Starting phenix.real_space_refine on Wed May 28 20:12:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j77_61196/05_2025/9j77_61196.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j77_61196/05_2025/9j77_61196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j77_61196/05_2025/9j77_61196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j77_61196/05_2025/9j77_61196.map" model { file = "/net/cci-nas-00/data/ceres_data/9j77_61196/05_2025/9j77_61196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j77_61196/05_2025/9j77_61196.cif" } resolution = 3.56 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= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6261 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 182 5.16 5 C 16576 2.51 5 N 4544 2.21 5 O 4901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26209 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "H" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 598 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 5947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5947 Classifications: {'peptide': 725} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 705} Chain breaks: 1 Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "D" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "E" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 703 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "A" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5953 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 706} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1762 SG CYS I 53 46.427 71.722 86.097 1.00 90.27 S ATOM 1785 SG CYS I 56 49.875 72.606 87.957 1.00 99.16 S ATOM 1813 SG CYS I 68 48.301 69.099 88.163 1.00 86.92 S ATOM 1676 SG CYS I 42 42.345 67.690 81.363 1.00 80.52 S ATOM 1695 SG CYS I 45 42.937 71.493 81.054 1.00 89.98 S ATOM 1931 SG CYS I 83 41.945 70.007 84.421 1.00 91.34 S ATOM 1863 SG CYS I 75 36.823 55.808 81.419 1.00117.13 S ATOM 2027 SG CYS I 94 35.211 57.851 83.556 1.00118.96 S ATOM 14789 SG CYS E 53 17.339 119.410 57.731 1.00 85.23 S ATOM 14812 SG CYS E 56 13.849 119.625 59.303 1.00 99.64 S ATOM 14896 SG CYS E 68 16.916 119.269 61.548 1.00 89.56 S ATOM 14703 SG CYS E 42 25.247 118.863 57.695 1.00 60.90 S ATOM 14722 SG CYS E 45 22.322 121.187 56.734 1.00 66.02 S ATOM 15014 SG CYS E 83 21.765 117.678 56.358 1.00 64.24 S ATOM 14946 SG CYS E 75 32.780 108.087 60.467 1.00 46.34 S ATOM 15110 SG CYS E 94 31.255 109.815 57.094 1.00 34.12 S Time building chain proxies: 14.07, per 1000 atoms: 0.54 Number of scatterers: 26209 At special positions: 0 Unit cell: (138.58, 177.12, 205, 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) Zn 6 29.99 S 182 16.00 O 4901 8.00 N 4544 7.00 C 16576 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: 5.63 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 200 " pdb="ZN ZN E 200 " - pdb=" NE2 HIS E 82 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 56 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 53 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 68 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 80 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 45 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 83 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 42 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 94 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 75 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 77 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" ND1 HIS I 82 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 68 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 53 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 56 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 80 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 83 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 45 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 94 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 77 " Number of angles added : 12 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 14 sheets defined 62.0% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 39 through 47 removed outlier: 3.503A pdb=" N LYS G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 83 Processing helix chain 'G' and resid 102 through 111 Processing helix chain 'H' and resid 23 through 36 removed outlier: 4.174A pdb=" N LEU H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE H 34 " --> pdb=" O ILE H 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 removed outlier: 4.226A pdb=" N ALA I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 91 Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.821A pdb=" N THR B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 54 through 79 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 138 through 152 removed outlier: 3.627A pdb=" N VAL B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 172 Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 207 through 230 Processing helix chain 'B' and resid 231 through 254 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 271 removed outlier: 3.578A pdb=" N VAL B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 263 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 289 removed outlier: 3.603A pdb=" N LEU B 278 " --> pdb=" O HIS B 274 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 304 removed outlier: 3.580A pdb=" N LEU B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 328 removed outlier: 4.045A pdb=" N MET B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 358 Processing helix chain 'B' and resid 361 through 377 Processing helix chain 'B' and resid 386 through 400 Processing helix chain 'B' and resid 407 through 424 removed outlier: 4.119A pdb=" N THR B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 445 removed outlier: 3.757A pdb=" N PHE B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 466 Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'B' and resid 482 through 496 Processing helix chain 'B' and resid 530 through 548 removed outlier: 3.518A pdb=" N GLU B 534 " --> pdb=" O PRO B 530 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER B 536 " --> pdb=" O GLU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 559 No H-bonds generated for 'chain 'B' and resid 557 through 559' Processing helix chain 'B' and resid 579 through 591 removed outlier: 3.511A pdb=" N SER B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 603 Processing helix chain 'B' and resid 606 through 620 Processing helix chain 'B' and resid 661 through 692 Processing helix chain 'B' and resid 695 through 708 Processing helix chain 'B' and resid 714 through 728 Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 83 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'D' and resid 24 through 36 Processing helix chain 'J' and resid 2 through 15 Processing helix chain 'J' and resid 17 through 24 Processing helix chain 'J' and resid 29 through 37 Processing helix chain 'J' and resid 48 through 56 Processing helix chain 'J' and resid 58 through 69 removed outlier: 4.146A pdb=" N VAL J 62 " --> pdb=" O HIS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 98 removed outlier: 3.643A pdb=" N CYS J 94 " --> pdb=" O THR J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 110 removed outlier: 3.700A pdb=" N VAL J 104 " --> pdb=" O HIS J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 132 removed outlier: 3.911A pdb=" N ALA J 127 " --> pdb=" O THR J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 143 Processing helix chain 'J' and resid 156 through 163 Processing helix chain 'J' and resid 166 through 175 Processing helix chain 'J' and resid 191 through 196 removed outlier: 3.733A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 209 Processing helix chain 'J' and resid 221 through 229 Processing helix chain 'J' and resid 231 through 240 Processing helix chain 'J' and resid 244 through 262 removed outlier: 4.094A pdb=" N SER J 248 " --> pdb=" O CYS J 244 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA J 261 " --> pdb=" O GLY J 257 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN J 262 " --> pdb=" O ALA J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 284 Processing helix chain 'J' and resid 299 through 303 Processing helix chain 'J' and resid 310 through 317 removed outlier: 3.549A pdb=" N LEU J 314 " --> pdb=" O ASN J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 337 Processing helix chain 'J' and resid 344 through 357 Processing helix chain 'J' and resid 359 through 377 Processing helix chain 'J' and resid 381 through 398 Processing helix chain 'J' and resid 403 through 428 Processing helix chain 'J' and resid 432 through 456 Processing helix chain 'J' and resid 460 through 476 Processing helix chain 'J' and resid 486 through 493 removed outlier: 3.533A pdb=" N ALA J 491 " --> pdb=" O LEU J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 501 through 506 Processing helix chain 'J' and resid 511 through 521 Processing helix chain 'J' and resid 534 through 541 removed outlier: 3.678A pdb=" N ILE J 538 " --> pdb=" O SER J 534 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE J 539 " --> pdb=" O ALA J 535 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN J 541 " --> pdb=" O HIS J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 563 removed outlier: 3.808A pdb=" N SER J 558 " --> pdb=" O SER J 554 " (cutoff:3.500A) Processing helix chain 'J' and resid 577 through 581 removed outlier: 4.243A pdb=" N THR J 581 " --> pdb=" O ASP J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 593 Processing helix chain 'J' and resid 596 through 609 Processing helix chain 'J' and resid 617 through 627 removed outlier: 4.110A pdb=" N GLU J 622 " --> pdb=" O ARG J 618 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE J 623 " --> pdb=" O THR J 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 removed outlier: 4.056A pdb=" N ALA E 58 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.532A pdb=" N VAL F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 23 removed outlier: 3.677A pdb=" N LEU F 20 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 37 removed outlier: 3.945A pdb=" N ILE F 32 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 56 removed outlier: 3.612A pdb=" N ILE F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.736A pdb=" N VAL F 62 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 65 " --> pdb=" O VAL F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 98 removed outlier: 3.958A pdb=" N CYS F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY F 97 " --> pdb=" O TRP F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 110 removed outlier: 3.729A pdb=" N VAL F 104 " --> pdb=" O HIS F 100 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 105 " --> pdb=" O PHE F 101 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU F 107 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 132 removed outlier: 4.056A pdb=" N ALA F 127 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.533A pdb=" N GLU F 142 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 164 removed outlier: 3.569A pdb=" N ILE F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.834A pdb=" N VAL F 170 " --> pdb=" O HIS F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 199 through 210 removed outlier: 3.593A pdb=" N VAL F 203 " --> pdb=" O HIS F 199 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS F 204 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 229 Processing helix chain 'F' and resid 231 through 239 removed outlier: 3.663A pdb=" N GLU F 236 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 237 " --> pdb=" O ASP F 233 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 239 " --> pdb=" O VAL F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 262 removed outlier: 3.716A pdb=" N ILE F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU F 251 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 252 " --> pdb=" O SER F 248 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 284 Processing helix chain 'F' and resid 310 through 317 removed outlier: 3.823A pdb=" N LEU F 314 " --> pdb=" O ASN F 310 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 317 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 337 removed outlier: 3.726A pdb=" N ILE F 330 " --> pdb=" O MET F 326 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 331 " --> pdb=" O GLU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'F' and resid 360 through 377 Processing helix chain 'F' and resid 381 through 398 Processing helix chain 'F' and resid 403 through 428 Processing helix chain 'F' and resid 432 through 456 Processing helix chain 'F' and resid 460 through 478 Processing helix chain 'F' and resid 486 through 493 Processing helix chain 'F' and resid 502 through 507 Processing helix chain 'F' and resid 511 through 522 Processing helix chain 'F' and resid 535 through 540 removed outlier: 3.524A pdb=" N ILE F 539 " --> pdb=" O ALA F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 563 Processing helix chain 'F' and resid 584 through 591 Processing helix chain 'F' and resid 596 through 609 Processing helix chain 'F' and resid 617 through 625 Processing helix chain 'A' and resid 9 through 26 Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.657A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.757A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.532A pdb=" N ILE A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.784A pdb=" N ASP A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.963A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.557A pdb=" N PHE A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 227 removed outlier: 3.697A pdb=" N GLN A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 254 removed outlier: 3.684A pdb=" N MET A 236 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 271 removed outlier: 3.547A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.507A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 327 removed outlier: 4.130A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 324 " --> pdb=" O HIS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.775A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.912A pdb=" N ALA A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 407 through 417 removed outlier: 3.894A pdb=" N SER A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 423 removed outlier: 4.021A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.713A pdb=" N GLU A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 496 removed outlier: 3.546A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 579 through 591 removed outlier: 3.745A pdb=" N VAL A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 603 removed outlier: 3.626A pdb=" N SER A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 620 removed outlier: 4.081A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 690 removed outlier: 4.161A pdb=" N GLN A 667 " --> pdb=" O GLN A 663 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 706 Processing helix chain 'A' and resid 714 through 728 Processing helix chain 'K' and resid 2 through 9 removed outlier: 4.110A pdb=" N UNK K 9 " --> pdb=" O UNK K 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 137 Processing sheet with id=AA1, first strand: chain 'G' and resid 28 through 32 removed outlier: 3.756A pdb=" N VAL G 60 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 18 removed outlier: 3.519A pdb=" N GLY H 76 " --> pdb=" O TYR H 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 506 through 507 removed outlier: 4.167A pdb=" N LYS I 26 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 513 removed outlier: 5.651A pdb=" N ALA I 31 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 554 " --> pdb=" O LEU I 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 41 through 42 removed outlier: 3.507A pdb=" N ASN I 47 " --> pdb=" O CYS I 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'B' and resid 510 through 513 removed outlier: 3.708A pdb=" N ALA E 31 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 574 through 578 removed outlier: 6.402A pdb=" N THR B 561 " --> pdb=" O TRP E 27 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP E 27 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU E 23 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 61 removed outlier: 5.008A pdb=" N LYS C 32 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N ASP D 17 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA D 73 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 78 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG D 43 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 40 through 42 Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 72 Processing sheet with id=AB3, first strand: chain 'F' and resid 40 through 42 Processing sheet with id=AB4, first strand: chain 'A' and resid 623 through 625 Processing sheet with id=AB5, first strand: chain 'A' and resid 693 through 694 1382 hydrogen bonds defined for protein. 4086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.82 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8550 1.34 - 1.46: 3738 1.46 - 1.58: 14135 1.58 - 1.70: 0 1.70 - 1.81: 284 Bond restraints: 26707 Sorted by residual: bond pdb=" C LEU A 308 " pdb=" N PRO A 309 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.33e+00 bond pdb=" CA ASN C 85 " pdb=" CB ASN C 85 " ideal model delta sigma weight residual 1.525 1.545 -0.020 1.77e-02 3.19e+03 1.26e+00 bond pdb=" C ALA B 387 " pdb=" N PRO B 388 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.21e+00 bond pdb=" C LEU B 308 " pdb=" N PRO B 309 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.19e+00 bond pdb=" CB PHE B 39 " pdb=" CG PHE B 39 " ideal model delta sigma weight residual 1.502 1.477 0.025 2.30e-02 1.89e+03 1.17e+00 ... (remaining 26702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 35596 1.98 - 3.97: 408 3.97 - 5.95: 73 5.95 - 7.94: 16 7.94 - 9.92: 3 Bond angle restraints: 36096 Sorted by residual: angle pdb=" N VAL B 620 " pdb=" CA VAL B 620 " pdb=" C VAL B 620 " ideal model delta sigma weight residual 112.29 107.29 5.00 9.40e-01 1.13e+00 2.83e+01 angle pdb=" N GLN J 420 " pdb=" CA GLN J 420 " pdb=" CB GLN J 420 " ideal model delta sigma weight residual 110.28 115.92 -5.64 1.55e+00 4.16e-01 1.32e+01 angle pdb=" C TYR J 84 " pdb=" N VAL J 85 " pdb=" CA VAL J 85 " ideal model delta sigma weight residual 121.97 128.49 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" C TYR F 84 " pdb=" N VAL F 85 " pdb=" CA VAL F 85 " ideal model delta sigma weight residual 121.97 128.49 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" CA TRP B 35 " pdb=" CB TRP B 35 " pdb=" CG TRP B 35 " ideal model delta sigma weight residual 113.60 120.38 -6.78 1.90e+00 2.77e-01 1.27e+01 ... (remaining 36091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 14382 17.80 - 35.60: 1527 35.60 - 53.41: 257 53.41 - 71.21: 58 71.21 - 89.01: 29 Dihedral angle restraints: 16253 sinusoidal: 6588 harmonic: 9665 Sorted by residual: dihedral pdb=" CA VAL A 47 " pdb=" C VAL A 47 " pdb=" N ALA A 48 " pdb=" CA ALA A 48 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ALA B 522 " pdb=" C ALA B 522 " pdb=" N PRO B 523 " pdb=" CA PRO B 523 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA PHE B 188 " pdb=" C PHE B 188 " pdb=" N VAL B 189 " pdb=" CA VAL B 189 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 16250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3078 0.044 - 0.089: 790 0.089 - 0.133: 179 0.133 - 0.177: 14 0.177 - 0.222: 3 Chirality restraints: 4064 Sorted by residual: chirality pdb=" CB ILE A 653 " pdb=" CA ILE A 653 " pdb=" CG1 ILE A 653 " pdb=" CG2 ILE A 653 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL A 620 " pdb=" CA VAL A 620 " pdb=" CG1 VAL A 620 " pdb=" CG2 VAL A 620 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB VAL B 620 " pdb=" CA VAL B 620 " pdb=" CG1 VAL B 620 " pdb=" CG2 VAL B 620 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 4061 not shown) Planarity restraints: 4635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 522 " 0.045 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO B 523 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 523 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 523 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 183 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C GLY B 183 " -0.038 2.00e-02 2.50e+03 pdb=" O GLY B 183 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 184 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR J 48 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO J 49 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO J 49 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 49 " -0.030 5.00e-02 4.00e+02 ... (remaining 4632 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 256 2.62 - 3.19: 22806 3.19 - 3.76: 42671 3.76 - 4.33: 55873 4.33 - 4.90: 91631 Nonbonded interactions: 213237 Sorted by model distance: nonbonded pdb=" OD1 ASP E 97 " pdb="ZN ZN E 202 " model vdw 2.055 2.230 nonbonded pdb=" O CYS J 244 " pdb=" OG SER J 248 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR J 275 " pdb=" O ILE F 546 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR C 79 " pdb=" O PRO C 91 " model vdw 2.238 3.040 nonbonded pdb=" NE1 TRP E 87 " pdb=" O VAL E 93 " model vdw 2.280 3.120 ... (remaining 213232 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 1 through 115 or resid 135 through 744)) selection = (chain 'B' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 744)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 24 through 59 or resid 68 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 104 or r \ esid 200 through 202)) selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.070 Extract box with map and model: 1.170 Check model and map are aligned: 0.290 Set scattering table: 0.300 Process input model: 60.820 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26729 Z= 0.125 Angle : 0.568 10.635 36108 Z= 0.302 Chirality : 0.041 0.222 4064 Planarity : 0.004 0.067 4635 Dihedral : 15.139 89.009 9965 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3218 helix: -0.29 (0.11), residues: 1898 sheet: -1.33 (0.56), residues: 79 loop : -1.66 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 33 HIS 0.006 0.001 HIS B 73 PHE 0.021 0.001 PHE B 507 TYR 0.017 0.001 TYR F 472 ARG 0.006 0.000 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.18949 ( 1382) hydrogen bonds : angle 6.47056 ( 4086) metal coordination : bond 0.00742 ( 22) metal coordination : angle 3.79513 ( 12) covalent geometry : bond 0.00255 (26707) covalent geometry : angle 0.56377 (36096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 LYS cc_start: 0.8591 (tttp) cc_final: 0.7866 (tmtt) REVERT: G 61 ASN cc_start: 0.7887 (t0) cc_final: 0.7635 (t0) REVERT: I 84 ILE cc_start: 0.7873 (mm) cc_final: 0.7649 (tp) REVERT: B 7 VAL cc_start: 0.8687 (t) cc_final: 0.8376 (m) REVERT: B 362 GLN cc_start: 0.8511 (tp40) cc_final: 0.7863 (tm-30) REVERT: B 377 ASN cc_start: 0.5930 (t0) cc_final: 0.5496 (t0) REVERT: B 379 ARG cc_start: 0.7678 (tpp80) cc_final: 0.7460 (ttt90) REVERT: B 389 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 652 LYS cc_start: 0.8939 (mttm) cc_final: 0.8719 (ttpt) REVERT: B 678 MET cc_start: 0.8010 (tpt) cc_final: 0.7781 (tpt) REVERT: B 741 TYR cc_start: 0.5042 (m-80) cc_final: 0.4297 (m-80) REVERT: D 2 ASP cc_start: 0.6016 (p0) cc_final: 0.5757 (m-30) REVERT: D 23 THR cc_start: 0.8327 (t) cc_final: 0.8111 (p) REVERT: J 93 TRP cc_start: 0.6609 (t60) cc_final: 0.6308 (t60) REVERT: J 196 GLU cc_start: 0.7321 (tp30) cc_final: 0.6990 (tp30) REVERT: E 62 SER cc_start: 0.4758 (p) cc_final: 0.4340 (t) REVERT: E 105 LYS cc_start: 0.6304 (mmpt) cc_final: 0.5007 (mtmm) REVERT: F 358 MET cc_start: 0.7902 (mmt) cc_final: 0.6745 (tmm) REVERT: F 391 VAL cc_start: 0.9284 (p) cc_final: 0.9044 (p) REVERT: F 468 ASN cc_start: 0.8279 (m-40) cc_final: 0.7388 (m-40) REVERT: A 236 MET cc_start: 0.8925 (mtm) cc_final: 0.8349 (mtm) REVERT: A 297 MET cc_start: 0.8591 (tpp) cc_final: 0.7622 (tpp) REVERT: A 396 ASP cc_start: 0.7836 (t70) cc_final: 0.7449 (t0) REVERT: A 604 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7370 (tp40) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.3907 time to fit residues: 375.9412 Evaluate side-chains 378 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 251 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 187 optimal weight: 20.0000 chunk 291 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN J 476 HIS J 553 HIS ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 292 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A 487 ASN A 497 GLN A 547 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.134749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.102580 restraints weight = 56656.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.100875 restraints weight = 63291.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.102251 restraints weight = 62561.834| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26729 Z= 0.170 Angle : 0.608 15.202 36108 Z= 0.314 Chirality : 0.040 0.250 4064 Planarity : 0.004 0.054 4635 Dihedral : 3.986 20.233 3546 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.56 % Allowed : 10.04 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3218 helix: 0.53 (0.12), residues: 1942 sheet: -1.21 (0.51), residues: 87 loop : -1.56 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 209 HIS 0.019 0.001 HIS B 190 PHE 0.025 0.002 PHE B 277 TYR 0.025 0.001 TYR G 79 ARG 0.007 0.001 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 1382) hydrogen bonds : angle 4.59851 ( 4086) metal coordination : bond 0.01876 ( 22) metal coordination : angle 5.72759 ( 12) covalent geometry : bond 0.00389 (26707) covalent geometry : angle 0.59921 (36096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 400 time to evaluate : 2.885 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: G 20 LYS cc_start: 0.8244 (tttp) cc_final: 0.7972 (tmtt) REVERT: I 55 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6523 (mt-10) REVERT: I 84 ILE cc_start: 0.7877 (mm) cc_final: 0.7456 (tp) REVERT: B 7 VAL cc_start: 0.8368 (t) cc_final: 0.8054 (m) REVERT: B 362 GLN cc_start: 0.8075 (tp40) cc_final: 0.7767 (tm-30) REVERT: B 741 TYR cc_start: 0.5139 (m-80) cc_final: 0.4436 (m-80) REVERT: C 69 VAL cc_start: 0.8634 (m) cc_final: 0.8277 (t) REVERT: J 196 GLU cc_start: 0.7084 (tp30) cc_final: 0.6805 (tp30) REVERT: J 499 ASP cc_start: 0.6270 (OUTLIER) cc_final: 0.6045 (t0) REVERT: J 593 MET cc_start: 0.7131 (mtm) cc_final: 0.6890 (mtp) REVERT: E 62 SER cc_start: 0.4787 (p) cc_final: 0.4259 (t) REVERT: E 105 LYS cc_start: 0.6542 (mmpt) cc_final: 0.5338 (mtmm) REVERT: F 280 MET cc_start: 0.2043 (tpp) cc_final: 0.1679 (ttm) REVERT: A 236 MET cc_start: 0.8915 (mtm) cc_final: 0.8578 (mtm) REVERT: A 297 MET cc_start: 0.8204 (tpp) cc_final: 0.7445 (tpp) REVERT: A 396 ASP cc_start: 0.7820 (t70) cc_final: 0.7384 (t0) outliers start: 45 outliers final: 31 residues processed: 423 average time/residue: 0.3701 time to fit residues: 247.2948 Evaluate side-chains 368 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 336 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 268 ASP Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 661 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 244 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 231 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN I 98 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 GLN ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS F 375 GLN A 318 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS A 547 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.133245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.099994 restraints weight = 56134.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.097353 restraints weight = 59275.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098665 restraints weight = 59928.260| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 26729 Z= 0.198 Angle : 0.606 14.255 36108 Z= 0.312 Chirality : 0.041 0.260 4064 Planarity : 0.004 0.057 4635 Dihedral : 4.066 20.010 3546 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.05 % Allowed : 12.40 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3218 helix: 0.74 (0.12), residues: 1952 sheet: -1.11 (0.53), residues: 82 loop : -1.53 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP J 209 HIS 0.011 0.001 HIS B 190 PHE 0.024 0.002 PHE J 626 TYR 0.022 0.001 TYR G 79 ARG 0.027 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 1382) hydrogen bonds : angle 4.45432 ( 4086) metal coordination : bond 0.01810 ( 22) metal coordination : angle 5.44376 ( 12) covalent geometry : bond 0.00461 (26707) covalent geometry : angle 0.59806 (36096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 352 time to evaluate : 2.840 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: G 20 LYS cc_start: 0.8291 (tttp) cc_final: 0.7029 (tttm) REVERT: H 49 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6653 (pm20) REVERT: I 55 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6695 (mt-10) REVERT: B 7 VAL cc_start: 0.8499 (t) cc_final: 0.8173 (m) REVERT: B 362 GLN cc_start: 0.8110 (tp40) cc_final: 0.7770 (tm-30) REVERT: B 377 ASN cc_start: 0.5925 (t0) cc_final: 0.5498 (t0) REVERT: B 741 TYR cc_start: 0.5562 (m-80) cc_final: 0.5018 (m-80) REVERT: D 26 GLU cc_start: 0.7438 (pm20) cc_final: 0.7183 (pm20) REVERT: J 196 GLU cc_start: 0.7223 (tp30) cc_final: 0.6945 (tp30) REVERT: E 62 SER cc_start: 0.4760 (p) cc_final: 0.4269 (t) REVERT: E 105 LYS cc_start: 0.6506 (mmpt) cc_final: 0.5329 (mtmm) REVERT: A 236 MET cc_start: 0.8934 (mtm) cc_final: 0.8665 (mtm) REVERT: A 297 MET cc_start: 0.8563 (tpp) cc_final: 0.7731 (tpp) REVERT: A 396 ASP cc_start: 0.8235 (t70) cc_final: 0.7877 (t0) outliers start: 59 outliers final: 35 residues processed: 383 average time/residue: 0.3592 time to fit residues: 221.0152 Evaluate side-chains 354 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 318 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 268 ASP Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 575 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 661 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 101 optimal weight: 0.0040 chunk 112 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 164 optimal weight: 0.0370 chunk 302 optimal weight: 7.9990 chunk 256 optimal weight: 0.9980 overall best weight: 0.3868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS C 27 HIS ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN A 274 HIS ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.134576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.101777 restraints weight = 56453.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098876 restraints weight = 62577.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.100268 restraints weight = 52784.697| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26729 Z= 0.125 Angle : 0.555 13.343 36108 Z= 0.285 Chirality : 0.039 0.239 4064 Planarity : 0.004 0.057 4635 Dihedral : 3.996 19.539 3546 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.05 % Allowed : 13.82 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3218 helix: 0.96 (0.12), residues: 1952 sheet: -0.94 (0.53), residues: 90 loop : -1.48 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 33 HIS 0.007 0.001 HIS B 190 PHE 0.026 0.001 PHE J 626 TYR 0.021 0.001 TYR G 79 ARG 0.008 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 1382) hydrogen bonds : angle 4.28227 ( 4086) metal coordination : bond 0.01063 ( 22) metal coordination : angle 4.28827 ( 12) covalent geometry : bond 0.00275 (26707) covalent geometry : angle 0.54969 (36096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 364 time to evaluate : 2.828 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: G 59 GLU cc_start: 0.7538 (pm20) cc_final: 0.7112 (pt0) REVERT: H 49 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: I 55 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6744 (mt-10) REVERT: B 7 VAL cc_start: 0.8342 (t) cc_final: 0.8008 (m) REVERT: B 362 GLN cc_start: 0.8060 (tp40) cc_final: 0.7734 (tm-30) REVERT: B 377 ASN cc_start: 0.5882 (t0) cc_final: 0.5452 (t0) REVERT: B 438 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7605 (mtm) REVERT: B 741 TYR cc_start: 0.5422 (m-80) cc_final: 0.4966 (m-80) REVERT: C 76 TYR cc_start: 0.8888 (t80) cc_final: 0.8662 (t80) REVERT: D 26 GLU cc_start: 0.7324 (pm20) cc_final: 0.7123 (pm20) REVERT: J 196 GLU cc_start: 0.7119 (tp30) cc_final: 0.6833 (tp30) REVERT: E 62 SER cc_start: 0.4803 (p) cc_final: 0.4326 (t) REVERT: E 105 LYS cc_start: 0.6484 (mmpt) cc_final: 0.5350 (mtmm) REVERT: A 219 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.8256 (m-10) REVERT: A 236 MET cc_start: 0.8849 (mtm) cc_final: 0.8634 (mtm) REVERT: A 297 MET cc_start: 0.8503 (tpp) cc_final: 0.7721 (tpp) REVERT: A 396 ASP cc_start: 0.7927 (t70) cc_final: 0.7519 (t0) REVERT: A 566 MET cc_start: 0.3387 (pmm) cc_final: 0.3174 (pmm) REVERT: A 694 LEU cc_start: 0.7942 (mt) cc_final: 0.7727 (mt) outliers start: 59 outliers final: 35 residues processed: 396 average time/residue: 0.3528 time to fit residues: 226.1971 Evaluate side-chains 360 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 322 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 266 ASN Chi-restraints excluded: chain J residue 268 ASP Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 575 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 654 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 169 optimal weight: 0.0980 chunk 268 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 305 optimal weight: 5.9990 chunk 311 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 278 optimal weight: 0.0370 chunk 303 optimal weight: 0.7980 chunk 304 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN I 48 HIS ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN C 68 HIS D 42 GLN J 266 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 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 = 0.4031 r_free = 0.4031 target = 0.133722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089857 restraints weight = 57859.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.092042 restraints weight = 35992.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093756 restraints weight = 25290.857| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26729 Z= 0.139 Angle : 0.564 10.931 36108 Z= 0.289 Chirality : 0.039 0.222 4064 Planarity : 0.004 0.057 4635 Dihedral : 3.971 19.291 3546 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.29 % Allowed : 15.25 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3218 helix: 1.05 (0.12), residues: 1950 sheet: -0.84 (0.54), residues: 90 loop : -1.47 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 33 HIS 0.007 0.001 HIS B 73 PHE 0.026 0.001 PHE J 626 TYR 0.037 0.001 TYR F 472 ARG 0.007 0.000 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 1382) hydrogen bonds : angle 4.24274 ( 4086) metal coordination : bond 0.01112 ( 22) metal coordination : angle 4.20652 ( 12) covalent geometry : bond 0.00320 (26707) covalent geometry : angle 0.55919 (36096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 348 time to evaluate : 2.924 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: G 20 LYS cc_start: 0.8380 (tttm) cc_final: 0.8180 (tptt) REVERT: H 49 GLN cc_start: 0.5991 (OUTLIER) cc_final: 0.5705 (pm20) REVERT: I 55 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6654 (mt-10) REVERT: I 92 GLN cc_start: 0.6917 (tp40) cc_final: 0.6234 (tp-100) REVERT: I 100 GLU cc_start: 0.7696 (tp30) cc_final: 0.7392 (tp30) REVERT: B 7 VAL cc_start: 0.8712 (t) cc_final: 0.8349 (m) REVERT: B 362 GLN cc_start: 0.8523 (tp40) cc_final: 0.7943 (tm-30) REVERT: B 377 ASN cc_start: 0.6103 (t0) cc_final: 0.5695 (t0) REVERT: B 438 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7674 (mtm) REVERT: B 741 TYR cc_start: 0.5715 (m-80) cc_final: 0.5299 (m-80) REVERT: J 196 GLU cc_start: 0.7563 (tp30) cc_final: 0.7210 (tp30) REVERT: E 62 SER cc_start: 0.4413 (p) cc_final: 0.4117 (t) REVERT: E 105 LYS cc_start: 0.6448 (mmpt) cc_final: 0.5239 (mtmm) REVERT: F 395 MET cc_start: 0.7967 (ppp) cc_final: 0.7575 (ppp) REVERT: A 219 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8291 (m-10) REVERT: A 236 MET cc_start: 0.8982 (mtm) cc_final: 0.8694 (mtm) REVERT: A 297 MET cc_start: 0.8539 (tpp) cc_final: 0.7609 (tpp) REVERT: A 300 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7974 (mp) REVERT: A 396 ASP cc_start: 0.8118 (t70) cc_final: 0.7685 (t0) REVERT: A 451 MET cc_start: 0.8831 (tpp) cc_final: 0.8359 (tpp) REVERT: A 694 LEU cc_start: 0.8392 (mt) cc_final: 0.8122 (mt) outliers start: 66 outliers final: 39 residues processed: 384 average time/residue: 0.3483 time to fit residues: 217.0509 Evaluate side-chains 361 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 318 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 193 PHE Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 575 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 654 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 262 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 252 optimal weight: 0.0470 chunk 269 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 242 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 229 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN A 547 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.133351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090241 restraints weight = 57075.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.092220 restraints weight = 38693.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094394 restraints weight = 27137.654| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26729 Z= 0.142 Angle : 0.568 10.857 36108 Z= 0.290 Chirality : 0.039 0.207 4064 Planarity : 0.004 0.051 4635 Dihedral : 3.935 23.531 3546 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.15 % Allowed : 16.36 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3218 helix: 1.12 (0.12), residues: 1949 sheet: -0.81 (0.54), residues: 90 loop : -1.48 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 209 HIS 0.005 0.001 HIS A 547 PHE 0.024 0.001 PHE J 626 TYR 0.028 0.001 TYR F 472 ARG 0.006 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 1382) hydrogen bonds : angle 4.19246 ( 4086) metal coordination : bond 0.01040 ( 22) metal coordination : angle 4.05177 ( 12) covalent geometry : bond 0.00325 (26707) covalent geometry : angle 0.56361 (36096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 341 time to evaluate : 2.971 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: H 49 GLN cc_start: 0.6274 (pm20) cc_final: 0.5961 (pm20) REVERT: I 55 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6774 (mt-10) REVERT: I 92 GLN cc_start: 0.6928 (tp40) cc_final: 0.6243 (tp-100) REVERT: I 100 GLU cc_start: 0.7634 (tp30) cc_final: 0.7326 (tp30) REVERT: B 7 VAL cc_start: 0.8590 (t) cc_final: 0.8236 (m) REVERT: B 362 GLN cc_start: 0.8438 (tp40) cc_final: 0.7902 (tm-30) REVERT: B 377 ASN cc_start: 0.6060 (t0) cc_final: 0.5631 (t0) REVERT: B 438 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7639 (mtm) REVERT: B 642 MET cc_start: 0.7013 (mmp) cc_final: 0.6758 (mmp) REVERT: B 741 TYR cc_start: 0.5619 (m-80) cc_final: 0.4803 (m-80) REVERT: J 1 MET cc_start: 0.4061 (ppp) cc_final: 0.3759 (ppp) REVERT: J 196 GLU cc_start: 0.7469 (tp30) cc_final: 0.7127 (tp30) REVERT: J 384 ASP cc_start: 0.8564 (t0) cc_final: 0.8290 (t0) REVERT: E 62 SER cc_start: 0.4573 (p) cc_final: 0.4216 (t) REVERT: E 105 LYS cc_start: 0.6405 (mmpt) cc_final: 0.5235 (mtmm) REVERT: F 395 MET cc_start: 0.8119 (ppp) cc_final: 0.7668 (ppp) REVERT: F 420 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8281 (tp-100) REVERT: A 86 MET cc_start: 0.7803 (tmm) cc_final: 0.7526 (tmm) REVERT: A 219 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8284 (m-10) REVERT: A 300 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8009 (mp) REVERT: A 396 ASP cc_start: 0.8103 (t70) cc_final: 0.7672 (t0) REVERT: A 451 MET cc_start: 0.8861 (tpp) cc_final: 0.8366 (tpp) REVERT: A 566 MET cc_start: 0.2711 (pmm) cc_final: 0.2330 (pmm) REVERT: A 694 LEU cc_start: 0.8403 (mt) cc_final: 0.8085 (mt) outliers start: 62 outliers final: 47 residues processed: 373 average time/residue: 0.3436 time to fit residues: 207.9103 Evaluate side-chains 369 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 318 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 193 PHE Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 268 ASP Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 575 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 390 GLN Chi-restraints excluded: chain F residue 420 GLN Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 595 MET Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 654 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 135 optimal weight: 0.0970 chunk 76 optimal weight: 0.4980 chunk 205 optimal weight: 7.9990 chunk 269 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN H 65 GLN ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.134450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.104911 restraints weight = 56780.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.106008 restraints weight = 94507.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.106807 restraints weight = 61147.111| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26729 Z= 0.141 Angle : 0.572 10.544 36108 Z= 0.292 Chirality : 0.039 0.195 4064 Planarity : 0.004 0.072 4635 Dihedral : 3.929 22.104 3546 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.40 % Allowed : 16.36 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3218 helix: 1.14 (0.12), residues: 1953 sheet: -0.81 (0.55), residues: 90 loop : -1.47 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 33 HIS 0.007 0.001 HIS B 68 PHE 0.027 0.002 PHE D 79 TYR 0.025 0.001 TYR J 472 ARG 0.017 0.000 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 1382) hydrogen bonds : angle 4.19727 ( 4086) metal coordination : bond 0.01012 ( 22) metal coordination : angle 3.93299 ( 12) covalent geometry : bond 0.00324 (26707) covalent geometry : angle 0.56775 (36096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 340 time to evaluate : 2.852 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: H 49 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: I 55 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6747 (mt-10) REVERT: I 92 GLN cc_start: 0.6474 (tp40) cc_final: 0.6194 (tp-100) REVERT: B 7 VAL cc_start: 0.8217 (t) cc_final: 0.7879 (m) REVERT: B 362 GLN cc_start: 0.8012 (tp40) cc_final: 0.7691 (tm-30) REVERT: B 377 ASN cc_start: 0.5900 (t0) cc_final: 0.5471 (t0) REVERT: B 438 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7495 (mtm) REVERT: B 741 TYR cc_start: 0.5290 (m-80) cc_final: 0.4667 (m-80) REVERT: D 46 LYS cc_start: 0.7049 (mtpt) cc_final: 0.6521 (mtpp) REVERT: J 172 TYR cc_start: 0.6623 (t80) cc_final: 0.6392 (t80) REVERT: J 196 GLU cc_start: 0.7017 (tp30) cc_final: 0.6763 (tp30) REVERT: J 384 ASP cc_start: 0.7725 (t0) cc_final: 0.7466 (t0) REVERT: E 50 MET cc_start: 0.7260 (mmm) cc_final: 0.7058 (mmt) REVERT: E 62 SER cc_start: 0.5097 (p) cc_final: 0.4560 (t) REVERT: E 105 LYS cc_start: 0.6612 (mmpt) cc_final: 0.5473 (mtmm) REVERT: F 395 MET cc_start: 0.7604 (ppp) cc_final: 0.7294 (ppp) REVERT: A 86 MET cc_start: 0.7595 (tmm) cc_final: 0.7288 (tmm) REVERT: A 151 MET cc_start: 0.9016 (tpp) cc_final: 0.8783 (tpt) REVERT: A 219 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8357 (m-10) REVERT: A 300 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7894 (mp) REVERT: A 396 ASP cc_start: 0.8059 (t70) cc_final: 0.7637 (t0) REVERT: A 451 MET cc_start: 0.8684 (tpp) cc_final: 0.8325 (tpp) REVERT: A 566 MET cc_start: 0.2858 (pmm) cc_final: 0.2593 (pmm) REVERT: A 694 LEU cc_start: 0.7974 (mt) cc_final: 0.7716 (mt) outliers start: 69 outliers final: 49 residues processed: 379 average time/residue: 0.3462 time to fit residues: 212.5973 Evaluate side-chains 377 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 324 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 193 PHE Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 561 GLU Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 575 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 504 ASN Chi-restraints excluded: chain F residue 595 MET Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 654 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 159 optimal weight: 0.2980 chunk 145 optimal weight: 0.3980 chunk 192 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 250 optimal weight: 0.5980 chunk 292 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 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 = 0.4035 r_free = 0.4035 target = 0.134530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.105156 restraints weight = 56736.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.106047 restraints weight = 98273.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.107060 restraints weight = 67760.505| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26729 Z= 0.139 Angle : 0.576 10.120 36108 Z= 0.295 Chirality : 0.039 0.183 4064 Planarity : 0.004 0.094 4635 Dihedral : 3.929 19.336 3546 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.40 % Allowed : 16.67 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3218 helix: 1.18 (0.12), residues: 1951 sheet: -0.81 (0.55), residues: 90 loop : -1.48 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 33 HIS 0.005 0.001 HIS J 476 PHE 0.024 0.001 PHE J 626 TYR 0.024 0.001 TYR J 472 ARG 0.008 0.000 ARG H 43 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 1382) hydrogen bonds : angle 4.19016 ( 4086) metal coordination : bond 0.00934 ( 22) metal coordination : angle 3.78264 ( 12) covalent geometry : bond 0.00319 (26707) covalent geometry : angle 0.57237 (36096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 336 time to evaluate : 2.831 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: G 52 PHE cc_start: 0.2426 (m-80) cc_final: 0.2110 (m-80) REVERT: H 49 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.7095 (pm20) REVERT: I 100 GLU cc_start: 0.7565 (tp30) cc_final: 0.7278 (tp30) REVERT: B 7 VAL cc_start: 0.8270 (t) cc_final: 0.7930 (m) REVERT: B 362 GLN cc_start: 0.8028 (tp40) cc_final: 0.7697 (tm-30) REVERT: B 377 ASN cc_start: 0.5913 (t0) cc_final: 0.5487 (t0) REVERT: B 438 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7492 (mtm) REVERT: B 741 TYR cc_start: 0.5275 (m-80) cc_final: 0.4729 (m-80) REVERT: D 46 LYS cc_start: 0.6936 (mtpt) cc_final: 0.6319 (mtpt) REVERT: J 196 GLU cc_start: 0.6982 (tp30) cc_final: 0.6742 (tp30) REVERT: J 384 ASP cc_start: 0.7685 (t0) cc_final: 0.7420 (t0) REVERT: E 62 SER cc_start: 0.5050 (p) cc_final: 0.4595 (t) REVERT: E 105 LYS cc_start: 0.6629 (mmpt) cc_final: 0.5504 (mtmm) REVERT: A 86 MET cc_start: 0.7576 (tmm) cc_final: 0.7293 (tmm) REVERT: A 219 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8343 (m-10) REVERT: A 236 MET cc_start: 0.8631 (mtm) cc_final: 0.8403 (mtm) REVERT: A 297 MET cc_start: 0.8660 (tpp) cc_final: 0.7614 (tpp) REVERT: A 396 ASP cc_start: 0.8007 (t70) cc_final: 0.7595 (t0) REVERT: A 451 MET cc_start: 0.8644 (tpp) cc_final: 0.8292 (tpp) REVERT: A 566 MET cc_start: 0.3192 (pmm) cc_final: 0.2989 (pmm) REVERT: A 582 MET cc_start: 0.8343 (tpt) cc_final: 0.8134 (tpt) REVERT: A 694 LEU cc_start: 0.7973 (mt) cc_final: 0.7705 (mt) outliers start: 69 outliers final: 51 residues processed: 374 average time/residue: 0.3781 time to fit residues: 230.9860 Evaluate side-chains 378 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 324 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 193 PHE Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 561 GLU Chi-restraints excluded: chain J residue 575 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 390 GLN Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 504 ASN Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 595 MET Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 654 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 112 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 260 optimal weight: 0.3980 chunk 237 optimal weight: 0.0470 chunk 279 optimal weight: 0.9990 chunk 254 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 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 = 0.4039 r_free = 0.4039 target = 0.134741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.105402 restraints weight = 56965.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.106844 restraints weight = 96631.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.107470 restraints weight = 60181.235| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26729 Z= 0.134 Angle : 0.586 10.159 36108 Z= 0.299 Chirality : 0.039 0.175 4064 Planarity : 0.004 0.077 4635 Dihedral : 3.939 22.244 3546 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.01 % Allowed : 17.47 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3218 helix: 1.21 (0.12), residues: 1950 sheet: -0.83 (0.58), residues: 81 loop : -1.47 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 33 HIS 0.005 0.001 HIS J 476 PHE 0.026 0.001 PHE J 626 TYR 0.024 0.001 TYR B 568 ARG 0.009 0.000 ARG I 86 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 1382) hydrogen bonds : angle 4.20159 ( 4086) metal coordination : bond 0.00900 ( 22) metal coordination : angle 3.80318 ( 12) covalent geometry : bond 0.00307 (26707) covalent geometry : angle 0.58238 (36096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 335 time to evaluate : 2.828 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: H 49 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: B 7 VAL cc_start: 0.8247 (t) cc_final: 0.7903 (m) REVERT: B 26 MET cc_start: 0.7820 (mmm) cc_final: 0.7605 (mmt) REVERT: B 362 GLN cc_start: 0.8030 (tp40) cc_final: 0.7699 (tm-30) REVERT: B 377 ASN cc_start: 0.5906 (t0) cc_final: 0.5474 (t0) REVERT: B 438 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7494 (mtm) REVERT: B 741 TYR cc_start: 0.5252 (m-80) cc_final: 0.4725 (m-80) REVERT: D 44 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6052 (mt) REVERT: D 46 LYS cc_start: 0.6966 (mtpt) cc_final: 0.5879 (mtpt) REVERT: D 49 GLN cc_start: 0.7603 (pp30) cc_final: 0.7366 (pp30) REVERT: J 117 THR cc_start: 0.6097 (p) cc_final: 0.5832 (p) REVERT: J 177 ARG cc_start: 0.7999 (mmp80) cc_final: 0.7276 (mmp80) REVERT: J 196 GLU cc_start: 0.6987 (tp30) cc_final: 0.6742 (tp30) REVERT: J 384 ASP cc_start: 0.7682 (t0) cc_final: 0.7401 (t0) REVERT: E 50 MET cc_start: 0.7238 (mmm) cc_final: 0.6994 (mmt) REVERT: E 62 SER cc_start: 0.5029 (p) cc_final: 0.4506 (t) REVERT: E 105 LYS cc_start: 0.6618 (mmpt) cc_final: 0.5525 (mtmm) REVERT: F 395 MET cc_start: 0.7573 (ppp) cc_final: 0.7271 (ppp) REVERT: A 86 MET cc_start: 0.7567 (tmm) cc_final: 0.7264 (tmm) REVERT: A 219 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8299 (m-10) REVERT: A 297 MET cc_start: 0.8626 (tpp) cc_final: 0.7619 (tpp) REVERT: A 396 ASP cc_start: 0.8067 (t70) cc_final: 0.7647 (t0) REVERT: A 451 MET cc_start: 0.8682 (tpp) cc_final: 0.8319 (tpp) REVERT: A 694 LEU cc_start: 0.7952 (mt) cc_final: 0.7677 (mt) outliers start: 58 outliers final: 48 residues processed: 371 average time/residue: 0.3640 time to fit residues: 216.9764 Evaluate side-chains 370 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 318 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 193 PHE Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 561 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 390 GLN Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 504 ASN Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 595 MET Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 654 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 269 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 173 optimal weight: 0.2980 chunk 139 optimal weight: 0.0030 chunk 254 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN ** A 487 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 = 0.4034 r_free = 0.4034 target = 0.134425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.105005 restraints weight = 56748.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.105624 restraints weight = 97795.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106771 restraints weight = 68540.591| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26729 Z= 0.144 Angle : 0.593 10.900 36108 Z= 0.302 Chirality : 0.040 0.189 4064 Planarity : 0.004 0.096 4635 Dihedral : 3.939 27.886 3546 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.08 % Allowed : 17.82 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3218 helix: 1.23 (0.12), residues: 1950 sheet: -0.86 (0.58), residues: 81 loop : -1.48 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 93 HIS 0.005 0.001 HIS J 476 PHE 0.025 0.001 PHE J 626 TYR 0.031 0.001 TYR J 172 ARG 0.017 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 1382) hydrogen bonds : angle 4.20145 ( 4086) metal coordination : bond 0.00989 ( 22) metal coordination : angle 3.79793 ( 12) covalent geometry : bond 0.00332 (26707) covalent geometry : angle 0.58929 (36096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 3.136 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: G 28 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 7 VAL cc_start: 0.8267 (t) cc_final: 0.7922 (m) REVERT: B 362 GLN cc_start: 0.8029 (tp40) cc_final: 0.7693 (tm-30) REVERT: B 377 ASN cc_start: 0.5763 (t0) cc_final: 0.5336 (t0) REVERT: B 438 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7515 (mtm) REVERT: D 46 LYS cc_start: 0.6952 (mtpt) cc_final: 0.6297 (mtpt) REVERT: D 49 GLN cc_start: 0.7678 (pp30) cc_final: 0.7456 (pp30) REVERT: J 117 THR cc_start: 0.6182 (p) cc_final: 0.5914 (p) REVERT: J 196 GLU cc_start: 0.7075 (tp30) cc_final: 0.6828 (tp30) REVERT: J 384 ASP cc_start: 0.7676 (t0) cc_final: 0.7388 (t0) REVERT: E 62 SER cc_start: 0.5018 (p) cc_final: 0.4548 (t) REVERT: E 105 LYS cc_start: 0.6635 (mmpt) cc_final: 0.5516 (mtmm) REVERT: A 86 MET cc_start: 0.7605 (tmm) cc_final: 0.7297 (tmm) REVERT: A 219 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8347 (m-10) REVERT: A 236 MET cc_start: 0.8380 (mtm) cc_final: 0.8077 (mtm) REVERT: A 297 MET cc_start: 0.8589 (tpp) cc_final: 0.7628 (tpp) REVERT: A 396 ASP cc_start: 0.7990 (t70) cc_final: 0.7581 (t0) REVERT: A 451 MET cc_start: 0.8645 (tpp) cc_final: 0.8304 (tpp) REVERT: A 566 MET cc_start: 0.2306 (pmm) cc_final: 0.1433 (pmm) REVERT: A 694 LEU cc_start: 0.8030 (mt) cc_final: 0.7732 (mt) outliers start: 60 outliers final: 51 residues processed: 371 average time/residue: 0.3473 time to fit residues: 210.3082 Evaluate side-chains 374 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 321 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 193 PHE Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 561 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 390 GLN Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 504 ASN Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 595 MET Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 654 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 161 optimal weight: 2.9990 chunk 296 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 266 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 257 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.134729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.105441 restraints weight = 56870.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.106783 restraints weight = 92829.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.107536 restraints weight = 65031.927| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26729 Z= 0.136 Angle : 0.604 10.743 36108 Z= 0.306 Chirality : 0.039 0.186 4064 Planarity : 0.004 0.109 4635 Dihedral : 3.954 26.305 3546 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.05 % Allowed : 18.41 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3218 helix: 1.27 (0.12), residues: 1944 sheet: -0.93 (0.57), residues: 81 loop : -1.46 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 33 HIS 0.005 0.001 HIS J 476 PHE 0.025 0.001 PHE J 626 TYR 0.032 0.001 TYR J 172 ARG 0.020 0.000 ARG J 133 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 1382) hydrogen bonds : angle 4.18345 ( 4086) metal coordination : bond 0.00831 ( 22) metal coordination : angle 3.78419 ( 12) covalent geometry : bond 0.00312 (26707) covalent geometry : angle 0.60006 (36096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8911.75 seconds wall clock time: 157 minutes 40.27 seconds (9460.27 seconds total)