 ASP cc_start: 0.5153 (t0) cc_final: 0.4758 (t0) REVERT: C 37 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8487 (pttt) REVERT: C 370 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.6889 (ptm) REVERT: C 445 ILE cc_start: 0.8443 (mt) cc_final: 0.8075 (pt) REVERT: C 775 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7093 (pt0) REVERT: C 872 TYR cc_start: 0.6578 (m-80) cc_final: 0.6370 (m-80) REVERT: C 1023 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.8178 (m-70) REVERT: C 1085 MET cc_start: 0.8182 (mmt) cc_final: 0.7942 (mmp) REVERT: C 1259 LEU cc_start: 0.7700 (mm) cc_final: 0.6834 (tp) REVERT: D 564 VAL cc_start: 0.8740 (t) cc_final: 0.8512 (m) REVERT: D 1260 MET cc_start: 0.6106 (ttt) cc_final: 0.5773 (mtt) outliers start: 89 outliers final: 52 residues processed: 372 average time/residue: 0.1338 time to fit residues: 83.4135 Evaluate side-chains 328 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 610 ARG Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1329 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 216 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 102 optimal weight: 0.0050 chunk 159 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 224 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 808 ASN D 158 GLN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN ** D1244 GLN ** 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 = 0.4218 r_free = 0.4218 target = 0.134850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.108780 restraints weight = 68607.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108116 restraints weight = 46227.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.108783 restraints weight = 35797.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.109017 restraints weight = 30513.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.109168 restraints weight = 28530.885| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25777 Z= 0.198 Angle : 0.719 12.071 35441 Z= 0.369 Chirality : 0.046 0.269 4398 Planarity : 0.005 0.061 4505 Dihedral : 13.878 165.097 4341 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.11 % Favored : 91.31 % Rotamer: Outliers : 5.51 % Allowed : 17.54 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % 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: -1.52 (0.14), residues: 3451 helix: 0.11 (0.15), residues: 1193 sheet: -0.89 (0.31), residues: 279 loop : -1.80 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 195 TYR 0.022 0.002 TYR D1363 PHE 0.021 0.002 PHE D 461 TRP 0.016 0.002 TRP C 807 HIS 0.010 0.002 HIS D 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (25777) covalent geometry : angle 0.71891 / 0.37 (35441) hydrogen bonds : bond 0.04754 / 3.35 ( 1047) hydrogen bonds : angle 5.43862 / 3.81 ( 2933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 267 time to evaluate : 0.882 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: A 67 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7851 (pt0) REVERT: A 132 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7761 (m-70) REVERT: B 212 ASP cc_start: 0.5205 (t0) cc_final: 0.4699 (t0) REVERT: C 37 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8699 (pttp) REVERT: C 445 ILE cc_start: 0.8362 (mt) cc_final: 0.8014 (pt) REVERT: C 514 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7294 (p90) REVERT: C 775 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7024 (pt0) REVERT: C 872 TYR cc_start: 0.6925 (m-80) cc_final: 0.6486 (m-80) REVERT: C 1023 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8285 (m-70) REVERT: C 1278 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8396 (mm) REVERT: D 564 VAL cc_start: 0.8784 (t) cc_final: 0.8547 (m) REVERT: D 1260 MET cc_start: 0.6547 (ttt) cc_final: 0.6258 (mtt) outliers start: 114 outliers final: 77 residues processed: 348 average time/residue: 0.1335 time to fit residues: 79.8696 Evaluate side-chains 328 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 244 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 610 ARG Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1319 PHE Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 312 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 292 optimal weight: 0.0470 chunk 40 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 249 optimal weight: 0.6980 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 808 ASN D 158 GLN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 ASN E 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.135847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.109477 restraints weight = 67858.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.108989 restraints weight = 44401.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.109611 restraints weight = 34116.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.109909 restraints weight = 28682.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.110020 restraints weight = 25927.639| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25777 Z= 0.129 Angle : 0.661 11.527 35441 Z= 0.333 Chirality : 0.045 0.302 4398 Planarity : 0.004 0.054 4505 Dihedral : 13.813 165.797 4341 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.27 % Favored : 92.18 % Rotamer: Outliers : 5.03 % Allowed : 18.41 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % 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: 3451 helix: 0.40 (0.15), residues: 1198 sheet: -0.86 (0.31), residues: 279 loop : -1.72 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 271 TYR 0.015 0.001 TYR D 679 PHE 0.013 0.001 PHE C 629 TRP 0.014 0.001 TRP D 580 HIS 0.007 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (25777) covalent geometry : angle 0.66134 / 0.33 (35441) hydrogen bonds : bond 0.04342 / 3.10 ( 1047) hydrogen bonds : angle 5.18804 / 3.65 ( 2933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 277 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8507 (mp) REVERT: B 78 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7555 (pp) REVERT: C 370 MET cc_start: 0.8280 (mmm) cc_final: 0.6830 (ptm) REVERT: C 445 ILE cc_start: 0.8395 (mt) cc_final: 0.8064 (pt) REVERT: C 775 GLU cc_start: 0.7554 (mp0) cc_final: 0.6974 (pt0) REVERT: C 872 TYR cc_start: 0.6826 (m-80) cc_final: 0.6503 (m-80) REVERT: C 965 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8712 (mp10) REVERT: C 1023 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.8186 (m-70) REVERT: C 1114 GLU cc_start: 0.7672 (tt0) cc_final: 0.7457 (tt0) REVERT: C 1291 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7998 (pp) REVERT: D 564 VAL cc_start: 0.8759 (t) cc_final: 0.8533 (m) REVERT: D 641 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7164 (mt) REVERT: D 1260 MET cc_start: 0.6336 (ttt) cc_final: 0.6054 (mtt) REVERT: M 250 VAL cc_start: 0.7640 (t) cc_final: 0.7406 (p) outliers start: 104 outliers final: 64 residues processed: 350 average time/residue: 0.1304 time to fit residues: 79.5273 Evaluate side-chains 324 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 254 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 610 ARG Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 250 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 234 optimal weight: 0.0470 chunk 162 optimal weight: 9.9990 chunk 330 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 293 optimal weight: 20.0000 chunk 328 optimal weight: 9.9990 overall best weight: 7.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS C 604 HIS C 752 ASN C 808 ASN D 158 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.125135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.099208 restraints weight = 70443.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.098920 restraints weight = 49330.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.099189 restraints weight = 43834.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099379 restraints weight = 37976.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.099598 restraints weight = 30798.893| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.128 25777 Z= 0.427 Angle : 1.075 18.663 35441 Z= 0.558 Chirality : 0.058 0.428 4398 Planarity : 0.008 0.079 4505 Dihedral : 14.558 169.851 4341 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.78 % Allowed : 11.01 % Favored : 88.21 % Rotamer: Outliers : 7.25 % Allowed : 17.59 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % 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: -2.54 (0.13), residues: 3451 helix: -0.85 (0.14), residues: 1188 sheet: -1.19 (0.30), residues: 301 loop : -2.39 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1177 TYR 0.032 0.004 TYR C 614 PHE 0.031 0.004 PHE C 188 TRP 0.018 0.003 TRP D 580 HIS 0.027 0.003 HIS D 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00964 / 0.43 (25777) covalent geometry : angle 1.07499 / 0.56 (35441) hydrogen bonds : bond 0.07034 / 4.84 ( 1047) hydrogen bonds : angle 6.20518 / 4.36 ( 2933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 232 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8179 (m-70) REVERT: C 33 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7671 (t0) REVERT: C 514 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7684 (p90) REVERT: C 573 ASN cc_start: 0.8825 (m110) cc_final: 0.8524 (m-40) REVERT: C 872 TYR cc_start: 0.7124 (m-80) cc_final: 0.6910 (m-80) REVERT: C 965 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8837 (mp10) REVERT: C 1269 ARG cc_start: 0.7284 (ptt-90) cc_final: 0.6817 (ptp-110) REVERT: D 425 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8059 (tpt90) REVERT: D 564 VAL cc_start: 0.8888 (t) cc_final: 0.8592 (m) REVERT: E 15 ASN cc_start: 0.8153 (t0) cc_final: 0.7564 (t0) REVERT: E 22 VAL cc_start: 0.8172 (m) cc_final: 0.7962 (p) REVERT: E 64 LEU cc_start: 0.8689 (mt) cc_final: 0.8428 (mt) outliers start: 150 outliers final: 84 residues processed: 357 average time/residue: 0.1303 time to fit residues: 80.2959 Evaluate side-chains 301 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 212 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 406 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1204 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 861 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1319 PHE Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 328 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 208 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 197 optimal weight: 8.9990 chunk 336 optimal weight: 50.0000 chunk 191 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 132 HIS C 808 ASN C1313 HIS ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.130450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.104729 restraints weight = 68941.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.103814 restraints weight = 47002.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.104508 restraints weight = 38398.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.104716 restraints weight = 31592.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104783 restraints weight = 29143.536| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 25777 Z= 0.155 Angle : 0.743 14.263 35441 Z= 0.375 Chirality : 0.047 0.279 4398 Planarity : 0.005 0.076 4505 Dihedral : 14.122 170.707 4341 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.82 % Favored : 91.63 % Rotamer: Outliers : 4.20 % Allowed : 20.78 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % 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: -1.84 (0.14), residues: 3451 helix: 0.06 (0.15), residues: 1209 sheet: -1.18 (0.30), residues: 282 loop : -2.16 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 101 TYR 0.015 0.002 TYR D 679 PHE 0.023 0.002 PHE C 38 TRP 0.021 0.001 TRP D 580 HIS 0.007 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (25777) covalent geometry : angle 0.74271 / 0.38 (35441) hydrogen bonds : bond 0.04961 / 3.50 ( 1047) hydrogen bonds : angle 5.36017 / 3.78 ( 2933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 248 time to evaluate : 0.927 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: A 83 LEU cc_start: 0.8919 (mm) cc_final: 0.8668 (mp) REVERT: A 132 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8197 (m90) REVERT: A 203 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7452 (mt) REVERT: C 130 MET cc_start: 0.6329 (ttp) cc_final: 0.6093 (ttp) REVERT: C 514 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7204 (p90) REVERT: C 872 TYR cc_start: 0.7136 (m-80) cc_final: 0.6811 (m-80) REVERT: C 964 LEU cc_start: 0.9327 (tp) cc_final: 0.9118 (tp) REVERT: C 965 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8803 (mp10) REVERT: C 1019 ASP cc_start: 0.7012 (t0) cc_final: 0.6700 (t0) REVERT: C 1180 MET cc_start: 0.7836 (tpt) cc_final: 0.7578 (tpt) REVERT: C 1269 ARG cc_start: 0.7236 (ptt-90) cc_final: 0.6752 (ptp-110) REVERT: C 1289 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8094 (mm-30) REVERT: D 347 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7749 (m) REVERT: D 564 VAL cc_start: 0.8819 (t) cc_final: 0.8547 (m) REVERT: D 1260 MET cc_start: 0.6592 (ttt) cc_final: 0.6151 (mtt) REVERT: E 15 ASN cc_start: 0.8248 (t0) cc_final: 0.7454 (t0) REVERT: E 22 VAL cc_start: 0.8085 (m) cc_final: 0.7845 (p) outliers start: 87 outliers final: 62 residues processed: 315 average time/residue: 0.1312 time to fit residues: 72.5187 Evaluate side-chains 290 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 406 ASN Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1319 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 185 optimal weight: 0.0040 chunk 4 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 250 optimal weight: 0.6980 chunk 247 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 311 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS D 702 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.131097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.105766 restraints weight = 68757.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105099 restraints weight = 46994.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.105612 restraints weight = 40273.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.105973 restraints weight = 31827.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.106030 restraints weight = 28589.005| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25777 Z= 0.139 Angle : 0.718 15.998 35441 Z= 0.357 Chirality : 0.046 0.261 4398 Planarity : 0.005 0.073 4505 Dihedral : 13.932 170.843 4341 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.20 % Favored : 91.13 % Rotamer: Outliers : 3.72 % Allowed : 21.22 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % 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: -1.58 (0.14), residues: 3451 helix: 0.34 (0.15), residues: 1216 sheet: -0.87 (0.32), residues: 262 loop : -2.08 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 271 TYR 0.014 0.001 TYR D 679 PHE 0.016 0.001 PHE C 38 TRP 0.018 0.001 TRP D 580 HIS 0.047 0.002 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (25777) covalent geometry : angle 0.71817 / 0.36 (35441) hydrogen bonds : bond 0.04637 / 3.28 ( 1047) hydrogen bonds : angle 5.16100 / 3.65 ( 2933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 244 time to evaluate : 0.759 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: A 83 LEU cc_start: 0.8916 (mm) cc_final: 0.8644 (mp) REVERT: C 130 MET cc_start: 0.6324 (ttp) cc_final: 0.6084 (ttp) REVERT: C 514 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7237 (p90) REVERT: C 872 TYR cc_start: 0.7084 (m-80) cc_final: 0.6701 (m-80) REVERT: C 964 LEU cc_start: 0.9301 (tp) cc_final: 0.9098 (tp) REVERT: C 965 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8810 (mp10) REVERT: C 1269 ARG cc_start: 0.7072 (ptt-90) cc_final: 0.6644 (ptp-110) REVERT: C 1289 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8058 (mm-30) REVERT: D 424 ASN cc_start: 0.8526 (t0) cc_final: 0.8310 (t0) REVERT: D 425 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7392 (tpt90) REVERT: D 564 VAL cc_start: 0.8758 (t) cc_final: 0.8520 (m) REVERT: D 1260 MET cc_start: 0.6533 (ttt) cc_final: 0.6118 (mtt) REVERT: E 15 ASN cc_start: 0.8274 (t0) cc_final: 0.7518 (t0) REVERT: E 22 VAL cc_start: 0.8165 (m) cc_final: 0.7952 (p) outliers start: 77 outliers final: 63 residues processed: 304 average time/residue: 0.1299 time to fit residues: 67.9665 Evaluate side-chains 296 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 230 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 406 ASN Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 166 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 122 optimal weight: 0.0670 chunk 3 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 61 optimal weight: 0.0370 chunk 269 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 702 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** 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 = 0.4177 r_free = 0.4177 target = 0.132059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.106418 restraints weight = 68498.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.105613 restraints weight = 46550.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.106323 restraints weight = 37474.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106571 restraints weight = 31095.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106632 restraints weight = 27961.890| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25777 Z= 0.131 Angle : 0.696 12.213 35441 Z= 0.347 Chirality : 0.045 0.345 4398 Planarity : 0.004 0.070 4505 Dihedral : 13.828 170.851 4341 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.48 % Favored : 91.89 % Rotamer: Outliers : 3.48 % Allowed : 21.60 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % 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: 3451 helix: 0.50 (0.15), residues: 1226 sheet: -0.83 (0.32), residues: 266 loop : -2.00 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 271 TYR 0.015 0.001 TYR D 679 PHE 0.014 0.001 PHE C 38 TRP 0.019 0.001 TRP D 580 HIS 0.009 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (25777) covalent geometry : angle 0.69576 / 0.35 (35441) hydrogen bonds : bond 0.04508 / 3.19 ( 1047) hydrogen bonds : angle 5.01541 / 3.56 ( 2933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 241 time to evaluate : 0.839 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: A 83 LEU cc_start: 0.8865 (mm) cc_final: 0.8602 (mp) REVERT: C 130 MET cc_start: 0.6296 (ttp) cc_final: 0.6036 (ttp) REVERT: C 514 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7334 (p90) REVERT: C 872 TYR cc_start: 0.7086 (m-80) cc_final: 0.6656 (m-80) REVERT: C 965 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8818 (mp10) REVERT: C 1269 ARG cc_start: 0.7018 (ptt-90) cc_final: 0.6582 (ptp-110) REVERT: C 1289 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8163 (mm-30) REVERT: C 1290 MET cc_start: 0.8343 (tmm) cc_final: 0.8100 (tmm) REVERT: D 425 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7456 (tpt90) REVERT: D 564 VAL cc_start: 0.8737 (t) cc_final: 0.8505 (m) REVERT: D 1260 MET cc_start: 0.6480 (ttt) cc_final: 0.6082 (mtt) REVERT: E 15 ASN cc_start: 0.8302 (t0) cc_final: 0.7551 (t0) REVERT: E 22 VAL cc_start: 0.8197 (m) cc_final: 0.7982 (p) outliers start: 72 outliers final: 63 residues processed: 296 average time/residue: 0.1360 time to fit residues: 69.3960 Evaluate side-chains 293 residues out of total 2978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 227 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 406 ASN Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 766 ASN Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain M residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 326 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 337 optimal weight: 50.0000 chunk 39 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS C 932 GLN D 702 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** 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 = 0.4170 r_free = 0.4170 target = 0.131167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.104692 restraints weight = 69046.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.104056 restraints weight = 45794.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.104481 restraints weight = 38537.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104734 restraints weight = 34283.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105235 restraints weight = 28138.390| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25777 Z= 0.140 Angle : 0.691 14.067 35441 Z= 0.345 Chirality : 0.045 0.333 4398 Planarity : 0.004 0.086 4505 Dihedral : 13.784 171.326 4341 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.06 % Favored : 91.31 % Rotamer: Outliers : 3.77 % Allowed : 21.46 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % 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: -1.36 (0.14), residues: 3451 helix: 0.56 (0.15), residues: 1234 sheet: -0.95 (0.31), residues: 275 loop : -1.97 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 271 TYR 0.014 0.001 TYR D 679 PHE 0.013 0.001 PHE C 38 TRP 0.017 0.001 TRP D 580 HIS 0.007 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (25777) covalent geometry : angle 0.69089 / 0.34 (35441) hydrogen bonds : bond 0.04483 / 3.17 ( 1047) hydrogen bonds : angle 4.97791 / 3.54 ( 2933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3988.80 seconds wall clock time: 69 minutes 28.96 seconds (4168.96 seconds total)