Starting phenix.real_space_refine on Tue Aug 26 21:32:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j79_61198/08_2025/9j79_61198.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j79_61198/08_2025/9j79_61198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j79_61198/08_2025/9j79_61198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j79_61198/08_2025/9j79_61198.map" model { file = "/net/cci-nas-00/data/ceres_data/9j79_61198/08_2025/9j79_61198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j79_61198/08_2025/9j79_61198.cif" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 236 5.16 5 C 23163 2.51 5 N 6428 2.21 5 O 6888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36721 Number of models: 1 Model: "" Number of chains: 21 Chain: "E" 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: "F" 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: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 585 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" 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: "L" 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: "M" 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: "N" 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: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 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: "A" 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: "B" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 495 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "G" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 517 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain: "D" 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: "O" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4562 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 577} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 33 Chain: "P" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4314 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 548} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "S" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 296 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 4, 'TRANS': 55} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 10, 'PHE:plan': 3, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 301 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 10, 'PHE:plan': 3, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 100 Chain: "Q" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "R" 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: "N" 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 7724 SG CYS I 53 63.670 98.636 141.278 1.00494.16 S ATOM 7747 SG CYS I 56 66.175 98.485 138.376 1.00496.07 S ATOM 7753 SG CYS I 68 66.103 101.492 140.698 1.00487.72 S ATOM 7638 SG CYS I 42 59.642 102.485 147.808 1.00462.06 S ATOM 7657 SG CYS I 45 60.388 98.669 147.804 1.00479.17 S ATOM 7871 SG CYS I 83 59.025 100.357 144.614 1.00466.97 S ATOM 7803 SG CYS I 75 53.188 112.464 148.071 1.00489.55 S ATOM 7967 SG CYS I 94 51.828 110.288 148.470 1.00513.96 S ATOM 15797 SG CYS N 53 38.910 46.068 162.901 1.00173.73 S ATOM 15820 SG CYS N 56 35.439 45.512 161.403 1.00196.56 S ATOM 15904 SG CYS N 68 38.394 46.422 159.115 1.00172.43 S ATOM 15711 SG CYS N 42 46.587 46.731 162.159 1.00157.48 S ATOM 15730 SG CYS N 45 43.554 45.527 164.128 1.00161.42 S ATOM 16022 SG CYS N 83 43.901 49.065 163.115 1.00159.57 S ATOM 15954 SG CYS N 75 52.391 57.264 161.598 1.00113.92 S ATOM 16118 SG CYS N 94 52.151 56.319 164.595 1.00112.60 S Time building chain proxies: 9.90, per 1000 atoms: 0.27 Number of scatterers: 36721 At special positions: 0 Unit cell: (159.9, 169.74, 220.58, 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 236 16.00 O 6888 8.00 N 6428 7.00 C 23163 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: 3.40 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination 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 45 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 83 " 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 " pdb=" ZN N 200 " pdb="ZN ZN N 200 " - pdb=" ND1 HIS N 82 " pdb="ZN ZN N 200 " - pdb=" SG CYS N 53 " pdb="ZN ZN N 200 " - pdb=" SG CYS N 56 " pdb="ZN ZN N 200 " - pdb=" SG CYS N 68 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" ND1 HIS N 80 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 83 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 42 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 45 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 75 " pdb="ZN ZN N 202 " - pdb=" ND1 HIS N 77 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 94 " Number of angles added : 12 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8956 Finding SS restraints... Secondary structure from input PDB file: 232 helices and 19 sheets defined 65.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'E' and resid 9 through 26 removed outlier: 3.519A pdb=" N THR E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 45 removed outlier: 3.658A pdb=" N ARG E 38 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 4.100A pdb=" N HIS E 71 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER E 79 " --> pdb=" O ARG E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.508A pdb=" N ARG E 89 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 138 through 151 Processing helix chain 'E' and resid 152 through 154 No H-bonds generated for 'chain 'E' and resid 152 through 154' Processing helix chain 'E' and resid 155 through 172 removed outlier: 3.513A pdb=" N ILE E 160 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET E 162 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU E 164 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 191 removed outlier: 3.948A pdb=" N VAL E 189 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 195 Processing helix chain 'E' and resid 200 through 207 Processing helix chain 'E' and resid 207 through 227 removed outlier: 3.512A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 254 removed outlier: 4.673A pdb=" N GLU E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG E 251 " --> pdb=" O GLU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 258 through 271 removed outlier: 3.558A pdb=" N VAL E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 289 removed outlier: 3.905A pdb=" N HIS E 283 " --> pdb=" O HIS E 279 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 286 " --> pdb=" O CYS E 282 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN E 288 " --> pdb=" O ASN E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 304 removed outlier: 3.674A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA E 303 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 327 removed outlier: 4.078A pdb=" N MET E 311 " --> pdb=" O GLY E 307 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN E 313 " --> pdb=" O PRO E 309 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP E 321 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU E 324 " --> pdb=" O HIS E 320 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG E 325 " --> pdb=" O ASP E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 357 Processing helix chain 'E' and resid 361 through 377 removed outlier: 3.763A pdb=" N ALA E 367 " --> pdb=" O HIS E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 400 removed outlier: 3.822A pdb=" N ALA E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 398 " --> pdb=" O TYR E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 423 removed outlier: 3.663A pdb=" N SER E 417 " --> pdb=" O ASP E 413 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR E 420 " --> pdb=" O THR E 416 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 421 " --> pdb=" O SER E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 445 removed outlier: 3.556A pdb=" N HIS E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 466 Processing helix chain 'E' and resid 470 through 492 removed outlier: 3.684A pdb=" N ASP E 479 " --> pdb=" O ARG E 475 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET E 480 " --> pdb=" O MET E 476 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA E 484 " --> pdb=" O MET E 480 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP E 485 " --> pdb=" O SER E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 497 Processing helix chain 'E' and resid 533 through 548 Processing helix chain 'E' and resid 578 through 587 removed outlier: 3.693A pdb=" N VAL E 584 " --> pdb=" O TYR E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 590 No H-bonds generated for 'chain 'E' and resid 588 through 590' Processing helix chain 'E' and resid 595 through 604 removed outlier: 3.905A pdb=" N LEU E 599 " --> pdb=" O SER E 595 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER E 602 " --> pdb=" O GLU E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 619 Processing helix chain 'E' and resid 661 through 692 removed outlier: 3.609A pdb=" N MET E 665 " --> pdb=" O THR E 661 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU E 666 " --> pdb=" O PRO E 662 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLN E 667 " --> pdb=" O GLN E 663 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR E 668 " --> pdb=" O GLU E 664 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 685 " --> pdb=" O GLN E 681 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA E 690 " --> pdb=" O ARG E 686 " (cutoff:3.500A) Processing helix chain 'E' and resid 695 through 708 removed outlier: 3.558A pdb=" N GLN E 701 " --> pdb=" O ASN E 697 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN E 706 " --> pdb=" O GLU E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 728 removed outlier: 3.506A pdb=" N ILE E 718 " --> pdb=" O SER E 714 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS E 720 " --> pdb=" O SER E 716 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 37 Processing helix chain 'F' and resid 39 through 47 Processing helix chain 'F' and resid 66 through 83 removed outlier: 4.066A pdb=" N LEU F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'H' and resid 24 through 36 removed outlier: 3.586A pdb=" N ILE H 30 " --> pdb=" O GLU H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 61 Processing helix chain 'I' and resid 81 through 91 removed outlier: 3.856A pdb=" N LYS I 89 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR I 90 " --> pdb=" O ARG I 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 26 removed outlier: 4.198A pdb=" N THR K 13 " --> pdb=" O ASP K 9 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR K 20 " --> pdb=" O LYS K 16 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS K 22 " --> pdb=" O LEU K 18 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 47 removed outlier: 3.636A pdb=" N PHE K 39 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER K 40 " --> pdb=" O ASN K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 79 Processing helix chain 'K' and resid 84 through 105 removed outlier: 3.632A pdb=" N LYS K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 112 Processing helix chain 'K' and resid 138 through 149 removed outlier: 3.629A pdb=" N MET K 146 " --> pdb=" O LEU K 142 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP K 147 " --> pdb=" O ALA K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 173 removed outlier: 3.678A pdb=" N ARG K 161 " --> pdb=" O ALA K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 189 removed outlier: 3.578A pdb=" N PHE K 188 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL K 189 " --> pdb=" O ILE K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 207 removed outlier: 3.533A pdb=" N GLU K 205 " --> pdb=" O LYS K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 230 removed outlier: 3.746A pdb=" N GLN K 221 " --> pdb=" O GLU K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 252 removed outlier: 3.711A pdb=" N MET K 236 " --> pdb=" O CYS K 232 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU K 237 " --> pdb=" O SER K 233 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS K 238 " --> pdb=" O GLN K 234 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE K 248 " --> pdb=" O LYS K 244 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS K 252 " --> pdb=" O ILE K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 257 No H-bonds generated for 'chain 'K' and resid 255 through 257' Processing helix chain 'K' and resid 258 through 271 Processing helix chain 'K' and resid 274 through 288 removed outlier: 4.003A pdb=" N GLU K 281 " --> pdb=" O PHE K 277 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS K 283 " --> pdb=" O HIS K 279 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASN K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE K 286 " --> pdb=" O CYS K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 304 removed outlier: 3.579A pdb=" N ALA K 303 " --> pdb=" O VAL K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 329 removed outlier: 3.887A pdb=" N MET K 311 " --> pdb=" O GLY K 307 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN K 329 " --> pdb=" O ARG K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 357 removed outlier: 3.696A pdb=" N VAL K 340 " --> pdb=" O PRO K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 377 removed outlier: 3.956A pdb=" N SER K 374 " --> pdb=" O LYS K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 400 Processing helix chain 'K' and resid 407 through 424 removed outlier: 3.549A pdb=" N VAL K 411 " --> pdb=" O THR K 407 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU K 412 " --> pdb=" O GLU K 408 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP K 413 " --> pdb=" O ASN K 409 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR K 420 " --> pdb=" O THR K 416 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR K 424 " --> pdb=" O THR K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 427 through 442 Processing helix chain 'K' and resid 450 through 466 removed outlier: 3.572A pdb=" N GLU K 454 " --> pdb=" O SER K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 496 removed outlier: 4.579A pdb=" N ALA K 484 " --> pdb=" O MET K 480 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP K 485 " --> pdb=" O SER K 481 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN K 488 " --> pdb=" O ALA K 484 " (cutoff:3.500A) Processing helix chain 'K' and resid 530 through 548 removed outlier: 4.283A pdb=" N LYS K 535 " --> pdb=" O GLN K 531 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER K 536 " --> pdb=" O GLU K 532 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN K 546 " --> pdb=" O LEU K 542 " (cutoff:3.500A) Processing helix chain 'K' and resid 579 through 591 removed outlier: 3.800A pdb=" N VAL K 584 " --> pdb=" O TYR K 580 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU K 585 " --> pdb=" O GLN K 581 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU K 586 " --> pdb=" O MET K 582 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA K 587 " --> pdb=" O ALA K 583 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE K 588 " --> pdb=" O VAL K 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 595 through 604 removed outlier: 3.591A pdb=" N LEU K 599 " --> pdb=" O SER K 595 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP K 601 " --> pdb=" O LYS K 597 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER K 602 " --> pdb=" O GLU K 598 " (cutoff:3.500A) Processing helix chain 'K' and resid 606 through 619 removed outlier: 3.530A pdb=" N ILE K 614 " --> pdb=" O LEU K 610 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP K 619 " --> pdb=" O LYS K 615 " (cutoff:3.500A) Processing helix chain 'K' and resid 661 through 692 removed outlier: 3.599A pdb=" N ALA K 682 " --> pdb=" O MET K 678 " (cutoff:3.500A) Processing helix chain 'K' and resid 695 through 707 removed outlier: 3.573A pdb=" N VAL K 703 " --> pdb=" O LEU K 699 " (cutoff:3.500A) Processing helix chain 'K' and resid 714 through 728 removed outlier: 3.521A pdb=" N CYS K 721 " --> pdb=" O MET K 717 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 37 Processing helix chain 'L' and resid 39 through 47 Processing helix chain 'L' and resid 66 through 83 Processing helix chain 'L' and resid 102 through 105 Processing helix chain 'L' and resid 106 through 111 Processing helix chain 'M' and resid 26 through 36 removed outlier: 3.832A pdb=" N VAL M 31 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 42 removed outlier: 3.883A pdb=" N GLU M 41 " --> pdb=" O PRO M 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN M 42 " --> pdb=" O PRO M 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 38 through 42' Processing helix chain 'N' and resid 53 through 58 removed outlier: 3.939A pdb=" N ALA N 58 " --> pdb=" O ILE N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 91 removed outlier: 3.648A pdb=" N LYS N 89 " --> pdb=" O SER N 85 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR N 90 " --> pdb=" O ARG N 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 14 Processing helix chain 'J' and resid 16 through 24 Processing helix chain 'J' and resid 29 through 37 Processing helix chain 'J' and resid 48 through 56 removed outlier: 3.806A pdb=" N ASN J 56 " --> pdb=" O ILE J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 69 removed outlier: 3.564A pdb=" N VAL J 62 " --> pdb=" O HIS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 98 removed outlier: 3.743A pdb=" N CYS J 94 " --> pdb=" O THR J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 111 removed outlier: 3.575A pdb=" N VAL J 104 " --> pdb=" O HIS J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 132 Processing helix chain 'J' and resid 133 through 143 Processing helix chain 'J' and resid 156 through 162 removed outlier: 3.555A pdb=" N ILE J 160 " --> pdb=" O THR J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 176 Processing helix chain 'J' and resid 189 through 198 Processing helix chain 'J' and resid 199 through 210 removed outlier: 3.518A pdb=" N TRP J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 229 removed outlier: 3.691A pdb=" N SER J 229 " --> pdb=" O VAL J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 231 through 242 Processing helix chain 'J' and resid 245 through 260 removed outlier: 3.554A pdb=" N PHE J 260 " --> pdb=" O LEU J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 285 Processing helix chain 'J' and resid 310 through 318 removed outlier: 3.673A 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 340 through 343 removed outlier: 3.662A pdb=" N VAL J 343 " --> pdb=" O ASN J 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 340 through 343' Processing helix chain 'J' and resid 344 through 357 Processing helix chain 'J' and resid 359 through 377 Processing helix chain 'J' and resid 382 through 398 Processing helix chain 'J' and resid 403 through 428 Processing helix chain 'J' and resid 432 through 457 Processing helix chain 'J' and resid 460 through 478 Processing helix chain 'J' and resid 486 through 493 Processing helix chain 'J' and resid 501 through 506 Processing helix chain 'J' and resid 511 through 522 Processing helix chain 'J' and resid 534 through 541 Processing helix chain 'J' and resid 548 through 563 Processing helix chain 'J' and resid 582 through 592 Processing helix chain 'J' and resid 596 through 609 Processing helix chain 'J' and resid 617 through 627 Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 58 through 68 removed outlier: 3.605A pdb=" N VAL A 62 " --> pdb=" O HIS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.502A pdb=" N VAL A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 262 removed outlier: 3.528A pdb=" N ASN A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 284 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.556A pdb=" N GLY A 303 " --> pdb=" O HIS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 320 through 337 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.062A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 378 Processing helix chain 'A' and resid 381 through 398 Processing helix chain 'A' and resid 403 through 428 Processing helix chain 'A' and resid 432 through 457 removed outlier: 3.573A pdb=" N ALA A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 Processing helix chain 'A' and resid 486 through 493 Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.568A pdb=" N VAL A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 522 Processing helix chain 'A' and resid 534 through 541 removed outlier: 3.564A pdb=" N GLN A 541 " --> pdb=" O HIS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.669A pdb=" N ILE A 557 " --> pdb=" O HIS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 593 Processing helix chain 'A' and resid 599 through 608 removed outlier: 4.495A pdb=" N ALA A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 627 removed outlier: 3.888A pdb=" N GLU A 622 " --> pdb=" O ARG A 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 84 removed outlier: 3.567A pdb=" N LEU B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 74 " --> pdb=" O PHE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 100 Processing helix chain 'B' and resid 105 through 111 removed outlier: 4.267A pdb=" N VAL B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 4.308A pdb=" N GLN B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N MET B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 84 Processing helix chain 'G' and resid 85 through 99 Processing helix chain 'G' and resid 102 through 114 removed outlier: 3.525A pdb=" N GLN G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL G 109 " --> pdb=" O GLN G 105 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLN G 112 " --> pdb=" O GLN G 108 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 114 " --> pdb=" O LEU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 126 removed outlier: 3.650A pdb=" N LYS G 125 " --> pdb=" O MET G 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 10 removed outlier: 3.525A pdb=" N UNK D 8 " --> pdb=" O UNK D 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 14 removed outlier: 3.618A pdb=" N ALA O 12 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU O 14 " --> pdb=" O LYS O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 25 removed outlier: 4.007A pdb=" N LEU O 20 " --> pdb=" O LYS O 16 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 36 removed outlier: 3.700A pdb=" N TYR O 34 " --> pdb=" O SER O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 45 removed outlier: 3.874A pdb=" N GLY O 44 " --> pdb=" O GLN O 41 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN O 45 " --> pdb=" O GLN O 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 41 through 45' Processing helix chain 'O' and resid 48 through 56 Processing helix chain 'O' and resid 58 through 69 removed outlier: 3.608A pdb=" N HIS O 68 " --> pdb=" O LEU O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 98 Processing helix chain 'O' and resid 100 through 111 removed outlier: 3.679A pdb=" N VAL O 104 " --> pdb=" O HIS O 100 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU O 106 " --> pdb=" O GLU O 102 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER O 109 " --> pdb=" O LYS O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 132 Processing helix chain 'O' and resid 133 through 143 removed outlier: 3.506A pdb=" N VAL O 141 " --> pdb=" O VAL O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 162 Processing helix chain 'O' and resid 166 through 176 removed outlier: 3.752A pdb=" N ARG O 171 " --> pdb=" O THR O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 197 removed outlier: 3.591A pdb=" N ALA O 197 " --> pdb=" O PHE O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 199 through 210 removed outlier: 3.530A pdb=" N ARG O 210 " --> pdb=" O LEU O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 228 Processing helix chain 'O' and resid 232 through 241 removed outlier: 3.553A pdb=" N SER O 240 " --> pdb=" O GLU O 236 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS O 241 " --> pdb=" O LEU O 237 " (cutoff:3.500A) Processing helix chain 'O' and resid 245 through 260 removed outlier: 3.690A pdb=" N LEU O 253 " --> pdb=" O ARG O 249 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA O 258 " --> pdb=" O GLU O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 268 through 284 removed outlier: 3.561A pdb=" N THR O 272 " --> pdb=" O ASP O 268 " (cutoff:3.500A) Processing helix chain 'O' and resid 285 through 287 No H-bonds generated for 'chain 'O' and resid 285 through 287' Processing helix chain 'O' and resid 312 through 317 removed outlier: 3.913A pdb=" N SER O 316 " --> pdb=" O GLN O 312 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE O 317 " --> pdb=" O GLU O 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 312 through 317' Processing helix chain 'O' and resid 320 through 337 removed outlier: 3.661A pdb=" N LEU O 324 " --> pdb=" O ASP O 320 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL O 331 " --> pdb=" O GLU O 327 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG O 332 " --> pdb=" O GLY O 328 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE O 335 " --> pdb=" O VAL O 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 357 Proline residue: O 346 - end of helix removed outlier: 3.645A pdb=" N GLY O 351 " --> pdb=" O ILE O 347 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 377 removed outlier: 4.177A pdb=" N HIS O 369 " --> pdb=" O LYS O 365 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA O 370 " --> pdb=" O LEU O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 381 through 399 removed outlier: 3.519A pdb=" N ILE O 396 " --> pdb=" O PHE O 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 428 removed outlier: 3.563A pdb=" N LEU O 411 " --> pdb=" O ILE O 407 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS O 426 " --> pdb=" O MET O 422 " (cutoff:3.500A) Processing helix chain 'O' and resid 432 through 457 Processing helix chain 'O' and resid 460 through 478 Processing helix chain 'O' and resid 486 through 493 removed outlier: 3.524A pdb=" N ALA O 491 " --> pdb=" O LEU O 487 " (cutoff:3.500A) Processing helix chain 'O' and resid 502 through 507 removed outlier: 3.606A pdb=" N VAL O 506 " --> pdb=" O HIS O 502 " (cutoff:3.500A) Processing helix chain 'O' and resid 511 through 520 removed outlier: 3.839A pdb=" N ASP O 520 " --> pdb=" O LYS O 516 " (cutoff:3.500A) Processing helix chain 'O' and resid 534 through 541 Processing helix chain 'O' and resid 548 through 562 removed outlier: 3.765A pdb=" N ILE O 557 " --> pdb=" O HIS O 553 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER O 558 " --> pdb=" O SER O 554 " (cutoff:3.500A) Processing helix chain 'O' and resid 582 through 592 removed outlier: 3.541A pdb=" N LEU O 588 " --> pdb=" O VAL O 584 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 removed outlier: 3.550A pdb=" N GLY P 6 " --> pdb=" O GLU P 2 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA P 12 " --> pdb=" O VAL P 8 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU P 14 " --> pdb=" O LYS P 10 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY P 15 " --> pdb=" O ALA P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 25 Processing helix chain 'P' and resid 28 through 36 removed outlier: 3.697A pdb=" N ARG P 33 " --> pdb=" O GLU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 57 Processing helix chain 'P' and resid 58 through 67 removed outlier: 3.569A pdb=" N VAL P 62 " --> pdb=" O HIS P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 98 removed outlier: 3.569A pdb=" N ALA P 98 " --> pdb=" O CYS P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 111 removed outlier: 3.670A pdb=" N VAL P 108 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER P 109 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 132 removed outlier: 3.664A pdb=" N ALA P 127 " --> pdb=" O THR P 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 133 through 144 Processing helix chain 'P' and resid 156 through 164 removed outlier: 3.562A pdb=" N LYS P 164 " --> pdb=" O ILE P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 174 Processing helix chain 'P' and resid 199 through 209 Processing helix chain 'P' and resid 221 through 229 removed outlier: 3.509A pdb=" N SER P 229 " --> pdb=" O VAL P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 240 removed outlier: 3.908A pdb=" N LEU P 237 " --> pdb=" O ASP P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 245 through 262 removed outlier: 4.009A pdb=" N GLU P 251 " --> pdb=" O ARG P 247 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU P 253 " --> pdb=" O ARG P 249 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER P 259 " --> pdb=" O LEU P 255 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE P 260 " --> pdb=" O LEU P 256 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA P 261 " --> pdb=" O GLY P 257 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN P 262 " --> pdb=" O ALA P 258 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 284 removed outlier: 3.583A pdb=" N PHE P 284 " --> pdb=" O MET P 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 317 Processing helix chain 'P' and resid 320 through 337 Processing helix chain 'P' and resid 343 through 357 removed outlier: 3.988A pdb=" N ILE P 347 " --> pdb=" O VAL P 343 " (cutoff:3.500A) Processing helix chain 'P' and resid 359 through 377 removed outlier: 3.611A pdb=" N ILE P 364 " --> pdb=" O PHE P 360 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS P 365 " --> pdb=" O GLU P 361 " (cutoff:3.500A) Processing helix chain 'P' and resid 381 through 398 removed outlier: 3.541A pdb=" N ALA P 389 " --> pdb=" O LEU P 385 " (cutoff:3.500A) Processing helix chain 'P' and resid 403 through 428 Processing helix chain 'P' and resid 432 through 457 removed outlier: 3.704A pdb=" N ALA P 436 " --> pdb=" O ASP P 432 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR P 449 " --> pdb=" O TYR P 445 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 478 removed outlier: 3.599A pdb=" N ILE P 471 " --> pdb=" O ILE P 467 " (cutoff:3.500A) Processing helix chain 'P' and resid 488 through 492 Processing helix chain 'P' and resid 502 through 507 removed outlier: 4.135A pdb=" N VAL P 506 " --> pdb=" O HIS P 502 " (cutoff:3.500A) Processing helix chain 'P' and resid 511 through 522 removed outlier: 3.521A pdb=" N LEU P 518 " --> pdb=" O VAL P 514 " (cutoff:3.500A) Processing helix chain 'P' and resid 534 through 542 removed outlier: 3.573A pdb=" N ILE P 539 " --> pdb=" O ALA P 535 " (cutoff:3.500A) Processing helix chain 'P' and resid 543 through 548 removed outlier: 3.660A pdb=" N SER P 547 " --> pdb=" O ASN P 543 " (cutoff:3.500A) Processing helix chain 'P' and resid 548 through 554 removed outlier: 3.840A pdb=" N LEU P 552 " --> pdb=" O ASP P 548 " (cutoff:3.500A) Processing helix chain 'P' and resid 555 through 560 Processing helix chain 'S' and resid 42 through 52 Processing helix chain 'S' and resid 53 through 58 removed outlier: 3.525A pdb=" N GLN S 58 " --> pdb=" O GLU S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 75 removed outlier: 3.536A pdb=" N GLY S 64 " --> pdb=" O GLU S 60 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP S 66 " --> pdb=" O GLU S 62 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS S 67 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN S 70 " --> pdb=" O ASP S 66 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA S 73 " --> pdb=" O THR S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 89 Processing helix chain 'S' and resid 90 through 100 removed outlier: 4.167A pdb=" N GLN S 95 " --> pdb=" O PRO S 91 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET S 96 " --> pdb=" O PRO S 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 removed outlier: 3.506A pdb=" N LEU C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.536A pdb=" N ASP C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 removed outlier: 3.727A pdb=" N LEU C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.753A pdb=" N THR C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 8 removed outlier: 3.868A pdb=" N UNK Q 8 " --> pdb=" O UNK Q 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 8 removed outlier: 4.092A pdb=" N UNK R 8 " --> pdb=" O UNK R 5 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 510 through 512 removed outlier: 6.893A pdb=" N TYR E 510 " --> pdb=" O ALA I 31 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TRP I 33 " --> pdb=" O TYR E 510 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU E 512 " --> pdb=" O TRP I 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 510 through 512 removed outlier: 6.893A pdb=" N TYR E 510 " --> pdb=" O ALA I 31 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TRP I 33 " --> pdb=" O TYR E 510 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU E 512 " --> pdb=" O TRP I 33 " (cutoff:3.500A) removed outlier: 12.871A pdb=" N ASN I 28 " --> pdb=" O TYR E 558 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N TYR E 558 " --> pdb=" O ASN I 28 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL I 30 " --> pdb=" O LEU E 556 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 593 through 594 Processing sheet with id=AA4, first strand: chain 'E' and resid 693 through 694 removed outlier: 3.505A pdb=" N LEU E 694 " --> pdb=" O TYR E 741 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AA6, first strand: chain 'F' and resid 21 through 22 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA8, first strand: chain 'H' and resid 13 through 14 Processing sheet with id=AA9, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AB1, first strand: chain 'K' and resid 512 through 513 removed outlier: 6.321A pdb=" N LEU K 512 " --> pdb=" O TRP N 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 650 through 652 removed outlier: 6.901A pdb=" N VAL K 574 " --> pdb=" O PHE K 651 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA K 575 " --> pdb=" O VAL K 564 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL K 564 " --> pdb=" O ALA K 575 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 623 through 625 Processing sheet with id=AB4, first strand: chain 'K' and resid 731 through 733 Processing sheet with id=AB5, first strand: chain 'L' and resid 60 through 61 removed outlier: 6.214A pdb=" N GLU L 28 " --> pdb=" O THR M 13 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE M 15 " --> pdb=" O GLU L 28 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE L 30 " --> pdb=" O PHE M 15 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N ASP M 17 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N LYS L 32 " --> pdb=" O ASP M 17 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 41 through 42 removed outlier: 3.525A pdb=" N ASN N 47 " --> pdb=" O CYS N 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 70 through 71 removed outlier: 3.598A pdb=" N PHE N 79 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 77 through 80 Processing sheet with id=AB9, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.714A pdb=" N GLN A 45 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 79 through 80 removed outlier: 3.603A pdb=" N ILE O 86 " --> pdb=" O VAL O 79 " (cutoff:3.500A) 1940 hydrogen bonds defined for protein. 5748 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: 7.97 Time building geometry restraints manager: 4.49 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: 12336 1.34 - 1.46: 8128 1.46 - 1.58: 16565 1.58 - 1.70: 0 1.70 - 1.82: 358 Bond restraints: 37387 Sorted by residual: bond pdb=" C LEU E 308 " pdb=" N PRO E 309 " ideal model delta sigma weight residual 1.337 1.370 -0.033 9.80e-03 1.04e+04 1.14e+01 bond pdb=" CA PRO O 297 " pdb=" C PRO O 297 " ideal model delta sigma weight residual 1.514 1.500 0.014 5.50e-03 3.31e+04 6.64e+00 bond pdb=" CB ASN K 712 " pdb=" CG ASN K 712 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.02e+00 bond pdb=" CA GLN E 604 " pdb=" C GLN E 604 " ideal model delta sigma weight residual 1.523 1.543 -0.021 1.49e-02 4.50e+03 1.92e+00 bond pdb=" CA GLN E 604 " pdb=" CB GLN E 604 " ideal model delta sigma weight residual 1.533 1.554 -0.021 1.66e-02 3.63e+03 1.54e+00 ... (remaining 37382 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 49596 1.68 - 3.36: 808 3.36 - 5.05: 140 5.05 - 6.73: 56 6.73 - 8.41: 15 Bond angle restraints: 50615 Sorted by residual: angle pdb=" N VAL O 103 " pdb=" CA VAL O 103 " pdb=" C VAL O 103 " ideal model delta sigma weight residual 112.96 108.79 4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" C SER A 596 " pdb=" N LEU A 597 " pdb=" CA LEU A 597 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C THR A 189 " pdb=" N ALA A 190 " pdb=" CA ALA A 190 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.45e+01 angle pdb=" N VAL P 492 " pdb=" CA VAL P 492 " pdb=" C VAL P 492 " ideal model delta sigma weight residual 113.71 110.26 3.45 9.50e-01 1.11e+00 1.32e+01 angle pdb=" C ILE A 616 " pdb=" CA ILE A 616 " pdb=" CB ILE A 616 " ideal model delta sigma weight residual 109.89 113.75 -3.86 1.08e+00 8.57e-01 1.28e+01 ... (remaining 50610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 20101 17.82 - 35.63: 2103 35.63 - 53.45: 333 53.45 - 71.27: 102 71.27 - 89.08: 46 Dihedral angle restraints: 22685 sinusoidal: 8904 harmonic: 13781 Sorted by residual: dihedral pdb=" CA MET A 595 " pdb=" C MET A 595 " pdb=" N SER A 596 " pdb=" CA SER A 596 " ideal model delta harmonic sigma weight residual 180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ALA A 195 " pdb=" C ALA A 195 " pdb=" N GLU A 196 " pdb=" CA GLU A 196 " ideal model delta harmonic sigma weight residual 180.00 157.45 22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LYS A 598 " pdb=" C LYS A 598 " pdb=" N CYS A 599 " pdb=" CA CYS A 599 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 22682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4564 0.048 - 0.096: 1022 0.096 - 0.145: 162 0.145 - 0.193: 17 0.193 - 0.241: 2 Chirality restraints: 5767 Sorted by residual: chirality pdb=" CB VAL P 39 " pdb=" CA VAL P 39 " pdb=" CG1 VAL P 39 " pdb=" CG2 VAL P 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB VAL A 39 " pdb=" CA VAL A 39 " pdb=" CG1 VAL A 39 " pdb=" CG2 VAL A 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB VAL L 31 " pdb=" CA VAL L 31 " pdb=" CG1 VAL L 31 " pdb=" CG2 VAL L 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 5764 not shown) Planarity restraints: 6546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG M 68 " 0.051 5.00e-02 4.00e+02 7.71e-02 9.52e+00 pdb=" N PRO M 69 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO M 69 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO M 69 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 616 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO A 617 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR O 123 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO O 124 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO O 124 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO O 124 " -0.032 5.00e-02 4.00e+02 ... (remaining 6543 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 438 2.62 - 3.19: 32849 3.19 - 3.76: 63081 3.76 - 4.33: 81352 4.33 - 4.90: 128555 Nonbonded interactions: 306275 Sorted by model distance: nonbonded pdb=" OD1 ASP N 97 " pdb="ZN ZN N 202 " model vdw 2.047 2.230 nonbonded pdb=" OD1 ASP I 97 " pdb="ZN ZN I 202 " model vdw 2.124 2.230 nonbonded pdb=" OH TYR E 219 " pdb=" OE2 GLU E 246 " model vdw 2.152 3.040 nonbonded pdb=" O THR O 73 " pdb=" OG1 THR O 90 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR A 569 " pdb=" O PHE A 626 " model vdw 2.214 3.040 ... (remaining 306270 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 523 or (resid 524 through 531 and (name N or nam \ e CA or name C or name O or name CB )) or resid 532 or (resid 533 through 562 an \ d (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and (resid 1 through 523 or (resid 524 through 531 and (name N or nam \ e CA or name C or name O or name CB )) or resid 532 or (resid 533 through 562 an \ d (name N or name CA or name C or name O or name CB )))) selection = (chain 'O' and (resid 1 through 523 or (resid 524 through 531 and (name N or nam \ e CA or name C or name O or name CB )) or resid 532 or (resid 533 through 562 an \ d (name N or name CA or name C or name O or name CB )))) selection = chain 'P' } ncs_group { reference = (chain 'B' and ((resid 66 through 76 and (name N or name CA or name C or name O \ or name CB )) or resid 77 or (resid 78 through 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 or (resid 85 through 88 and (name N or na \ me CA or name C or name O or name CB )) or resid 89 or (resid 90 through 100 and \ (name N or name CA or name C or name O or name CB )) or resid 101 or (resid 102 \ through 125 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and resid 41 through 100) selection = (chain 'G' and ((resid 66 through 76 and (name N or name CA or name C or name O \ or name CB )) or resid 77 or (resid 78 through 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 or (resid 85 through 88 and (name N or na \ me CA or name C or name O or name CB )) or resid 89 or (resid 90 through 100 and \ (name N or name CA or name C or name O or name CB )) or resid 101 or (resid 102 \ through 125 and (name N or name CA or name C or name O or name CB )))) selection = chain 'S' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = (chain 'E' and (resid 1 through 115 or resid 135 through 744)) selection = (chain 'K' 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 'F' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'M' } 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: 23.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.050 Extract box with map and model: 0.780 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 42.410 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 37409 Z= 0.120 Angle : 0.575 8.410 50627 Z= 0.305 Chirality : 0.040 0.241 5767 Planarity : 0.004 0.077 6546 Dihedral : 15.328 89.083 13729 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.12), residues: 4608 helix: -0.46 (0.09), residues: 2754 sheet: -1.90 (0.49), residues: 104 loop : -1.19 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 387 TYR 0.025 0.001 TYR J 7 PHE 0.030 0.001 PHE J 388 TRP 0.012 0.001 TRP O 367 HIS 0.004 0.001 HIS O 434 Details of bonding type rmsd covalent geometry : bond 0.00233 (37387) covalent geometry : angle 0.57323 (50615) hydrogen bonds : bond 0.24321 ( 1940) hydrogen bonds : angle 7.29354 ( 5748) metal coordination : bond 0.00820 ( 22) metal coordination : angle 2.71066 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: E 18 LEU cc_start: 0.8734 (tp) cc_final: 0.8362 (tt) REVERT: E 151 MET cc_start: 0.9265 (tpt) cc_final: 0.9031 (tpp) REVERT: E 294 MET cc_start: 0.8781 (ttm) cc_final: 0.8500 (ttm) REVERT: E 358 LEU cc_start: 0.9224 (mt) cc_final: 0.8998 (mt) REVERT: E 576 MET cc_start: 0.8809 (mpp) cc_final: 0.7715 (mpp) REVERT: E 650 LYS cc_start: 0.9541 (pttp) cc_final: 0.9327 (tptt) REVERT: E 688 MET cc_start: 0.8614 (mmm) cc_final: 0.8381 (mmm) REVERT: H 6 MET cc_start: 0.6394 (tmm) cc_final: 0.6137 (tmm) REVERT: K 39 PHE cc_start: 0.8908 (t80) cc_final: 0.8396 (t80) REVERT: K 96 LYS cc_start: 0.9702 (mmtt) cc_final: 0.9479 (tppp) REVERT: K 101 MET cc_start: 0.9304 (mmm) cc_final: 0.8941 (mmm) REVERT: K 137 MET cc_start: 0.8564 (ptp) cc_final: 0.8273 (ptp) REVERT: K 138 GLU cc_start: 0.8491 (pt0) cc_final: 0.8282 (mp0) REVERT: K 282 CYS cc_start: 0.8355 (t) cc_final: 0.6640 (t) REVERT: K 311 MET cc_start: 0.9017 (ttt) cc_final: 0.8457 (tpp) REVERT: K 476 MET cc_start: 0.9200 (mtp) cc_final: 0.8902 (mtm) REVERT: K 479 ASP cc_start: 0.8995 (m-30) cc_final: 0.8508 (t0) REVERT: K 678 MET cc_start: 0.9216 (tpt) cc_final: 0.8990 (tpp) REVERT: K 695 ARG cc_start: 0.9341 (ptp90) cc_final: 0.9117 (ptp90) REVERT: K 697 ASN cc_start: 0.9510 (t0) cc_final: 0.9234 (t0) REVERT: L 112 CYS cc_start: 0.8289 (m) cc_final: 0.8045 (m) REVERT: J 300 HIS cc_start: 0.8602 (t70) cc_final: 0.8169 (p90) REVERT: J 371 LEU cc_start: 0.9393 (tp) cc_final: 0.9157 (pp) REVERT: A 64 LEU cc_start: 0.8712 (mm) cc_final: 0.8341 (tp) REVERT: A 70 ARG cc_start: 0.5621 (mmp80) cc_final: 0.4192 (tmm-80) REVERT: A 130 PHE cc_start: 0.9150 (t80) cc_final: 0.8929 (t80) REVERT: A 204 LYS cc_start: 0.9498 (tppp) cc_final: 0.9259 (tptp) REVERT: A 236 GLU cc_start: 0.8957 (tt0) cc_final: 0.8737 (tm-30) REVERT: A 326 MET cc_start: 0.9033 (mmt) cc_final: 0.8124 (mmt) REVERT: A 530 ASN cc_start: 0.8972 (m-40) cc_final: 0.8669 (m110) REVERT: B 87 GLU cc_start: 0.8289 (pm20) cc_final: 0.7840 (pm20) REVERT: B 88 LYS cc_start: 0.8927 (tttt) cc_final: 0.8671 (ttpt) REVERT: O 358 MET cc_start: 0.6872 (mmp) cc_final: 0.6072 (ptp) REVERT: O 386 LEU cc_start: 0.7014 (tp) cc_final: 0.6588 (pp) REVERT: P 220 MET cc_start: 0.6003 (mtm) cc_final: 0.5193 (mmt) REVERT: P 280 MET cc_start: 0.5577 (mmp) cc_final: 0.5130 (tpp) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.2539 time to fit residues: 194.8160 Evaluate side-chains 259 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 ASN ** K 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 320 HIS K 658 GLN ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN N 104 GLN ** J 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 GLN A 553 HIS A 613 GLN O 380 ASN O 443 ASN O 476 HIS O 489 HIS O 495 ASN P 42 GLN ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 420 GLN ** P 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.075865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.053245 restraints weight = 255052.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.053369 restraints weight = 171185.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.053097 restraints weight = 121504.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.053397 restraints weight = 115514.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.053582 restraints weight = 97738.565| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 37409 Z= 0.268 Angle : 0.684 10.569 50627 Z= 0.363 Chirality : 0.042 0.195 5767 Planarity : 0.005 0.065 6546 Dihedral : 4.407 25.877 5057 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.47 % Favored : 94.51 % Rotamer: Outliers : 0.20 % Allowed : 6.55 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.12), residues: 4608 helix: 0.24 (0.09), residues: 2870 sheet: -2.11 (0.47), residues: 121 loop : -1.09 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 321 TYR 0.027 0.002 TYR A 7 PHE 0.022 0.002 PHE K 431 TRP 0.017 0.002 TRP N 27 HIS 0.015 0.001 HIS P 476 Details of bonding type rmsd covalent geometry : bond 0.00560 (37387) covalent geometry : angle 0.68088 (50615) hydrogen bonds : bond 0.05154 ( 1940) hydrogen bonds : angle 5.02883 ( 5748) metal coordination : bond 0.02240 ( 22) metal coordination : angle 4.31919 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 310 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 ASP cc_start: 0.8681 (t0) cc_final: 0.8441 (t0) REVERT: E 162 MET cc_start: 0.8980 (ppp) cc_final: 0.8678 (ppp) REVERT: E 233 SER cc_start: 0.8974 (m) cc_final: 0.8694 (t) REVERT: E 311 MET cc_start: 0.9196 (ttp) cc_final: 0.8908 (ttm) REVERT: E 576 MET cc_start: 0.8767 (mpp) cc_final: 0.7893 (mmm) REVERT: E 581 GLN cc_start: 0.8924 (mt0) cc_final: 0.8437 (mm-40) REVERT: E 688 MET cc_start: 0.9005 (mmm) cc_final: 0.8560 (mmm) REVERT: F 45 MET cc_start: 0.9248 (mmm) cc_final: 0.8693 (mmm) REVERT: I 40 ASP cc_start: 0.8102 (t70) cc_final: 0.7872 (t0) REVERT: K 476 MET cc_start: 0.9261 (mtp) cc_final: 0.8806 (mtm) REVERT: K 479 ASP cc_start: 0.8536 (m-30) cc_final: 0.8308 (m-30) REVERT: K 539 MET cc_start: 0.8809 (mmp) cc_final: 0.8579 (mmm) REVERT: K 576 MET cc_start: 0.8497 (mmp) cc_final: 0.8084 (mmm) REVERT: K 657 MET cc_start: 0.7922 (pmm) cc_final: 0.7713 (pmm) REVERT: K 678 MET cc_start: 0.9259 (tpt) cc_final: 0.9036 (tpp) REVERT: K 688 MET cc_start: 0.5857 (tmm) cc_final: 0.5492 (tmm) REVERT: K 697 ASN cc_start: 0.9433 (t0) cc_final: 0.8938 (t0) REVERT: J 300 HIS cc_start: 0.8623 (t70) cc_final: 0.8248 (p90) REVERT: J 371 LEU cc_start: 0.9544 (tp) cc_final: 0.9230 (pp) REVERT: A 64 LEU cc_start: 0.8853 (mm) cc_final: 0.8467 (tp) REVERT: A 70 ARG cc_start: 0.5416 (mmp80) cc_final: 0.3980 (ttp80) REVERT: A 76 THR cc_start: 0.9020 (p) cc_final: 0.8818 (p) REVERT: A 130 PHE cc_start: 0.9190 (t80) cc_final: 0.8976 (t80) REVERT: A 326 MET cc_start: 0.8950 (mmt) cc_final: 0.8036 (mmt) REVERT: A 422 MET cc_start: 0.9353 (ttm) cc_final: 0.9033 (mtp) REVERT: A 530 ASN cc_start: 0.8965 (m-40) cc_final: 0.8677 (m110) REVERT: A 586 GLU cc_start: 0.9026 (pp20) cc_final: 0.8314 (pp20) REVERT: A 590 LYS cc_start: 0.9532 (mttp) cc_final: 0.9280 (mtmm) REVERT: B 86 TYR cc_start: 0.7429 (m-10) cc_final: 0.7043 (m-80) REVERT: O 326 MET cc_start: 0.5788 (tmm) cc_final: 0.5479 (tpt) REVERT: O 386 LEU cc_start: 0.7271 (tp) cc_final: 0.6883 (pp) REVERT: O 476 HIS cc_start: 0.8589 (OUTLIER) cc_final: 0.8176 (m-70) REVERT: P 220 MET cc_start: 0.7048 (mtm) cc_final: 0.6053 (mmt) REVERT: P 280 MET cc_start: 0.5706 (mmp) cc_final: 0.5216 (tpp) REVERT: P 367 TRP cc_start: 0.8461 (m-10) cc_final: 0.8232 (m-10) outliers start: 8 outliers final: 2 residues processed: 318 average time/residue: 0.2378 time to fit residues: 125.7279 Evaluate side-chains 235 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 232 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 150 optimal weight: 1.9990 chunk 176 optimal weight: 0.0030 chunk 437 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 413 optimal weight: 40.0000 chunk 363 optimal weight: 0.0170 chunk 212 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 345 optimal weight: 20.0000 chunk 201 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 overall best weight: 1.6032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN E 317 ASN ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 ASN ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 HIS ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 310 HIS K 701 GLN ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** J 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 HIS A 439 ASN A 608 ASN O 504 ASN O 511 ASN P 420 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.076815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.054226 restraints weight = 255575.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.055143 restraints weight = 160111.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.054579 restraints weight = 101455.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.054917 restraints weight = 112080.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.055067 restraints weight = 93520.539| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37409 Z= 0.169 Angle : 0.586 10.511 50627 Z= 0.308 Chirality : 0.040 0.184 5767 Planarity : 0.004 0.064 6546 Dihedral : 4.353 25.606 5057 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.12), residues: 4608 helix: 0.43 (0.09), residues: 2880 sheet: -1.74 (0.52), residues: 102 loop : -1.10 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 68 TYR 0.030 0.001 TYR O 440 PHE 0.041 0.001 PHE O 388 TRP 0.016 0.001 TRP N 27 HIS 0.010 0.001 HIS O 489 Details of bonding type rmsd covalent geometry : bond 0.00357 (37387) covalent geometry : angle 0.58119 (50615) hydrogen bonds : bond 0.04621 ( 1940) hydrogen bonds : angle 4.72182 ( 5748) metal coordination : bond 0.01330 ( 22) metal coordination : angle 5.04807 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 162 MET cc_start: 0.8825 (ppp) cc_final: 0.8563 (ppp) REVERT: E 233 SER cc_start: 0.8963 (m) cc_final: 0.8687 (t) REVERT: E 476 MET cc_start: 0.8877 (mtm) cc_final: 0.8650 (mtm) REVERT: E 581 GLN cc_start: 0.8929 (mt0) cc_final: 0.8435 (mm-40) REVERT: E 688 MET cc_start: 0.9014 (mmm) cc_final: 0.8527 (mmm) REVERT: I 40 ASP cc_start: 0.8083 (t70) cc_final: 0.7865 (t0) REVERT: I 46 ARG cc_start: 0.8872 (tpp-160) cc_final: 0.8563 (tpp-160) REVERT: K 137 MET cc_start: 0.8499 (ptp) cc_final: 0.8212 (ptp) REVERT: K 270 MET cc_start: 0.9069 (ptp) cc_final: 0.8521 (ptt) REVERT: K 476 MET cc_start: 0.9117 (mtp) cc_final: 0.8776 (mtm) REVERT: K 479 ASP cc_start: 0.8500 (m-30) cc_final: 0.8270 (m-30) REVERT: K 539 MET cc_start: 0.8819 (mmp) cc_final: 0.8559 (mmm) REVERT: K 576 MET cc_start: 0.8492 (mmp) cc_final: 0.8109 (mmm) REVERT: K 678 MET cc_start: 0.9222 (tpt) cc_final: 0.8974 (tpp) REVERT: K 688 MET cc_start: 0.5719 (tmm) cc_final: 0.5484 (tmm) REVERT: K 695 ARG cc_start: 0.9266 (ptt-90) cc_final: 0.8940 (ttp80) REVERT: L 98 GLU cc_start: 0.8270 (pp20) cc_final: 0.8000 (pp20) REVERT: J 280 MET cc_start: -0.2273 (tmm) cc_final: -0.2613 (tmm) REVERT: J 300 HIS cc_start: 0.8626 (t70) cc_final: 0.8261 (p90) REVERT: J 371 LEU cc_start: 0.9530 (tp) cc_final: 0.9226 (pp) REVERT: J 395 MET cc_start: 0.9052 (ptm) cc_final: 0.8652 (ppp) REVERT: A 64 LEU cc_start: 0.8975 (mm) cc_final: 0.8494 (tp) REVERT: A 70 ARG cc_start: 0.5260 (mmp80) cc_final: 0.3907 (ttp80) REVERT: A 130 PHE cc_start: 0.9215 (t80) cc_final: 0.8995 (t80) REVERT: A 326 MET cc_start: 0.8877 (mmt) cc_final: 0.7950 (mmt) REVERT: A 422 MET cc_start: 0.9279 (ttm) cc_final: 0.9018 (mtp) REVERT: A 530 ASN cc_start: 0.8924 (m-40) cc_final: 0.8627 (m110) REVERT: A 593 MET cc_start: 0.8655 (mtm) cc_final: 0.8442 (mtt) REVERT: O 326 MET cc_start: 0.5917 (tmm) cc_final: 0.5661 (tpt) REVERT: O 358 MET cc_start: 0.6592 (mmp) cc_final: 0.5861 (ptp) REVERT: P 220 MET cc_start: 0.7077 (mtm) cc_final: 0.6076 (mmt) REVERT: P 280 MET cc_start: 0.5740 (mmp) cc_final: 0.5254 (tpp) REVERT: P 326 MET cc_start: 0.9338 (ptp) cc_final: 0.9044 (mmm) REVERT: P 397 HIS cc_start: 0.9416 (t70) cc_final: 0.9170 (t-90) outliers start: 1 outliers final: 1 residues processed: 307 average time/residue: 0.2315 time to fit residues: 119.3542 Evaluate side-chains 228 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 86 optimal weight: 8.9990 chunk 231 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 272 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 456 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 HIS ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN N 104 GLN J 110 HIS ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 HIS O 476 HIS O 511 ASN P 420 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.077378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.056216 restraints weight = 254391.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.056179 restraints weight = 147762.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.055671 restraints weight = 120614.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.055898 restraints weight = 121375.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.056619 restraints weight = 102001.048| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37409 Z= 0.141 Angle : 0.566 8.527 50627 Z= 0.295 Chirality : 0.039 0.169 5767 Planarity : 0.004 0.061 6546 Dihedral : 4.293 26.756 5057 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.12), residues: 4608 helix: 0.57 (0.10), residues: 2878 sheet: -1.71 (0.52), residues: 102 loop : -1.09 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 475 TYR 0.027 0.001 TYR K 544 PHE 0.024 0.001 PHE J 388 TRP 0.037 0.002 TRP P 93 HIS 0.010 0.001 HIS J 325 Details of bonding type rmsd covalent geometry : bond 0.00300 (37387) covalent geometry : angle 0.56257 (50615) hydrogen bonds : bond 0.04165 ( 1940) hydrogen bonds : angle 4.53282 ( 5748) metal coordination : bond 0.00883 ( 22) metal coordination : angle 3.80604 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 233 SER cc_start: 0.8899 (m) cc_final: 0.8641 (t) REVERT: E 246 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8050 (tp30) REVERT: E 576 MET cc_start: 0.8697 (mpp) cc_final: 0.8097 (mpp) REVERT: E 688 MET cc_start: 0.8985 (mmm) cc_final: 0.8502 (mmm) REVERT: F 45 MET cc_start: 0.9059 (mmm) cc_final: 0.8182 (mmm) REVERT: F 64 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6932 (mt-10) REVERT: I 40 ASP cc_start: 0.8042 (t70) cc_final: 0.7836 (t0) REVERT: I 46 ARG cc_start: 0.8839 (tpp-160) cc_final: 0.8543 (tpp-160) REVERT: K 270 MET cc_start: 0.9036 (ptp) cc_final: 0.8434 (ptt) REVERT: K 479 ASP cc_start: 0.8248 (m-30) cc_final: 0.8033 (m-30) REVERT: K 539 MET cc_start: 0.8742 (mmp) cc_final: 0.8534 (mmm) REVERT: K 576 MET cc_start: 0.8382 (mmp) cc_final: 0.8053 (mmm) REVERT: K 657 MET cc_start: 0.7972 (pmm) cc_final: 0.7768 (pmm) REVERT: K 688 MET cc_start: 0.5663 (tmm) cc_final: 0.5458 (tmm) REVERT: K 695 ARG cc_start: 0.9289 (ptt-90) cc_final: 0.8917 (ttp80) REVERT: K 697 ASN cc_start: 0.9552 (m-40) cc_final: 0.9352 (m-40) REVERT: L 98 GLU cc_start: 0.8256 (pp20) cc_final: 0.7970 (pp20) REVERT: J 300 HIS cc_start: 0.8637 (t70) cc_final: 0.8262 (p90) REVERT: J 371 LEU cc_start: 0.9483 (tp) cc_final: 0.9179 (pp) REVERT: A 64 LEU cc_start: 0.8989 (mm) cc_final: 0.8537 (tp) REVERT: A 70 ARG cc_start: 0.5108 (mmp80) cc_final: 0.3920 (ttp80) REVERT: A 130 PHE cc_start: 0.9155 (t80) cc_final: 0.8920 (t80) REVERT: A 326 MET cc_start: 0.8832 (mmt) cc_final: 0.7907 (mmt) REVERT: A 553 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.8028 (t-90) REVERT: A 590 LYS cc_start: 0.9424 (mttp) cc_final: 0.9076 (mtmm) REVERT: O 326 MET cc_start: 0.5994 (tmm) cc_final: 0.5749 (tpt) REVERT: O 358 MET cc_start: 0.6539 (mmp) cc_final: 0.5794 (ptp) REVERT: P 220 MET cc_start: 0.6959 (mtm) cc_final: 0.5940 (mmt) REVERT: P 280 MET cc_start: 0.5639 (mmp) cc_final: 0.5203 (tpp) REVERT: P 326 MET cc_start: 0.9319 (ptp) cc_final: 0.9045 (mmm) REVERT: P 395 MET cc_start: 0.6600 (ptm) cc_final: 0.6387 (ptm) REVERT: P 397 HIS cc_start: 0.9349 (t70) cc_final: 0.9089 (t-90) outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.2271 time to fit residues: 121.1566 Evaluate side-chains 231 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 150 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 340 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 405 optimal weight: 0.0980 chunk 89 optimal weight: 8.9990 chunk 268 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 HIS E 234 GLN ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 HIS ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 ASN A 74 GLN ** O 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 420 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.076954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.055133 restraints weight = 254759.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.054926 restraints weight = 167918.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.054974 restraints weight = 132269.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.055370 restraints weight = 107850.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.055683 restraints weight = 91842.806| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37409 Z= 0.162 Angle : 0.570 7.703 50627 Z= 0.298 Chirality : 0.040 0.280 5767 Planarity : 0.004 0.060 6546 Dihedral : 4.268 25.905 5057 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.73 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.12), residues: 4608 helix: 0.68 (0.10), residues: 2878 sheet: -1.75 (0.50), residues: 102 loop : -1.09 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 475 TYR 0.034 0.001 TYR A 7 PHE 0.017 0.001 PHE J 549 TRP 0.026 0.002 TRP P 367 HIS 0.019 0.001 HIS J 325 Details of bonding type rmsd covalent geometry : bond 0.00346 (37387) covalent geometry : angle 0.56831 (50615) hydrogen bonds : bond 0.04017 ( 1940) hydrogen bonds : angle 4.47928 ( 5748) metal coordination : bond 0.01112 ( 22) metal coordination : angle 3.21781 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 688 MET cc_start: 0.8951 (mmm) cc_final: 0.8510 (mmm) REVERT: F 64 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6760 (mt-10) REVERT: I 46 ARG cc_start: 0.8783 (tpp-160) cc_final: 0.8446 (tpp-160) REVERT: K 270 MET cc_start: 0.8888 (ptp) cc_final: 0.8551 (ttp) REVERT: K 294 MET cc_start: 0.8983 (mtm) cc_final: 0.8703 (mtp) REVERT: K 297 MET cc_start: 0.8209 (ppp) cc_final: 0.7996 (ppp) REVERT: K 476 MET cc_start: 0.8845 (mtp) cc_final: 0.8481 (mtm) REVERT: K 479 ASP cc_start: 0.8024 (m-30) cc_final: 0.7620 (t0) REVERT: K 576 MET cc_start: 0.8184 (mmp) cc_final: 0.7897 (mmm) REVERT: K 688 MET cc_start: 0.5819 (tmm) cc_final: 0.5610 (tmm) REVERT: K 695 ARG cc_start: 0.9166 (ptt-90) cc_final: 0.8831 (ttp80) REVERT: K 697 ASN cc_start: 0.9478 (m-40) cc_final: 0.9256 (m-40) REVERT: J 300 HIS cc_start: 0.8654 (t70) cc_final: 0.8300 (p90) REVERT: J 371 LEU cc_start: 0.9427 (tp) cc_final: 0.9146 (pp) REVERT: J 395 MET cc_start: 0.8976 (ppp) cc_final: 0.8488 (ppp) REVERT: J 550 LEU cc_start: 0.9055 (tp) cc_final: 0.8821 (tp) REVERT: A 64 LEU cc_start: 0.8898 (mm) cc_final: 0.8506 (tp) REVERT: A 70 ARG cc_start: 0.5045 (mmp80) cc_final: 0.3910 (ttp80) REVERT: A 130 PHE cc_start: 0.9108 (t80) cc_final: 0.8864 (t80) REVERT: A 326 MET cc_start: 0.8729 (mmt) cc_final: 0.7929 (mmt) REVERT: A 590 LYS cc_start: 0.9340 (mttp) cc_final: 0.9128 (mtmm) REVERT: B 83 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7271 (tp-100) REVERT: B 92 HIS cc_start: 0.7460 (m90) cc_final: 0.7147 (m170) REVERT: G 119 PHE cc_start: 0.7140 (t80) cc_final: 0.6778 (t80) REVERT: O 159 MET cc_start: -0.0252 (mmp) cc_final: -0.0564 (mmp) REVERT: O 358 MET cc_start: 0.6549 (mmp) cc_final: 0.5863 (ptp) REVERT: P 220 MET cc_start: 0.6894 (mtm) cc_final: 0.5870 (mmt) REVERT: P 280 MET cc_start: 0.5609 (mmp) cc_final: 0.5086 (mtp) REVERT: P 326 MET cc_start: 0.9306 (ptp) cc_final: 0.9043 (mmm) REVERT: P 395 MET cc_start: 0.6640 (ptm) cc_final: 0.6327 (ptm) REVERT: P 397 HIS cc_start: 0.9331 (t70) cc_final: 0.9068 (t-90) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2304 time to fit residues: 116.2106 Evaluate side-chains 225 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 140 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 336 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 444 optimal weight: 30.0000 chunk 372 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 237 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 234 GLN ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 HIS ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS O 511 ASN ** P 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 420 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.077826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.059865 restraints weight = 255179.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.057790 restraints weight = 156161.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.058348 restraints weight = 138516.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.058299 restraints weight = 110272.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.058329 restraints weight = 105608.686| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37409 Z= 0.150 Angle : 0.562 7.386 50627 Z= 0.295 Chirality : 0.040 0.318 5767 Planarity : 0.004 0.061 6546 Dihedral : 4.275 25.898 5057 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.12), residues: 4608 helix: 0.74 (0.10), residues: 2872 sheet: -1.92 (0.48), residues: 112 loop : -1.12 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 475 TYR 0.020 0.001 TYR O 472 PHE 0.018 0.001 PHE E 651 TRP 0.021 0.002 TRP P 367 HIS 0.009 0.001 HIS L 68 Details of bonding type rmsd covalent geometry : bond 0.00324 (37387) covalent geometry : angle 0.56043 (50615) hydrogen bonds : bond 0.03873 ( 1940) hydrogen bonds : angle 4.43237 ( 5748) metal coordination : bond 0.01034 ( 22) metal coordination : angle 2.82038 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 688 MET cc_start: 0.8775 (mmm) cc_final: 0.8420 (mmm) REVERT: I 46 ARG cc_start: 0.8739 (tpp-160) cc_final: 0.8397 (tpp-160) REVERT: K 270 MET cc_start: 0.8775 (ptp) cc_final: 0.8399 (ttp) REVERT: K 294 MET cc_start: 0.8912 (mtm) cc_final: 0.8670 (mtp) REVERT: K 297 MET cc_start: 0.8093 (ppp) cc_final: 0.7887 (ppp) REVERT: K 451 MET cc_start: 0.7471 (tpp) cc_final: 0.7255 (mmm) REVERT: K 479 ASP cc_start: 0.7789 (m-30) cc_final: 0.7451 (t0) REVERT: K 688 MET cc_start: 0.5799 (tmm) cc_final: 0.5582 (tmm) REVERT: K 695 ARG cc_start: 0.9143 (ptt-90) cc_final: 0.8804 (ttp80) REVERT: N 36 ASP cc_start: 0.8060 (t70) cc_final: 0.7354 (t0) REVERT: J 300 HIS cc_start: 0.8691 (t70) cc_final: 0.8281 (p90) REVERT: J 371 LEU cc_start: 0.9332 (tp) cc_final: 0.9096 (pp) REVERT: J 395 MET cc_start: 0.8951 (ppp) cc_final: 0.8510 (ppp) REVERT: J 550 LEU cc_start: 0.9095 (tp) cc_final: 0.8888 (tp) REVERT: A 64 LEU cc_start: 0.8878 (mm) cc_final: 0.8485 (tp) REVERT: A 326 MET cc_start: 0.8652 (mmt) cc_final: 0.7889 (mmt) REVERT: B 83 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7181 (tp-100) REVERT: G 83 GLN cc_start: 0.7530 (pt0) cc_final: 0.7222 (pt0) REVERT: G 119 PHE cc_start: 0.7086 (t80) cc_final: 0.6746 (t80) REVERT: O 358 MET cc_start: 0.6512 (mmp) cc_final: 0.5844 (ptp) REVERT: O 386 LEU cc_start: 0.7327 (tp) cc_final: 0.7070 (pp) REVERT: P 220 MET cc_start: 0.6629 (mtm) cc_final: 0.5610 (mmt) REVERT: P 280 MET cc_start: 0.5592 (mmp) cc_final: 0.5240 (tpp) REVERT: P 326 MET cc_start: 0.9215 (ptp) cc_final: 0.8996 (mmm) REVERT: P 395 MET cc_start: 0.6773 (ptm) cc_final: 0.6421 (ptm) REVERT: P 397 HIS cc_start: 0.9214 (t70) cc_final: 0.8973 (t-90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2203 time to fit residues: 111.9979 Evaluate side-chains 219 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 361 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 308 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 295 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 434 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 388 optimal weight: 0.9990 chunk 326 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 234 GLN E 377 ASN I 48 HIS ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 511 ASN ** P 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 420 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.078363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.060516 restraints weight = 255421.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.058272 restraints weight = 153686.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.058740 restraints weight = 134243.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.058707 restraints weight = 108924.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.058857 restraints weight = 104970.992| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37409 Z= 0.125 Angle : 0.559 13.913 50627 Z= 0.289 Chirality : 0.039 0.162 5767 Planarity : 0.004 0.062 6546 Dihedral : 4.232 26.334 5057 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.36 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.12), residues: 4608 helix: 0.76 (0.10), residues: 2881 sheet: -1.88 (0.47), residues: 112 loop : -1.06 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.017 0.001 TYR O 472 PHE 0.032 0.001 PHE O 485 TRP 0.041 0.002 TRP P 367 HIS 0.006 0.001 HIS O 489 Details of bonding type rmsd covalent geometry : bond 0.00269 (37387) covalent geometry : angle 0.55184 (50615) hydrogen bonds : bond 0.03718 ( 1940) hydrogen bonds : angle 4.34563 ( 5748) metal coordination : bond 0.01420 ( 22) metal coordination : angle 5.94921 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.613 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: E 11 ASP cc_start: 0.8446 (t70) cc_final: 0.8218 (t0) REVERT: E 39 PHE cc_start: 0.8273 (m-80) cc_final: 0.8050 (m-80) REVERT: E 246 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8163 (mm-30) REVERT: E 576 MET cc_start: 0.9178 (mmp) cc_final: 0.8312 (mmp) REVERT: F 45 MET cc_start: 0.9379 (mmm) cc_final: 0.8722 (mmm) REVERT: F 75 MET cc_start: 0.9224 (mtp) cc_final: 0.8980 (mtp) REVERT: F 105 MET cc_start: 0.8646 (mmt) cc_final: 0.8431 (mmm) REVERT: I 40 ASP cc_start: 0.7932 (t70) cc_final: 0.7731 (t0) REVERT: I 46 ARG cc_start: 0.8772 (tpp-160) cc_final: 0.8376 (tpp-160) REVERT: K 146 MET cc_start: 0.8067 (mmm) cc_final: 0.7833 (mmp) REVERT: K 270 MET cc_start: 0.8932 (ptp) cc_final: 0.8232 (ptt) REVERT: K 294 MET cc_start: 0.9114 (mtm) cc_final: 0.8835 (mtp) REVERT: K 297 MET cc_start: 0.8398 (ppp) cc_final: 0.7972 (ppp) REVERT: K 451 MET cc_start: 0.7788 (tpp) cc_final: 0.7467 (mmm) REVERT: K 479 ASP cc_start: 0.8284 (m-30) cc_final: 0.7861 (t0) REVERT: K 539 MET cc_start: 0.8872 (mmp) cc_final: 0.8602 (mmm) REVERT: K 576 MET cc_start: 0.8149 (mmp) cc_final: 0.7901 (mmm) REVERT: K 688 MET cc_start: 0.5728 (tmm) cc_final: 0.5520 (tmm) REVERT: K 695 ARG cc_start: 0.9273 (ptt-90) cc_final: 0.8834 (ttp80) REVERT: K 697 ASN cc_start: 0.9490 (m-40) cc_final: 0.9262 (m110) REVERT: L 112 CYS cc_start: 0.8368 (m) cc_final: 0.7967 (t) REVERT: J 300 HIS cc_start: 0.8713 (t70) cc_final: 0.8259 (p90) REVERT: J 371 LEU cc_start: 0.9464 (tp) cc_final: 0.9180 (pp) REVERT: J 395 MET cc_start: 0.9092 (ppp) cc_final: 0.8629 (ppp) REVERT: J 550 LEU cc_start: 0.9100 (tp) cc_final: 0.8878 (tp) REVERT: A 64 LEU cc_start: 0.8881 (mm) cc_final: 0.8482 (tp) REVERT: A 326 MET cc_start: 0.8880 (mmt) cc_final: 0.8046 (mmt) REVERT: A 586 GLU cc_start: 0.8972 (pp20) cc_final: 0.8679 (tm-30) REVERT: A 593 MET cc_start: 0.8714 (mtm) cc_final: 0.8483 (mtt) REVERT: B 83 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7306 (tp-100) REVERT: G 83 GLN cc_start: 0.7686 (pt0) cc_final: 0.7271 (pt0) REVERT: G 119 PHE cc_start: 0.6968 (t80) cc_final: 0.6615 (t80) REVERT: O 358 MET cc_start: 0.6564 (mmp) cc_final: 0.5938 (ptp) REVERT: O 386 LEU cc_start: 0.7421 (tp) cc_final: 0.7172 (pp) REVERT: P 220 MET cc_start: 0.6776 (mtm) cc_final: 0.5724 (mmt) REVERT: P 280 MET cc_start: 0.5613 (mmp) cc_final: 0.5214 (tpp) REVERT: P 326 MET cc_start: 0.9297 (ptp) cc_final: 0.9036 (mmm) REVERT: P 395 MET cc_start: 0.6631 (ptm) cc_final: 0.6261 (ptm) REVERT: P 397 HIS cc_start: 0.9285 (t70) cc_final: 0.9049 (t-90) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2259 time to fit residues: 111.0285 Evaluate side-chains 223 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 374 optimal weight: 20.0000 chunk 250 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 198 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 0.1980 chunk 230 optimal weight: 1.9990 chunk 454 optimal weight: 8.9990 chunk 254 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 234 GLN I 48 HIS ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 511 ASN P 42 GLN ** P 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 420 GLN P 502 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.078684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.060560 restraints weight = 255117.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.058058 restraints weight = 153034.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.058599 restraints weight = 137587.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.058510 restraints weight = 112387.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.058664 restraints weight = 108837.334| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 37409 Z= 0.115 Angle : 0.562 14.456 50627 Z= 0.288 Chirality : 0.039 0.207 5767 Planarity : 0.004 0.062 6546 Dihedral : 4.192 21.917 5057 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.13), residues: 4608 helix: 0.85 (0.10), residues: 2881 sheet: -1.86 (0.45), residues: 122 loop : -1.09 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 46 TYR 0.034 0.001 TYR A 7 PHE 0.028 0.001 PHE J 392 TRP 0.017 0.002 TRP E 91 HIS 0.005 0.001 HIS P 476 Details of bonding type rmsd covalent geometry : bond 0.00244 (37387) covalent geometry : angle 0.55415 (50615) hydrogen bonds : bond 0.03575 ( 1940) hydrogen bonds : angle 4.26986 ( 5748) metal coordination : bond 0.02296 ( 22) metal coordination : angle 6.13334 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 576 MET cc_start: 0.9182 (mmp) cc_final: 0.8563 (mmp) REVERT: I 40 ASP cc_start: 0.7966 (t70) cc_final: 0.7753 (t0) REVERT: I 46 ARG cc_start: 0.8760 (tpp-160) cc_final: 0.8362 (tpp-160) REVERT: K 146 MET cc_start: 0.7949 (mmm) cc_final: 0.7711 (mmp) REVERT: K 270 MET cc_start: 0.8852 (ptp) cc_final: 0.8161 (ptt) REVERT: K 294 MET cc_start: 0.8985 (mtm) cc_final: 0.8766 (mtp) REVERT: K 297 MET cc_start: 0.8340 (ppp) cc_final: 0.8132 (ppp) REVERT: K 479 ASP cc_start: 0.7983 (m-30) cc_final: 0.7595 (t0) REVERT: K 539 MET cc_start: 0.8792 (mmp) cc_final: 0.8484 (mmm) REVERT: K 576 MET cc_start: 0.8062 (mmp) cc_final: 0.7818 (mmm) REVERT: K 605 MET cc_start: 0.7882 (ppp) cc_final: 0.7595 (ppp) REVERT: K 695 ARG cc_start: 0.9210 (ptt-90) cc_final: 0.8810 (ttp80) REVERT: L 112 CYS cc_start: 0.8291 (m) cc_final: 0.7869 (t) REVERT: J 300 HIS cc_start: 0.8694 (t70) cc_final: 0.8225 (p90) REVERT: J 371 LEU cc_start: 0.9422 (tp) cc_final: 0.9150 (pp) REVERT: J 395 MET cc_start: 0.9031 (ppp) cc_final: 0.8603 (ppp) REVERT: J 550 LEU cc_start: 0.9096 (tp) cc_final: 0.8865 (tp) REVERT: A 64 LEU cc_start: 0.8975 (mm) cc_final: 0.8441 (tp) REVERT: A 326 MET cc_start: 0.8681 (mmt) cc_final: 0.7950 (mmt) REVERT: A 586 GLU cc_start: 0.8811 (pp20) cc_final: 0.8453 (tm-30) REVERT: A 598 LYS cc_start: 0.6951 (ptpt) cc_final: 0.6713 (mtmm) REVERT: B 83 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7690 (tp-100) REVERT: G 83 GLN cc_start: 0.7533 (pt0) cc_final: 0.7323 (pt0) REVERT: G 119 PHE cc_start: 0.7012 (t80) cc_final: 0.6645 (t80) REVERT: O 159 MET cc_start: -0.0499 (mmp) cc_final: -0.0979 (mmp) REVERT: O 358 MET cc_start: 0.6585 (mmp) cc_final: 0.5973 (ptp) REVERT: O 386 LEU cc_start: 0.7459 (tp) cc_final: 0.7213 (pp) REVERT: P 220 MET cc_start: 0.6812 (mtm) cc_final: 0.5758 (mmt) REVERT: P 280 MET cc_start: 0.5600 (mmp) cc_final: 0.5195 (tpp) REVERT: P 326 MET cc_start: 0.9300 (ptp) cc_final: 0.9051 (mmm) REVERT: P 395 MET cc_start: 0.6711 (ptm) cc_final: 0.6406 (ptm) REVERT: P 397 HIS cc_start: 0.9299 (t70) cc_final: 0.9086 (t-90) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.2219 time to fit residues: 108.9847 Evaluate side-chains 221 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 380 optimal weight: 20.0000 chunk 233 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 337 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 350 optimal weight: 30.0000 chunk 249 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 234 GLN E 320 HIS I 48 HIS ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 511 ASN ** P 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 420 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.076881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.055493 restraints weight = 255210.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.055471 restraints weight = 145682.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.055177 restraints weight = 105740.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.055524 restraints weight = 118373.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.055711 restraints weight = 92774.945| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 37409 Z= 0.175 Angle : 0.597 11.673 50627 Z= 0.308 Chirality : 0.040 0.235 5767 Planarity : 0.004 0.063 6546 Dihedral : 4.204 23.323 5057 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.75 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.13), residues: 4608 helix: 0.85 (0.10), residues: 2882 sheet: -1.78 (0.47), residues: 112 loop : -1.11 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 37 TYR 0.020 0.001 TYR L 76 PHE 0.022 0.002 PHE N 79 TRP 0.016 0.002 TRP P 209 HIS 0.006 0.001 HIS K 310 Details of bonding type rmsd covalent geometry : bond 0.00374 (37387) covalent geometry : angle 0.59098 (50615) hydrogen bonds : bond 0.03651 ( 1940) hydrogen bonds : angle 4.36729 ( 5748) metal coordination : bond 0.02120 ( 22) metal coordination : angle 5.67249 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 576 MET cc_start: 0.9203 (mmp) cc_final: 0.8586 (mmp) REVERT: I 46 ARG cc_start: 0.8781 (tpp-160) cc_final: 0.8421 (tpp-160) REVERT: K 146 MET cc_start: 0.8203 (mmm) cc_final: 0.7947 (mmp) REVERT: K 270 MET cc_start: 0.8949 (ptp) cc_final: 0.8251 (ptt) REVERT: K 294 MET cc_start: 0.9101 (mtm) cc_final: 0.8810 (mtt) REVERT: K 297 MET cc_start: 0.8527 (ppp) cc_final: 0.8215 (ppp) REVERT: K 566 MET cc_start: 0.6563 (pmm) cc_final: 0.6234 (pmm) REVERT: K 576 MET cc_start: 0.8200 (mmp) cc_final: 0.7855 (mmm) REVERT: K 695 ARG cc_start: 0.9215 (ptt-90) cc_final: 0.8914 (ttp80) REVERT: K 701 GLN cc_start: 0.9323 (mp10) cc_final: 0.9082 (mp10) REVERT: L 112 CYS cc_start: 0.8234 (m) cc_final: 0.8009 (t) REVERT: J 300 HIS cc_start: 0.8722 (t70) cc_final: 0.8251 (p90) REVERT: J 371 LEU cc_start: 0.9466 (tp) cc_final: 0.9205 (pp) REVERT: J 395 MET cc_start: 0.9060 (ppp) cc_final: 0.8621 (ppp) REVERT: J 550 LEU cc_start: 0.9188 (tp) cc_final: 0.8980 (tp) REVERT: A 64 LEU cc_start: 0.8975 (mm) cc_final: 0.8436 (tp) REVERT: A 326 MET cc_start: 0.8784 (mmt) cc_final: 0.7971 (mmt) REVERT: A 586 GLU cc_start: 0.8836 (pp20) cc_final: 0.8459 (tm-30) REVERT: B 83 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7702 (tp-100) REVERT: G 83 GLN cc_start: 0.7489 (pt0) cc_final: 0.7288 (pt0) REVERT: G 119 PHE cc_start: 0.7018 (t80) cc_final: 0.6654 (t80) REVERT: O 358 MET cc_start: 0.6501 (mmp) cc_final: 0.5834 (ptp) REVERT: O 386 LEU cc_start: 0.7499 (tp) cc_final: 0.7245 (pp) REVERT: P 220 MET cc_start: 0.6813 (mtm) cc_final: 0.5767 (mmt) REVERT: P 280 MET cc_start: 0.5600 (mmp) cc_final: 0.5162 (tpp) REVERT: P 326 MET cc_start: 0.9311 (ptp) cc_final: 0.9058 (mmm) REVERT: P 397 HIS cc_start: 0.9245 (t70) cc_final: 0.9030 (t-90) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1863 time to fit residues: 89.5531 Evaluate side-chains 217 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 179 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 339 optimal weight: 30.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 234 GLN I 48 HIS ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 511 ASN P 241 HIS ** P 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 420 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.077431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.056017 restraints weight = 254920.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.056026 restraints weight = 146209.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.055929 restraints weight = 112458.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.056315 restraints weight = 106225.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.056731 restraints weight = 86585.065| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37409 Z= 0.134 Angle : 0.591 12.020 50627 Z= 0.302 Chirality : 0.040 0.240 5767 Planarity : 0.004 0.062 6546 Dihedral : 4.221 24.676 5057 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.13), residues: 4608 helix: 0.85 (0.10), residues: 2886 sheet: -1.81 (0.47), residues: 112 loop : -1.12 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 475 TYR 0.022 0.001 TYR F 76 PHE 0.023 0.001 PHE J 388 TRP 0.017 0.002 TRP J 93 HIS 0.006 0.001 HIS I 48 Details of bonding type rmsd covalent geometry : bond 0.00291 (37387) covalent geometry : angle 0.58562 (50615) hydrogen bonds : bond 0.03549 ( 1940) hydrogen bonds : angle 4.31222 ( 5748) metal coordination : bond 0.01708 ( 22) metal coordination : angle 5.40249 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 1.341 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: E 438 MET cc_start: 0.8877 (tpp) cc_final: 0.8676 (tpp) REVERT: E 576 MET cc_start: 0.9208 (mmp) cc_final: 0.8354 (mmp) REVERT: F 45 MET cc_start: 0.9216 (mmm) cc_final: 0.8698 (mmm) REVERT: F 64 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6765 (mt-10) REVERT: F 105 MET cc_start: 0.8510 (mmt) cc_final: 0.8299 (mmm) REVERT: I 46 ARG cc_start: 0.8764 (tpp-160) cc_final: 0.8386 (tpp-160) REVERT: K 146 MET cc_start: 0.8142 (mmm) cc_final: 0.7853 (mmp) REVERT: K 236 MET cc_start: 0.8935 (ptm) cc_final: 0.8563 (ptm) REVERT: K 270 MET cc_start: 0.8928 (ptp) cc_final: 0.8303 (ptt) REVERT: K 294 MET cc_start: 0.9058 (mtm) cc_final: 0.8729 (mtt) REVERT: K 297 MET cc_start: 0.8482 (ppp) cc_final: 0.8232 (ppp) REVERT: K 479 ASP cc_start: 0.8102 (m-30) cc_final: 0.7882 (m-30) REVERT: K 566 MET cc_start: 0.6571 (pmm) cc_final: 0.6235 (pmm) REVERT: K 576 MET cc_start: 0.8191 (mmp) cc_final: 0.7819 (mmm) REVERT: K 605 MET cc_start: 0.7800 (ppp) cc_final: 0.7498 (ppp) REVERT: K 695 ARG cc_start: 0.9147 (ptt-90) cc_final: 0.8834 (ttp80) REVERT: K 697 ASN cc_start: 0.9422 (m110) cc_final: 0.9055 (m-40) REVERT: K 701 GLN cc_start: 0.9294 (mp10) cc_final: 0.9082 (mp10) REVERT: L 112 CYS cc_start: 0.8139 (m) cc_final: 0.7762 (t) REVERT: J 300 HIS cc_start: 0.8707 (t70) cc_final: 0.8208 (p90) REVERT: J 371 LEU cc_start: 0.9454 (tp) cc_final: 0.9194 (pp) REVERT: J 395 MET cc_start: 0.9051 (ppp) cc_final: 0.8623 (ppp) REVERT: J 550 LEU cc_start: 0.9028 (tp) cc_final: 0.8805 (tp) REVERT: A 64 LEU cc_start: 0.8949 (mm) cc_final: 0.8427 (tp) REVERT: A 326 MET cc_start: 0.8755 (mmt) cc_final: 0.8007 (mmt) REVERT: A 586 GLU cc_start: 0.8804 (pp20) cc_final: 0.8441 (tm-30) REVERT: B 83 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7709 (tp-100) REVERT: G 119 PHE cc_start: 0.7043 (t80) cc_final: 0.6663 (t80) REVERT: O 358 MET cc_start: 0.6552 (mmp) cc_final: 0.5908 (ptp) REVERT: O 386 LEU cc_start: 0.7490 (tp) cc_final: 0.7249 (pp) REVERT: P 220 MET cc_start: 0.6785 (mtm) cc_final: 0.5690 (mmt) REVERT: P 280 MET cc_start: 0.5579 (mmp) cc_final: 0.5140 (tpp) REVERT: P 326 MET cc_start: 0.9303 (ptp) cc_final: 0.9059 (mmm) REVERT: P 397 HIS cc_start: 0.9237 (t70) cc_final: 0.9027 (t-90) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1808 time to fit residues: 87.1938 Evaluate side-chains 222 residues out of total 4087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 76 optimal weight: 3.9990 chunk 427 optimal weight: 4.9990 chunk 385 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 276 optimal weight: 4.9990 chunk 443 optimal weight: 0.0070 chunk 362 optimal weight: 5.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 234 GLN ** I 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN ** O 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 511 ASN ** P 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 420 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.077370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.055200 restraints weight = 254384.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.055577 restraints weight = 155680.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.055481 restraints weight = 104643.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.055779 restraints weight = 109715.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.055935 restraints weight = 91307.784| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 0.066 37409 Z= 0.136 Angle : 0.587 10.543 50627 Z= 0.301 Chirality : 0.040 0.156 5767 Planarity : 0.004 0.062 6546 Dihedral : 4.222 25.417 5057 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.13), residues: 4608 helix: 0.88 (0.10), residues: 2902 sheet: -1.79 (0.46), residues: 112 loop : -1.10 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 33 TYR 0.019 0.001 TYR F 79 PHE 0.024 0.001 PHE J 388 TRP 0.017 0.002 TRP J 93 HIS 0.006 0.001 HIS O 489 Details of bonding type rmsd covalent geometry : bond 0.00295 (37387) covalent geometry : angle 0.58238 (50615) hydrogen bonds : bond 0.03529 ( 1940) hydrogen bonds : angle 4.29561 ( 5748) metal coordination : bond 0.01732 ( 22) metal coordination : angle 5.02090 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7392.08 seconds wall clock time: 129 minutes 13.08 seconds (7753.08 seconds total)