Starting phenix.real_space_refine on Tue Jun 24 05:12:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gh6_0002/06_2025/6gh6_0002.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gh6_0002/06_2025/6gh6_0002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gh6_0002/06_2025/6gh6_0002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gh6_0002/06_2025/6gh6_0002.map" model { file = "/net/cci-nas-00/data/ceres_data/6gh6_0002/06_2025/6gh6_0002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gh6_0002/06_2025/6gh6_0002.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 96 5.16 5 C 17252 2.51 5 N 4960 2.21 5 O 5647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28051 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1776 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1729 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 10068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10068 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 333 Chain: "D" Number of atoms: 10063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10063 Classifications: {'peptide': 1334} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 65} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 51, 'TRANS': 1279} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 398 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 11, 'GLU:plan': 4, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 206 Chain: "E" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 568 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "M" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 958 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 3, 'TRANS': 139} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 144 Chain: "M" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 536 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 35, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 128 Chain: "M" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 381 Classifications: {'peptide': 75} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 61} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'TYR:plan': 1, 'UNK:plan-1': 16, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 Chain: "N" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 988 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "T" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 984 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N ASP M 168 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP M 168 " occ=0.20 residue: pdb=" N GLU M 169 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU M 169 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 17.22, per 1000 atoms: 0.61 Number of scatterers: 28051 At special positions: 0 Unit cell: (137.16, 171.72, 165.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 96 15.00 O 5647 8.00 N 4960 7.00 C 17252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.59 Conformation dependent library (CDL) restraints added in 3.7 seconds 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6558 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 36 sheets defined 38.4% alpha, 11.5% beta 38 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 10.07 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.970A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.657A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.600A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.829A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.961A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.609A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 28 through 39 removed outlier: 4.064A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.620A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 159 through 163 removed outlier: 4.014A pdb=" N GLY C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.060A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.753A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.532A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.700A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 4.083A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.705A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 388 removed outlier: 3.660A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 removed outlier: 4.112A pdb=" N ARG C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.522A pdb=" N GLY C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.548A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 4.435A pdb=" N ASP C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 487 through 492' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.899A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 607 through 613 removed outlier: 4.151A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.160A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.751A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.646A pdb=" N GLN C 686 " --> pdb=" O GLY C 682 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.623A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 removed outlier: 3.710A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 911 removed outlier: 4.575A pdb=" N ALA C 910 " --> pdb=" O GLY C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 979 removed outlier: 4.159A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.538A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1037 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.095A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.911A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1168 through 1177 Processing helix chain 'C' and resid 1191 through 1201 removed outlier: 3.785A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1310 removed outlier: 4.063A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1321 through 1333 removed outlier: 4.098A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.793A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.511A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.730A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.583A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.530A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.792A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 4.245A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 376 " --> pdb=" O MET D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 removed outlier: 3.878A pdb=" N GLY D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.022A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.653A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 483 removed outlier: 4.179A pdb=" N LEU D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.713A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 539 removed outlier: 4.328A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.822A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.697A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.741A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 701 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.812A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 783 removed outlier: 4.365A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 805 removed outlier: 3.875A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR D 797 " --> pdb=" O SER D 793 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.103A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 916 through 925 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.815A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.397A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1291 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.977A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1353 Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 3.702A pdb=" N MET D1370 " --> pdb=" O HIS D1366 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D1372 " --> pdb=" O ASP D1368 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.909A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.561A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 120 through 131 removed outlier: 3.582A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 146 removed outlier: 3.805A pdb=" N ASP M 146 " --> pdb=" O THR M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 164 removed outlier: 3.675A pdb=" N ILE M 161 " --> pdb=" O GLN M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 3.787A pdb=" N ALA M 177 " --> pdb=" O GLU M 173 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 207 removed outlier: 4.747A pdb=" N ALA M 207 " --> pdb=" O LEU M 203 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.834A pdb=" N ALA M 216 " --> pdb=" O TRP M 212 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS M 223 " --> pdb=" O ILE M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 231 removed outlier: 4.592A pdb=" N HIS M 230 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP M 231 " --> pdb=" O LEU M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 255 removed outlier: 4.230A pdb=" N LYS M 247 " --> pdb=" O GLU M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 355 removed outlier: 3.716A pdb=" N SER M 344 " --> pdb=" O LEU M 340 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 374 removed outlier: 3.960A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 388 removed outlier: 3.958A pdb=" N GLN M 387 " --> pdb=" O ARG M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 428 Processing helix chain 'M' and resid 438 through 449 removed outlier: 3.642A pdb=" N GLN M 449 " --> pdb=" O MET M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 455 through 463 removed outlier: 3.608A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 5.153A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 105 removed outlier: 8.377A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 105 removed outlier: 3.568A pdb=" N LEU B 102 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA6, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.440A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.534A pdb=" N GLU C 67 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 103 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.534A pdb=" N GLU C 67 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 103 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 145 removed outlier: 3.689A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 454 removed outlier: 7.007A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 154 through 158 removed outlier: 4.177A pdb=" N ALA C 174 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 285 through 286 removed outlier: 4.001A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.796A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.606A pdb=" N VAL C 296 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 336 " --> pdb=" O VAL C 296 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.741A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.741A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 616 through 617 removed outlier: 3.637A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.731A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 724 through 727 removed outlier: 4.896A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC3, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 5.093A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AC5, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.974A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.974A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 865 through 866 removed outlier: 3.503A pdb=" N ILE C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1335 through 1336 removed outlier: 3.965A pdb=" N ALA D 23 " --> pdb=" O ASN C1336 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 104 through 106 Processing sheet with id=AD1, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.488A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 435 through 437 removed outlier: 3.570A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 366 through 369 Processing sheet with id=AD4, first strand: chain 'D' and resid 527 through 528 removed outlier: 7.233A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD6, first strand: chain 'D' and resid 959 through 961 removed outlier: 4.311A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1160 through 1163 removed outlier: 4.418A pdb=" N ILE D1162 " --> pdb=" O GLU D1202 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU D1202 " --> pdb=" O ILE D1162 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AD9, first strand: chain 'M' and resid 279 through 281 964 hydrogen bonds defined for protein. 2736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 15.62 Time building geometry restraints manager: 8.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 1 1.13 - 1.30: 4748 1.30 - 1.47: 11003 1.47 - 1.64: 12712 1.64 - 1.81: 170 Bond restraints: 28634 Sorted by residual: bond pdb=" C THR D 514 " pdb=" N ARG D 515 " ideal model delta sigma weight residual 1.329 0.964 0.365 1.36e-02 5.41e+03 7.22e+02 bond pdb=" C GLU M 356 " pdb=" N GLN M 357 " ideal model delta sigma weight residual 1.332 1.507 -0.175 1.40e-02 5.10e+03 1.56e+02 bond pdb=" C THR M 210 " pdb=" N PRO M 211 " ideal model delta sigma weight residual 1.334 1.511 -0.177 2.34e-02 1.83e+03 5.75e+01 bond pdb=" O3' DA T 1 " pdb=" P DG T 2 " ideal model delta sigma weight residual 1.607 1.686 -0.079 1.50e-02 4.44e+03 2.77e+01 bond pdb=" C LYS M 363 " pdb=" N PRO M 364 " ideal model delta sigma weight residual 1.332 1.390 -0.059 1.30e-02 5.92e+03 2.05e+01 ... (remaining 28629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.35: 39209 6.35 - 12.71: 70 12.71 - 19.06: 12 19.06 - 25.41: 4 25.41 - 31.76: 2 Bond angle restraints: 39297 Sorted by residual: angle pdb=" CA GLU M 356 " pdb=" C GLU M 356 " pdb=" N GLN M 357 " ideal model delta sigma weight residual 116.51 85.96 30.55 1.34e+00 5.57e-01 5.20e+02 angle pdb=" O GLU M 356 " pdb=" C GLU M 356 " pdb=" N GLN M 357 " ideal model delta sigma weight residual 123.12 146.82 -23.70 1.32e+00 5.74e-01 3.22e+02 angle pdb=" C GLU M 356 " pdb=" N GLN M 357 " pdb=" CA GLN M 357 " ideal model delta sigma weight residual 121.54 89.78 31.76 1.91e+00 2.74e-01 2.77e+02 angle pdb=" O3' DC T 5 " pdb=" P DT T 6 " pdb=" O5' DT T 6 " ideal model delta sigma weight residual 104.00 125.91 -21.91 1.50e+00 4.44e-01 2.13e+02 angle pdb=" C5' DC T 5 " pdb=" C4' DC T 5 " pdb=" O4' DC T 5 " ideal model delta sigma weight residual 109.40 128.95 -19.55 1.50e+00 4.44e-01 1.70e+02 ... (remaining 39292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 16615 35.29 - 70.58: 557 70.58 - 105.87: 24 105.87 - 141.17: 3 141.17 - 176.46: 4 Dihedral angle restraints: 17203 sinusoidal: 7047 harmonic: 10156 Sorted by residual: dihedral pdb=" CA ALA C1263 " pdb=" C ALA C1263 " pdb=" N GLN C1264 " pdb=" CA GLN C1264 " ideal model delta harmonic sigma weight residual -180.00 -139.71 -40.29 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" CA LEU D 343 " pdb=" C LEU D 343 " pdb=" N GLY D 344 " pdb=" CA GLY D 344 " ideal model delta harmonic sigma weight residual 180.00 -146.65 -33.35 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA PRO D1026 " pdb=" C PRO D1026 " pdb=" N VAL D1027 " pdb=" CA VAL D1027 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 17200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 4642 0.206 - 0.411: 25 0.411 - 0.617: 3 0.617 - 0.823: 0 0.823 - 1.028: 1 Chirality restraints: 4671 Sorted by residual: chirality pdb=" C4' DC T 5 " pdb=" C5' DC T 5 " pdb=" O4' DC T 5 " pdb=" C3' DC T 5 " both_signs ideal model delta sigma weight residual False -2.53 -1.50 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" C4' DT T 6 " pdb=" C5' DT T 6 " pdb=" O4' DT T 6 " pdb=" C3' DT T 6 " both_signs ideal model delta sigma weight residual False -2.53 -1.94 -0.58 2.00e-01 2.50e+01 8.55e+00 chirality pdb=" CA UNK M 270 " pdb=" N UNK M 270 " pdb=" C UNK M 270 " pdb=" CB UNK M 270 " both_signs ideal model delta sigma weight residual False 2.52 2.02 0.50 2.00e-01 2.50e+01 6.24e+00 ... (remaining 4668 not shown) Planarity restraints: 4826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU M 356 " 0.026 2.00e-02 2.50e+03 7.98e-02 6.37e+01 pdb=" C GLU M 356 " -0.136 2.00e-02 2.50e+03 pdb=" O GLU M 356 " 0.066 2.00e-02 2.50e+03 pdb=" N GLN M 357 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N -8 " -0.051 2.00e-02 2.50e+03 2.31e-02 1.60e+01 pdb=" N9 DG N -8 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG N -8 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG N -8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG N -8 " 0.014 2.00e-02 2.50e+03 pdb=" C6 DG N -8 " -0.020 2.00e-02 2.50e+03 pdb=" O6 DG N -8 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG N -8 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DG N -8 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG N -8 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG N -8 " 0.027 2.00e-02 2.50e+03 pdb=" C4 DG N -8 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N -7 " -0.050 2.00e-02 2.50e+03 2.31e-02 1.46e+01 pdb=" N9 DA N -7 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA N -7 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA N -7 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA N -7 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA N -7 " -0.014 2.00e-02 2.50e+03 pdb=" N6 DA N -7 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DA N -7 " -0.019 2.00e-02 2.50e+03 pdb=" C2 DA N -7 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA N -7 " 0.023 2.00e-02 2.50e+03 pdb=" C4 DA N -7 " 0.028 2.00e-02 2.50e+03 ... (remaining 4823 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 172 2.53 - 3.12: 22138 3.12 - 3.71: 41188 3.71 - 4.31: 55642 4.31 - 4.90: 90379 Nonbonded interactions: 209519 Sorted by model distance: nonbonded pdb=" OE1 GLU D 523 " pdb=" N GLY D 524 " model vdw 1.934 3.120 nonbonded pdb=" C1' DC N -11 " pdb=" OP1 DT N -10 " model vdw 2.124 3.470 nonbonded pdb=" C GLU M 356 " pdb=" C GLN M 357 " model vdw 2.209 2.800 nonbonded pdb=" OG SER C1322 " pdb=" NZ LYS D 332 " model vdw 2.215 3.120 nonbonded pdb=" C4' DA N -12 " pdb=" OP1 DC N -11 " model vdw 2.220 3.470 ... (remaining 209514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 65 or (resid 66 through 68 and (nam \ e N or name CA or name C or name O or name CB )) or resid 69 through 70 or (resi \ d 71 through 72 and (name N or name CA or name C or name O or name CB )) or resi \ d 73 through 79 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 134 or (resid 135 through 138 and (name N or name CA o \ r name C or name O or name CB )) or resid 139 through 142 or (resid 143 and (nam \ e N or name CA or name C or name O or name CB )) or resid 144 through 159 or (re \ sid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 or \ (resid 162 through 166 and (name N or name CA or name C or name O or name CB )) \ or resid 167 through 169 or (resid 170 and (name N or name CA or name C or name \ O or name CB )) or resid 171 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 232 or (resid 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 through 237)) selection = (chain 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 71 or (resid 72 and (name N or name CA or name C or name O \ or name CB )) or resid 73 through 92 or (resid 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 or (resid 95 and (name N or name CA or na \ me C or name O or name CB )) or resid 96 through 190 or (resid 191 and (name N o \ r name CA or name C or name O or name CB )) or resid 192 or (resid 193 and (name \ N or name CA or name C or name O or name CB )) or resid 194 through 236 or (res \ id 237 and (name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.040 Extract box with map and model: 1.140 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 77.030 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.365 28634 Z= 0.267 Angle : 0.910 31.765 39297 Z= 0.551 Chirality : 0.051 1.028 4671 Planarity : 0.004 0.080 4826 Dihedral : 14.496 176.458 10645 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.93 % Allowed : 9.75 % Favored : 89.33 % Rotamer: Outliers : 0.38 % Allowed : 1.49 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.11), residues: 3458 helix: -2.82 (0.11), residues: 1112 sheet: -1.21 (0.26), residues: 285 loop : -2.40 (0.11), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1193 HIS 0.006 0.001 HIS D 104 PHE 0.015 0.001 PHE C 828 TYR 0.013 0.001 TYR C1229 ARG 0.006 0.000 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.16556 ( 1054) hydrogen bonds : angle 10.22205 ( 2914) covalent geometry : bond 0.00426 (28634) covalent geometry : angle 0.90986 (39297) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 570 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8252 (mt) cc_final: 0.7511 (mt) REVERT: A 51 MET cc_start: 0.8819 (mmm) cc_final: 0.8549 (mmm) REVERT: A 80 GLU cc_start: 0.9072 (tt0) cc_final: 0.8842 (tt0) REVERT: A 97 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8477 (tm-30) REVERT: A 115 ILE cc_start: 0.9595 (mt) cc_final: 0.9225 (tp) REVERT: A 173 VAL cc_start: 0.9058 (m) cc_final: 0.8429 (p) REVERT: B 29 GLU cc_start: 0.9433 (tt0) cc_final: 0.9155 (tt0) REVERT: B 77 ASP cc_start: 0.9687 (t0) cc_final: 0.9447 (t70) REVERT: B 147 GLN cc_start: 0.9538 (pt0) cc_final: 0.9204 (pp30) REVERT: B 199 ASP cc_start: 0.8543 (m-30) cc_final: 0.8025 (m-30) REVERT: B 212 ASP cc_start: 0.8891 (t0) cc_final: 0.8458 (t0) REVERT: C 124 MET cc_start: 0.9053 (ptp) cc_final: 0.8776 (ptp) REVERT: C 562 GLU cc_start: 0.9315 (mt-10) cc_final: 0.9079 (mt-10) REVERT: C 741 MET cc_start: 0.9205 (ttm) cc_final: 0.8654 (ttm) REVERT: C 816 ILE cc_start: 0.8893 (mt) cc_final: 0.8534 (tt) REVERT: C 876 GLU cc_start: 0.9423 (tt0) cc_final: 0.9172 (mp0) REVERT: C 1046 VAL cc_start: 0.8958 (p) cc_final: 0.8737 (m) REVERT: C 1199 LEU cc_start: 0.9070 (tt) cc_final: 0.8596 (tp) REVERT: C 1226 THR cc_start: 0.9053 (p) cc_final: 0.8738 (t) REVERT: C 1297 ASP cc_start: 0.7788 (t0) cc_final: 0.6968 (t70) REVERT: C 1319 MET cc_start: 0.7962 (ptp) cc_final: 0.7717 (mtm) REVERT: C 1323 PHE cc_start: 0.8682 (t80) cc_final: 0.8438 (t80) REVERT: D 337 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7527 (mpp-170) REVERT: D 461 PHE cc_start: 0.8295 (m-10) cc_final: 0.7682 (m-80) REVERT: D 641 ILE cc_start: 0.9257 (pt) cc_final: 0.8833 (tp) REVERT: D 686 TRP cc_start: 0.7582 (m100) cc_final: 0.7365 (m100) REVERT: D 701 LEU cc_start: 0.5972 (mt) cc_final: 0.5653 (tt) REVERT: D 786 THR cc_start: 0.8602 (m) cc_final: 0.7782 (p) REVERT: D 901 ARG cc_start: 0.7375 (tpt90) cc_final: 0.6905 (tpm170) REVERT: D 917 VAL cc_start: 0.9105 (m) cc_final: 0.8029 (t) REVERT: D 918 ILE cc_start: 0.8322 (pt) cc_final: 0.7874 (mt) REVERT: D 1040 MET cc_start: 0.5240 (mtm) cc_final: 0.4822 (mtt) REVERT: E 5 THR cc_start: 0.9146 (m) cc_final: 0.8822 (t) REVERT: E 53 GLU cc_start: 0.9611 (mt-10) cc_final: 0.9324 (mt-10) REVERT: E 59 ILE cc_start: 0.8815 (mm) cc_final: 0.8583 (mt) REVERT: M 133 PHE cc_start: 0.1967 (m-10) cc_final: 0.1623 (m-10) REVERT: M 205 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8162 (mp10) outliers start: 10 outliers final: 3 residues processed: 580 average time/residue: 0.4301 time to fit residues: 391.4032 Evaluate side-chains 294 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 291 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 50.0000 chunk 259 optimal weight: 4.9990 chunk 143 optimal weight: 30.0000 chunk 88 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 0.0670 chunk 268 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 310 optimal weight: 4.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 132 HIS A 227 GLN B 23 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 582 ASN C 604 HIS C 686 GLN C 760 ASN C 799 ASN C1038 GLN C1072 ASN C1111 GLN C1256 GLN C1264 GLN D 94 GLN D 104 HIS D 209 ASN D 477 GLN D 702 GLN D 897 HIS D 910 ASN D1218 HIS D1244 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.119080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.088503 restraints weight = 96791.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085553 restraints weight = 81719.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086380 restraints weight = 83083.319| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1237 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28634 Z= 0.202 Angle : 0.728 11.008 39297 Z= 0.382 Chirality : 0.045 0.238 4671 Planarity : 0.005 0.076 4826 Dihedral : 17.725 179.670 4819 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.69 % Favored : 91.76 % Rotamer: Outliers : 0.30 % Allowed : 2.48 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.13), residues: 3458 helix: -0.63 (0.14), residues: 1174 sheet: -0.53 (0.29), residues: 279 loop : -2.17 (0.12), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D1193 HIS 0.006 0.001 HIS D 104 PHE 0.019 0.002 PHE D 437 TYR 0.040 0.002 TYR C 810 ARG 0.009 0.001 ARG C1034 Details of bonding type rmsd hydrogen bonds : bond 0.05158 ( 1054) hydrogen bonds : angle 5.39937 ( 2914) covalent geometry : bond 0.00438 (28634) covalent geometry : angle 0.72837 (39297) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 330 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8474 (pm20) cc_final: 0.8182 (pm20) REVERT: B 15 ASP cc_start: 0.8642 (t0) cc_final: 0.8249 (t0) REVERT: B 77 ASP cc_start: 0.8922 (t0) cc_final: 0.8643 (t70) REVERT: B 147 GLN cc_start: 0.8944 (pt0) cc_final: 0.8707 (pt0) REVERT: B 236 ASP cc_start: 0.5968 (t70) cc_final: 0.5586 (p0) REVERT: C 369 MET cc_start: 0.9003 (tmm) cc_final: 0.8624 (tmm) REVERT: C 805 MET cc_start: 0.9073 (ptm) cc_final: 0.8868 (ptm) REVERT: C 959 ASP cc_start: 0.8471 (m-30) cc_final: 0.6853 (m-30) REVERT: C 968 GLU cc_start: 0.9223 (tt0) cc_final: 0.8948 (tp30) REVERT: C 1088 ASP cc_start: 0.8665 (p0) cc_final: 0.8361 (p0) REVERT: C 1131 MET cc_start: 0.8540 (tpp) cc_final: 0.8279 (tpp) REVERT: C 1170 MET cc_start: 0.7868 (pmm) cc_final: 0.7613 (pmm) REVERT: C 1274 GLU cc_start: 0.8061 (mp0) cc_final: 0.7828 (mp0) REVERT: C 1281 TYR cc_start: 0.8654 (m-10) cc_final: 0.8335 (m-10) REVERT: D 29 MET cc_start: 0.9219 (mtp) cc_final: 0.8951 (mtp) REVERT: D 35 PHE cc_start: 0.6576 (t80) cc_final: 0.6314 (t80) REVERT: D 151 MET cc_start: 0.7907 (pmm) cc_final: 0.7390 (pmm) REVERT: D 239 LEU cc_start: 0.8373 (pt) cc_final: 0.8172 (pt) REVERT: D 339 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7891 (mpt-90) REVERT: D 466 MET cc_start: 0.8994 (tpp) cc_final: 0.8674 (ttp) REVERT: D 725 MET cc_start: 0.8205 (mtm) cc_final: 0.7969 (mtm) REVERT: D 743 MET cc_start: 0.8123 (mtp) cc_final: 0.7650 (mmm) REVERT: D 744 ARG cc_start: 0.8772 (ttt180) cc_final: 0.8367 (mmm-85) REVERT: D 901 ARG cc_start: 0.7943 (tpt90) cc_final: 0.7594 (tpm170) REVERT: D 1040 MET cc_start: 0.0006 (mtm) cc_final: -0.0695 (mtt) REVERT: E 5 THR cc_start: 0.8404 (m) cc_final: 0.8202 (t) REVERT: E 30 MET cc_start: 0.8574 (mmm) cc_final: 0.8211 (mmm) REVERT: E 53 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8165 (mt-10) REVERT: M 126 TRP cc_start: 0.9241 (t60) cc_final: 0.8921 (t60) REVERT: M 205 GLN cc_start: 0.8502 (mm-40) cc_final: 0.7890 (mp10) outliers start: 8 outliers final: 3 residues processed: 338 average time/residue: 0.4363 time to fit residues: 240.8687 Evaluate side-chains 225 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 222 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 88 optimal weight: 20.0000 chunk 164 optimal weight: 1.9990 chunk 262 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 183 optimal weight: 0.1980 chunk 281 optimal weight: 0.6980 chunk 197 optimal weight: 0.2980 chunk 167 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 265 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.120215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089763 restraints weight = 96164.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086832 restraints weight = 78509.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.087614 restraints weight = 73517.441| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28634 Z= 0.119 Angle : 0.624 10.757 39297 Z= 0.324 Chirality : 0.043 0.259 4671 Planarity : 0.004 0.057 4826 Dihedral : 17.354 179.662 4819 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.13 % Favored : 91.24 % Rotamer: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.13), residues: 3458 helix: 0.19 (0.15), residues: 1181 sheet: -0.31 (0.30), residues: 279 loop : -2.01 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1276 HIS 0.013 0.001 HIS C1023 PHE 0.013 0.001 PHE C 405 TYR 0.017 0.001 TYR C1229 ARG 0.006 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 1054) hydrogen bonds : angle 4.92043 ( 2914) covalent geometry : bond 0.00245 (28634) covalent geometry : angle 0.62398 (39297) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 291 time to evaluate : 4.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7750 (mp0) cc_final: 0.7219 (mp0) REVERT: A 103 ASN cc_start: 0.8597 (m-40) cc_final: 0.8353 (m-40) REVERT: B 15 ASP cc_start: 0.8731 (t0) cc_final: 0.8340 (t0) REVERT: B 77 ASP cc_start: 0.8801 (t0) cc_final: 0.8535 (t0) REVERT: B 196 THR cc_start: 0.8270 (p) cc_final: 0.7744 (t) REVERT: B 236 ASP cc_start: 0.5698 (t70) cc_final: 0.5379 (p0) REVERT: C 195 PHE cc_start: 0.8727 (m-80) cc_final: 0.8362 (m-10) REVERT: C 503 LYS cc_start: 0.9253 (tttp) cc_final: 0.9013 (ttpt) REVERT: C 800 MET cc_start: 0.8578 (mtp) cc_final: 0.8167 (mtt) REVERT: C 805 MET cc_start: 0.8824 (ptm) cc_final: 0.8549 (ptm) REVERT: C 960 LEU cc_start: 0.9000 (pp) cc_final: 0.8577 (tp) REVERT: C 1088 ASP cc_start: 0.8856 (p0) cc_final: 0.8538 (p0) REVERT: C 1170 MET cc_start: 0.7834 (pmm) cc_final: 0.7561 (pmm) REVERT: D 29 MET cc_start: 0.9167 (mtp) cc_final: 0.8932 (mtp) REVERT: D 151 MET cc_start: 0.7866 (pmm) cc_final: 0.7289 (pmm) REVERT: D 298 MET cc_start: 0.9282 (mtp) cc_final: 0.9076 (mtp) REVERT: D 466 MET cc_start: 0.8850 (tpp) cc_final: 0.8509 (tpp) REVERT: D 901 ARG cc_start: 0.7884 (tpt90) cc_final: 0.7607 (tpm170) REVERT: D 1040 MET cc_start: -0.0228 (mtm) cc_final: -0.1133 (mmm) REVERT: D 1144 LEU cc_start: 0.9423 (mt) cc_final: 0.9151 (mp) REVERT: E 7 GLN cc_start: 0.8632 (pt0) cc_final: 0.8413 (tt0) REVERT: E 53 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8097 (mt-10) REVERT: M 179 LEU cc_start: 0.8698 (mm) cc_final: 0.8420 (mt) REVERT: M 205 GLN cc_start: 0.8490 (mm-40) cc_final: 0.7808 (mp10) outliers start: 3 outliers final: 2 residues processed: 293 average time/residue: 0.5715 time to fit residues: 279.8767 Evaluate side-chains 221 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 150 optimal weight: 4.9990 chunk 277 optimal weight: 0.0050 chunk 92 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 186 optimal weight: 0.0070 chunk 165 optimal weight: 7.9990 chunk 206 optimal weight: 20.0000 chunk 289 optimal weight: 0.2980 chunk 171 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN C 148 GLN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.119120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082533 restraints weight = 95650.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081238 restraints weight = 60611.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.081056 restraints weight = 55158.375| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28634 Z= 0.126 Angle : 0.609 10.379 39297 Z= 0.317 Chirality : 0.042 0.256 4671 Planarity : 0.004 0.056 4826 Dihedral : 17.157 177.212 4819 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.10 % Favored : 91.30 % Rotamer: Outliers : 0.08 % Allowed : 1.87 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3458 helix: 0.59 (0.15), residues: 1204 sheet: -0.23 (0.31), residues: 274 loop : -1.92 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1020 HIS 0.007 0.001 HIS C1023 PHE 0.011 0.001 PHE D 172 TYR 0.014 0.001 TYR C 73 ARG 0.007 0.000 ARG C 470 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 1054) hydrogen bonds : angle 4.57933 ( 2914) covalent geometry : bond 0.00273 (28634) covalent geometry : angle 0.60942 (39297) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASP cc_start: 0.8932 (t0) cc_final: 0.8574 (t0) REVERT: B 77 ASP cc_start: 0.8961 (t0) cc_final: 0.8672 (t70) REVERT: B 196 THR cc_start: 0.8438 (p) cc_final: 0.7926 (t) REVERT: B 236 ASP cc_start: 0.5880 (t70) cc_final: 0.5491 (p0) REVERT: C 195 PHE cc_start: 0.8962 (m-80) cc_final: 0.8563 (m-10) REVERT: C 503 LYS cc_start: 0.9381 (tttp) cc_final: 0.9098 (tppt) REVERT: C 790 ASP cc_start: 0.8615 (t0) cc_final: 0.8402 (t0) REVERT: C 1023 HIS cc_start: 0.9128 (m-70) cc_final: 0.8876 (m90) REVERT: C 1088 ASP cc_start: 0.8910 (p0) cc_final: 0.8599 (p0) REVERT: D 29 MET cc_start: 0.9312 (mtp) cc_final: 0.9039 (mtp) REVERT: D 151 MET cc_start: 0.7935 (pmm) cc_final: 0.7396 (pmm) REVERT: D 237 MET cc_start: 0.8784 (tpp) cc_final: 0.8532 (tpp) REVERT: D 298 MET cc_start: 0.9408 (mtp) cc_final: 0.9169 (mtp) REVERT: D 466 MET cc_start: 0.8964 (tpp) cc_final: 0.8622 (tpp) REVERT: D 725 MET cc_start: 0.8123 (mtm) cc_final: 0.7813 (mtm) REVERT: D 901 ARG cc_start: 0.7983 (tpt90) cc_final: 0.7619 (tpm170) REVERT: D 1040 MET cc_start: -0.0096 (mtm) cc_final: -0.0941 (mtt) REVERT: E 53 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8211 (mt-10) REVERT: E 65 ASP cc_start: 0.9073 (m-30) cc_final: 0.8855 (m-30) REVERT: M 205 GLN cc_start: 0.8559 (mm-40) cc_final: 0.7948 (mp10) outliers start: 2 outliers final: 1 residues processed: 271 average time/residue: 0.3708 time to fit residues: 167.1265 Evaluate side-chains 209 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 219 optimal weight: 0.0060 chunk 60 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 313 optimal weight: 10.0000 chunk 338 optimal weight: 40.0000 chunk 171 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 202 optimal weight: 0.8980 chunk 316 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 ASN C1264 GLN C1288 GLN ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS D 477 GLN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.118522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.080406 restraints weight = 94394.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079007 restraints weight = 66292.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079402 restraints weight = 56174.212| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1239 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28634 Z= 0.124 Angle : 0.594 10.433 39297 Z= 0.308 Chirality : 0.042 0.229 4671 Planarity : 0.004 0.052 4826 Dihedral : 17.095 176.122 4819 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.04 % Favored : 91.32 % Rotamer: Outliers : 0.08 % Allowed : 1.49 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3458 helix: 0.88 (0.15), residues: 1197 sheet: -0.31 (0.30), residues: 295 loop : -1.89 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1020 HIS 0.005 0.001 HIS C1023 PHE 0.012 0.001 PHE C1323 TYR 0.016 0.001 TYR D 631 ARG 0.004 0.000 ARG C 706 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 1054) hydrogen bonds : angle 4.41425 ( 2914) covalent geometry : bond 0.00269 (28634) covalent geometry : angle 0.59432 (39297) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 263 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8775 (m-40) cc_final: 0.8550 (m-40) REVERT: B 15 ASP cc_start: 0.9014 (t0) cc_final: 0.8586 (t0) REVERT: B 77 ASP cc_start: 0.9057 (t0) cc_final: 0.8743 (t70) REVERT: B 196 THR cc_start: 0.8762 (p) cc_final: 0.8202 (t) REVERT: B 236 ASP cc_start: 0.6041 (t70) cc_final: 0.5575 (p0) REVERT: C 195 PHE cc_start: 0.9099 (m-80) cc_final: 0.8631 (m-10) REVERT: C 503 LYS cc_start: 0.9419 (tttp) cc_final: 0.9131 (tppt) REVERT: C 805 MET cc_start: 0.8498 (ptm) cc_final: 0.8278 (ptm) REVERT: C 1023 HIS cc_start: 0.9136 (m-70) cc_final: 0.8910 (m90) REVERT: C 1122 LYS cc_start: 0.8914 (tttp) cc_final: 0.8697 (tppt) REVERT: D 29 MET cc_start: 0.9331 (mtp) cc_final: 0.9059 (mtp) REVERT: D 35 PHE cc_start: 0.6901 (t80) cc_final: 0.6572 (t80) REVERT: D 102 MET cc_start: 0.8659 (pmm) cc_final: 0.8443 (pmm) REVERT: D 151 MET cc_start: 0.8022 (pmm) cc_final: 0.7544 (pmm) REVERT: D 237 MET cc_start: 0.8856 (tpp) cc_final: 0.8638 (tpp) REVERT: D 298 MET cc_start: 0.9450 (mtp) cc_final: 0.9173 (mtp) REVERT: D 466 MET cc_start: 0.9011 (tpp) cc_final: 0.8740 (tpp) REVERT: D 725 MET cc_start: 0.8036 (mtm) cc_final: 0.7784 (mtm) REVERT: D 901 ARG cc_start: 0.7902 (tpt90) cc_final: 0.7429 (tpm170) REVERT: D 1040 MET cc_start: -0.0021 (mtm) cc_final: -0.0892 (mmm) REVERT: E 6 VAL cc_start: 0.8568 (t) cc_final: 0.8356 (t) REVERT: E 30 MET cc_start: 0.8577 (mmm) cc_final: 0.8347 (mmm) REVERT: E 41 GLU cc_start: 0.8715 (tt0) cc_final: 0.8365 (pp20) REVERT: E 43 ASN cc_start: 0.7787 (m-40) cc_final: 0.7531 (m-40) REVERT: E 53 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8255 (mt-10) REVERT: E 65 ASP cc_start: 0.9070 (m-30) cc_final: 0.8861 (m-30) REVERT: M 205 GLN cc_start: 0.8573 (mm-40) cc_final: 0.7955 (mp10) outliers start: 2 outliers final: 2 residues processed: 265 average time/residue: 0.3901 time to fit residues: 170.9315 Evaluate side-chains 216 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 10 optimal weight: 0.0020 chunk 219 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 328 optimal weight: 8.9990 chunk 249 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 243 optimal weight: 30.0000 overall best weight: 3.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS D 435 GLN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.115802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.075847 restraints weight = 95493.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.075765 restraints weight = 73062.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.075293 restraints weight = 60104.724| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28634 Z= 0.183 Angle : 0.656 9.656 39297 Z= 0.341 Chirality : 0.044 0.266 4671 Planarity : 0.004 0.057 4826 Dihedral : 17.202 175.443 4819 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.62 % Favored : 90.75 % Rotamer: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3458 helix: 1.02 (0.15), residues: 1189 sheet: -0.56 (0.28), residues: 327 loop : -1.92 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D1020 HIS 0.005 0.001 HIS D 907 PHE 0.014 0.001 PHE C1270 TYR 0.022 0.002 TYR C1281 ARG 0.010 0.001 ARG D 431 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 1054) hydrogen bonds : angle 4.47925 ( 2914) covalent geometry : bond 0.00414 (28634) covalent geometry : angle 0.65625 (39297) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7736 (mp0) cc_final: 0.7414 (mt-10) REVERT: B 15 ASP cc_start: 0.9012 (t0) cc_final: 0.8620 (t0) REVERT: B 77 ASP cc_start: 0.9110 (t0) cc_final: 0.8711 (t0) REVERT: B 196 THR cc_start: 0.9044 (p) cc_final: 0.8698 (t) REVERT: B 236 ASP cc_start: 0.6301 (t70) cc_final: 0.5872 (p0) REVERT: C 195 PHE cc_start: 0.9165 (m-80) cc_final: 0.8649 (m-10) REVERT: C 503 LYS cc_start: 0.9437 (tttp) cc_final: 0.9119 (tppt) REVERT: C 959 ASP cc_start: 0.8414 (m-30) cc_final: 0.8018 (m-30) REVERT: C 967 LEU cc_start: 0.9654 (mm) cc_final: 0.9356 (pp) REVERT: C 968 GLU cc_start: 0.9521 (tt0) cc_final: 0.9259 (tp30) REVERT: C 1023 HIS cc_start: 0.9210 (m-70) cc_final: 0.8949 (m90) REVERT: C 1274 GLU cc_start: 0.8256 (mp0) cc_final: 0.8034 (mp0) REVERT: C 1281 TYR cc_start: 0.8997 (m-10) cc_final: 0.8721 (m-10) REVERT: D 29 MET cc_start: 0.9367 (mtp) cc_final: 0.9098 (mtp) REVERT: D 102 MET cc_start: 0.8886 (pmm) cc_final: 0.8634 (pmm) REVERT: D 151 MET cc_start: 0.8206 (pmm) cc_final: 0.7722 (pmm) REVERT: D 298 MET cc_start: 0.9459 (mtp) cc_final: 0.9123 (mtm) REVERT: D 466 MET cc_start: 0.9065 (tpp) cc_final: 0.8663 (tpp) REVERT: D 725 MET cc_start: 0.8214 (mtm) cc_final: 0.7916 (mtm) REVERT: D 1040 MET cc_start: 0.0183 (mtm) cc_final: -0.0519 (mtt) REVERT: E 15 ASN cc_start: 0.8095 (t0) cc_final: 0.7260 (t0) REVERT: E 30 MET cc_start: 0.8627 (mmm) cc_final: 0.8363 (mmm) REVERT: E 41 GLU cc_start: 0.8729 (tt0) cc_final: 0.8361 (pp20) REVERT: E 43 ASN cc_start: 0.7967 (m-40) cc_final: 0.7703 (m-40) REVERT: E 53 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8367 (mt-10) REVERT: E 65 ASP cc_start: 0.9129 (m-30) cc_final: 0.8895 (m-30) REVERT: M 205 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8034 (mp10) outliers start: 1 outliers final: 1 residues processed: 260 average time/residue: 0.3756 time to fit residues: 159.4785 Evaluate side-chains 197 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 287 optimal weight: 50.0000 chunk 311 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 0.0030 chunk 274 optimal weight: 0.8980 chunk 290 optimal weight: 7.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 504 GLN D 910 ASN E 15 ASN ** M 229 ASN ** 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 = 0.4030 r_free = 0.4030 target = 0.117458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079030 restraints weight = 95801.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.077772 restraints weight = 69777.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.077722 restraints weight = 60664.878| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28634 Z= 0.118 Angle : 0.603 10.930 39297 Z= 0.312 Chirality : 0.042 0.226 4671 Planarity : 0.004 0.051 4826 Dihedral : 17.108 176.561 4819 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.69 % Favored : 91.67 % Rotamer: Outliers : 0.04 % Allowed : 1.26 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3458 helix: 1.25 (0.16), residues: 1187 sheet: -0.34 (0.29), residues: 315 loop : -1.88 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP M 126 HIS 0.006 0.001 HIS D 907 PHE 0.031 0.001 PHE D 17 TYR 0.017 0.001 TYR D 360 ARG 0.007 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 1054) hydrogen bonds : angle 4.29619 ( 2914) covalent geometry : bond 0.00253 (28634) covalent geometry : angle 0.60298 (39297) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ASP cc_start: 0.9001 (t0) cc_final: 0.8535 (t0) REVERT: B 77 ASP cc_start: 0.9043 (t0) cc_final: 0.8683 (t0) REVERT: B 196 THR cc_start: 0.9053 (p) cc_final: 0.8706 (t) REVERT: B 236 ASP cc_start: 0.6145 (t70) cc_final: 0.5720 (p0) REVERT: C 195 PHE cc_start: 0.9069 (m-80) cc_final: 0.8549 (m-10) REVERT: C 503 LYS cc_start: 0.9443 (tttp) cc_final: 0.9114 (tppt) REVERT: C 959 ASP cc_start: 0.8219 (m-30) cc_final: 0.7829 (m-30) REVERT: C 967 LEU cc_start: 0.9589 (mm) cc_final: 0.9378 (mt) REVERT: C 1023 HIS cc_start: 0.9131 (m-70) cc_final: 0.8895 (m90) REVERT: C 1170 MET cc_start: 0.7960 (pmm) cc_final: 0.7681 (pmm) REVERT: D 17 PHE cc_start: 0.6052 (m-80) cc_final: 0.5751 (m-80) REVERT: D 29 MET cc_start: 0.9357 (mtp) cc_final: 0.9106 (mtp) REVERT: D 151 MET cc_start: 0.8202 (pmm) cc_final: 0.7765 (pmm) REVERT: D 237 MET cc_start: 0.8990 (tpp) cc_final: 0.8637 (tpp) REVERT: D 298 MET cc_start: 0.9452 (mtp) cc_final: 0.9140 (mtm) REVERT: D 641 ILE cc_start: 0.9413 (pt) cc_final: 0.9063 (tp) REVERT: D 725 MET cc_start: 0.8161 (mtm) cc_final: 0.7844 (mtm) REVERT: D 1040 MET cc_start: -0.0050 (mtm) cc_final: -0.0907 (mmm) REVERT: E 15 ASN cc_start: 0.8104 (t0) cc_final: 0.7350 (t0) REVERT: E 30 MET cc_start: 0.8615 (mmm) cc_final: 0.8356 (mmm) REVERT: E 41 GLU cc_start: 0.8732 (tt0) cc_final: 0.8334 (pp20) REVERT: E 43 ASN cc_start: 0.8046 (m-40) cc_final: 0.7620 (m-40) REVERT: E 53 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8330 (mt-10) REVERT: E 65 ASP cc_start: 0.9067 (m-30) cc_final: 0.8855 (m-30) REVERT: M 205 GLN cc_start: 0.8645 (mm-40) cc_final: 0.7964 (mp10) outliers start: 1 outliers final: 1 residues processed: 259 average time/residue: 0.3672 time to fit residues: 157.5975 Evaluate side-chains 198 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 133 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 245 optimal weight: 50.0000 chunk 13 optimal weight: 0.8980 chunk 330 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 262 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 339 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 ASN C1244 HIS D 335 GLN D1218 HIS D1227 HIS ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.113813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.074110 restraints weight = 97048.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.073311 restraints weight = 70905.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.072709 restraints weight = 69961.325| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 28634 Z= 0.252 Angle : 0.728 10.612 39297 Z= 0.376 Chirality : 0.046 0.301 4671 Planarity : 0.005 0.057 4826 Dihedral : 17.357 177.976 4819 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.31 % Favored : 90.05 % Rotamer: Outliers : 0.04 % Allowed : 0.72 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3458 helix: 1.05 (0.15), residues: 1203 sheet: -0.45 (0.29), residues: 324 loop : -1.98 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D1020 HIS 0.010 0.001 HIS D 907 PHE 0.020 0.002 PHE C 506 TYR 0.038 0.002 TYR C1281 ARG 0.014 0.001 ARG C 470 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 1054) hydrogen bonds : angle 4.59583 ( 2914) covalent geometry : bond 0.00572 (28634) covalent geometry : angle 0.72842 (39297) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7698 (mp0) cc_final: 0.7200 (mt-10) REVERT: A 226 GLU cc_start: 0.8673 (pp20) cc_final: 0.8382 (tm-30) REVERT: B 15 ASP cc_start: 0.8979 (t0) cc_final: 0.8521 (t0) REVERT: B 77 ASP cc_start: 0.9118 (t0) cc_final: 0.8825 (t70) REVERT: B 196 THR cc_start: 0.9081 (p) cc_final: 0.8822 (t) REVERT: B 236 ASP cc_start: 0.6375 (t70) cc_final: 0.6012 (p0) REVERT: C 195 PHE cc_start: 0.9034 (m-80) cc_final: 0.8426 (m-10) REVERT: C 628 HIS cc_start: 0.9030 (m90) cc_final: 0.8804 (m-70) REVERT: C 959 ASP cc_start: 0.8269 (m-30) cc_final: 0.7866 (m-30) REVERT: C 967 LEU cc_start: 0.9637 (mm) cc_final: 0.9407 (mt) REVERT: C 968 GLU cc_start: 0.9474 (tt0) cc_final: 0.9200 (tp30) REVERT: C 1023 HIS cc_start: 0.9199 (m-70) cc_final: 0.8942 (m90) REVERT: C 1170 MET cc_start: 0.8027 (pmm) cc_final: 0.7823 (pmm) REVERT: C 1274 GLU cc_start: 0.8291 (mp0) cc_final: 0.8039 (mp0) REVERT: C 1281 TYR cc_start: 0.9048 (m-10) cc_final: 0.8723 (m-10) REVERT: C 1319 MET cc_start: 0.7226 (mtm) cc_final: 0.6881 (mtm) REVERT: D 29 MET cc_start: 0.9377 (mtp) cc_final: 0.9108 (mtp) REVERT: D 102 MET cc_start: 0.8771 (pmm) cc_final: 0.8566 (pmm) REVERT: D 298 MET cc_start: 0.9461 (mtp) cc_final: 0.9113 (mtm) REVERT: D 641 ILE cc_start: 0.9371 (pt) cc_final: 0.9060 (tp) REVERT: D 725 MET cc_start: 0.8356 (mtm) cc_final: 0.8102 (mtm) REVERT: D 1040 MET cc_start: -0.0022 (mtm) cc_final: -0.0682 (mtt) REVERT: E 15 ASN cc_start: 0.7685 (t0) cc_final: 0.6992 (t0) REVERT: E 30 MET cc_start: 0.8691 (mmm) cc_final: 0.8403 (mmm) REVERT: E 41 GLU cc_start: 0.8641 (tt0) cc_final: 0.8300 (pp20) REVERT: E 42 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6948 (mm-30) REVERT: E 43 ASN cc_start: 0.8016 (m-40) cc_final: 0.7624 (m-40) REVERT: E 53 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8544 (tt0) REVERT: E 58 LEU cc_start: 0.9216 (tt) cc_final: 0.8941 (tt) REVERT: E 59 ILE cc_start: 0.7532 (tp) cc_final: 0.7174 (tp) REVERT: E 65 ASP cc_start: 0.9171 (m-30) cc_final: 0.8939 (m-30) REVERT: M 205 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8079 (mp10) outliers start: 1 outliers final: 1 residues processed: 239 average time/residue: 0.3769 time to fit residues: 151.1107 Evaluate side-chains 188 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 5 optimal weight: 5.9990 chunk 247 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 203 optimal weight: 30.0000 chunk 306 optimal weight: 9.9990 chunk 229 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 279 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 213 optimal weight: 0.8980 chunk 301 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** M 229 ASN ** 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 = 0.3990 r_free = 0.3990 target = 0.115112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.074452 restraints weight = 95705.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.074233 restraints weight = 71991.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.073940 restraints weight = 60670.577| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28634 Z= 0.157 Angle : 0.647 11.571 39297 Z= 0.335 Chirality : 0.043 0.296 4671 Planarity : 0.004 0.073 4826 Dihedral : 17.285 178.679 4819 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.39 % Favored : 90.98 % Rotamer: Outliers : 0.04 % Allowed : 0.50 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3458 helix: 1.21 (0.15), residues: 1204 sheet: -0.41 (0.30), residues: 299 loop : -1.93 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1020 HIS 0.012 0.001 HIS D 907 PHE 0.018 0.001 PHE D 17 TYR 0.019 0.001 TYR D 360 ARG 0.008 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 1054) hydrogen bonds : angle 4.40207 ( 2914) covalent geometry : bond 0.00351 (28634) covalent geometry : angle 0.64659 (39297) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7608 (mp0) cc_final: 0.7186 (mt-10) REVERT: B 15 ASP cc_start: 0.8981 (t0) cc_final: 0.8544 (t0) REVERT: B 77 ASP cc_start: 0.9148 (t0) cc_final: 0.8773 (t0) REVERT: B 196 THR cc_start: 0.9005 (p) cc_final: 0.8780 (t) REVERT: B 236 ASP cc_start: 0.6292 (t70) cc_final: 0.5881 (p0) REVERT: C 195 PHE cc_start: 0.9012 (m-80) cc_final: 0.8403 (m-10) REVERT: C 959 ASP cc_start: 0.8231 (m-30) cc_final: 0.7799 (m-30) REVERT: C 967 LEU cc_start: 0.9627 (mm) cc_final: 0.9402 (mt) REVERT: C 1023 HIS cc_start: 0.9205 (m-70) cc_final: 0.8924 (m90) REVERT: D 29 MET cc_start: 0.9356 (mtp) cc_final: 0.9077 (mtp) REVERT: D 102 MET cc_start: 0.8820 (pmm) cc_final: 0.8614 (pmm) REVERT: D 237 MET cc_start: 0.8993 (tpp) cc_final: 0.8605 (tpp) REVERT: D 298 MET cc_start: 0.9449 (mtp) cc_final: 0.9082 (mtm) REVERT: D 479 GLU cc_start: 0.8728 (tt0) cc_final: 0.8502 (tt0) REVERT: D 641 ILE cc_start: 0.9370 (pt) cc_final: 0.9080 (tp) REVERT: D 725 MET cc_start: 0.8332 (mtm) cc_final: 0.8074 (mtm) REVERT: D 1040 MET cc_start: 0.0026 (mtm) cc_final: -0.0766 (mtt) REVERT: E 41 GLU cc_start: 0.8685 (tt0) cc_final: 0.8381 (tm-30) REVERT: E 42 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6858 (mm-30) REVERT: E 43 ASN cc_start: 0.8131 (m-40) cc_final: 0.7658 (m-40) REVERT: E 53 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8503 (tt0) REVERT: E 58 LEU cc_start: 0.9254 (tt) cc_final: 0.8988 (tt) REVERT: E 59 ILE cc_start: 0.7545 (tp) cc_final: 0.7090 (tp) REVERT: E 65 ASP cc_start: 0.9171 (m-30) cc_final: 0.8953 (m-30) REVERT: M 205 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8053 (mp10) outliers start: 1 outliers final: 1 residues processed: 241 average time/residue: 0.3828 time to fit residues: 152.4086 Evaluate side-chains 190 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 184 optimal weight: 40.0000 chunk 164 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 12 optimal weight: 0.0370 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 319 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 331 optimal weight: 50.0000 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.115922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.076581 restraints weight = 95474.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.075762 restraints weight = 69656.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075441 restraints weight = 63926.964| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28634 Z= 0.129 Angle : 0.627 10.236 39297 Z= 0.324 Chirality : 0.043 0.275 4671 Planarity : 0.004 0.080 4826 Dihedral : 17.190 178.571 4819 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.65 % Favored : 90.72 % Rotamer: Outliers : 0.04 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3458 helix: 1.31 (0.16), residues: 1208 sheet: -0.35 (0.29), residues: 322 loop : -1.89 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 126 HIS 0.012 0.001 HIS D 907 PHE 0.014 0.001 PHE D 17 TYR 0.017 0.001 TYR C1229 ARG 0.009 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 1054) hydrogen bonds : angle 4.29532 ( 2914) covalent geometry : bond 0.00283 (28634) covalent geometry : angle 0.62669 (39297) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6916 Ramachandran restraints generated. 3458 Oldfield, 0 Emsley, 3458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN D1049 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7589 (mp0) cc_final: 0.6987 (mp0) REVERT: B 15 ASP cc_start: 0.8975 (t0) cc_final: 0.8557 (t0) REVERT: B 77 ASP cc_start: 0.9109 (t0) cc_final: 0.8737 (t0) REVERT: B 196 THR cc_start: 0.8991 (p) cc_final: 0.8772 (t) REVERT: B 236 ASP cc_start: 0.6367 (t70) cc_final: 0.5957 (p0) REVERT: C 195 PHE cc_start: 0.8951 (m-80) cc_final: 0.8319 (m-10) REVERT: C 459 MET cc_start: 0.9096 (mpp) cc_final: 0.8856 (mpp) REVERT: C 723 VAL cc_start: 0.9293 (t) cc_final: 0.9026 (p) REVERT: C 959 ASP cc_start: 0.8180 (m-30) cc_final: 0.7735 (m-30) REVERT: C 967 LEU cc_start: 0.9597 (mm) cc_final: 0.9383 (mt) REVERT: C 1023 HIS cc_start: 0.9178 (m-70) cc_final: 0.8915 (m90) REVERT: D 29 MET cc_start: 0.9371 (mtp) cc_final: 0.9093 (mtp) REVERT: D 237 MET cc_start: 0.9006 (tpp) cc_final: 0.8771 (tpp) REVERT: D 298 MET cc_start: 0.9473 (mtp) cc_final: 0.9107 (mtm) REVERT: D 641 ILE cc_start: 0.9377 (pt) cc_final: 0.9032 (tp) REVERT: D 725 MET cc_start: 0.8327 (mtm) cc_final: 0.8075 (mtm) REVERT: D 1040 MET cc_start: -0.0014 (mtm) cc_final: -0.0816 (mtt) REVERT: E 41 GLU cc_start: 0.8616 (tt0) cc_final: 0.8339 (tm-30) REVERT: E 42 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7152 (mp0) REVERT: E 43 ASN cc_start: 0.8141 (m-40) cc_final: 0.7668 (m-40) REVERT: E 53 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8341 (mt-10) REVERT: E 65 ASP cc_start: 0.9135 (m-30) cc_final: 0.8932 (m-30) REVERT: M 205 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8005 (mp10) outliers start: 1 outliers final: 1 residues processed: 239 average time/residue: 0.3704 time to fit residues: 148.0917 Evaluate side-chains 187 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 113 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 140 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 145 optimal weight: 50.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** M 229 ASN ** 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 = 0.3964 r_free = 0.3964 target = 0.113562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.073573 restraints weight = 96978.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.072789 restraints weight = 70668.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.072419 restraints weight = 67319.970| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1240 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28634 Z= 0.236 Angle : 0.707 10.181 39297 Z= 0.366 Chirality : 0.045 0.273 4671 Planarity : 0.005 0.071 4826 Dihedral : 17.352 179.316 4819 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.66 % Favored : 89.73 % Rotamer: Outliers : 0.04 % Allowed : 0.34 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3458 helix: 1.11 (0.15), residues: 1223 sheet: -0.59 (0.30), residues: 311 loop : -1.95 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D1020 HIS 0.012 0.001 HIS D 907 PHE 0.024 0.002 PHE D 17 TYR 0.022 0.002 TYR C1229 ARG 0.010 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 1054) hydrogen bonds : angle 4.48470 ( 2914) covalent geometry : bond 0.00537 (28634) covalent geometry : angle 0.70651 (39297) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9754.44 seconds wall clock time: 173 minutes 52.65 seconds (10432.65 seconds total)