Starting phenix.real_space_refine on Tue Aug 26 10:49:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ioz_60750/08_2025/9ioz_60750.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ioz_60750/08_2025/9ioz_60750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ioz_60750/08_2025/9ioz_60750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ioz_60750/08_2025/9ioz_60750.map" model { file = "/net/cci-nas-00/data/ceres_data/9ioz_60750/08_2025/9ioz_60750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ioz_60750/08_2025/9ioz_60750.cif" } resolution = 3.9 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 23215 2.51 5 N 6044 2.21 5 O 7076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s 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: 36407 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2379 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 278} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2379 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 278} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2379 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 278} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1609 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "E" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1609 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1609 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "G" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1609 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "H" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1609 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "I" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1609 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "J" Number of atoms: 6536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6536 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 31, 'TRANS': 784} Chain breaks: 2 Chain: "K" Number of atoms: 6536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6536 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 31, 'TRANS': 784} Chain breaks: 2 Chain: "L" Number of atoms: 6544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6544 Classifications: {'peptide': 817} Link IDs: {'PTRANS': 31, 'TRANS': 785} Chain breaks: 2 Time building chain proxies: 7.72, per 1000 atoms: 0.21 Number of scatterers: 36407 At special positions: 0 Unit cell: (133.9, 139.1, 197.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 7076 8.00 N 6044 7.00 C 23215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8492 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 55 sheets defined 16.6% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.619A pdb=" N ASP A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 76 through 82 removed outlier: 3.628A pdb=" N ASP B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 76 through 82 removed outlier: 3.650A pdb=" N ASP C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'D' and resid 58 through 75 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.524A pdb=" N TYR D 86 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 75 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'G' and resid 58 through 75 Processing helix chain 'H' and resid 58 through 75 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 58 through 75 Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 85 through 94 Processing helix chain 'J' and resid 174 through 180 Processing helix chain 'J' and resid 196 through 202 removed outlier: 3.545A pdb=" N GLN J 200 " --> pdb=" O ARG J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 218 removed outlier: 3.784A pdb=" N TYR J 218 " --> pdb=" O ILE J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 249 Processing helix chain 'J' and resid 258 through 263 removed outlier: 3.528A pdb=" N ALA J 261 " --> pdb=" O ASN J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 325 Processing helix chain 'J' and resid 337 through 344 removed outlier: 3.568A pdb=" N LEU J 341 " --> pdb=" O THR J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 389 Processing helix chain 'J' and resid 392 through 399 removed outlier: 3.558A pdb=" N ASN J 396 " --> pdb=" O PHE J 392 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 469 removed outlier: 3.930A pdb=" N LEU J 464 " --> pdb=" O GLY J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 483 through 495 Processing helix chain 'J' and resid 502 through 506 Processing helix chain 'J' and resid 508 through 513 removed outlier: 3.953A pdb=" N GLY J 513 " --> pdb=" O TRP J 509 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 549 Processing helix chain 'J' and resid 574 through 579 removed outlier: 3.637A pdb=" N THR J 578 " --> pdb=" O ASN J 574 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR J 579 " --> pdb=" O PHE J 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 574 through 579' Processing helix chain 'J' and resid 587 through 592 removed outlier: 4.036A pdb=" N LYS J 592 " --> pdb=" O THR J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 603 through 606 removed outlier: 3.611A pdb=" N SER J 606 " --> pdb=" O PRO J 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 603 through 606' Processing helix chain 'J' and resid 616 through 624 Processing helix chain 'J' and resid 639 through 657 removed outlier: 3.626A pdb=" N SER J 657 " --> pdb=" O LYS J 653 " (cutoff:3.500A) Processing helix chain 'J' and resid 665 through 669 Processing helix chain 'J' and resid 712 through 718 removed outlier: 4.522A pdb=" N PHE J 716 " --> pdb=" O GLY J 712 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN J 718 " --> pdb=" O ASP J 714 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 85 through 94 Processing helix chain 'K' and resid 174 through 180 Processing helix chain 'K' and resid 195 through 201 removed outlier: 4.373A pdb=" N TYR K 199 " --> pdb=" O LYS K 195 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN K 200 " --> pdb=" O ARG K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 removed outlier: 3.792A pdb=" N TYR K 218 " --> pdb=" O ILE K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 249 Processing helix chain 'K' and resid 258 through 263 removed outlier: 3.561A pdb=" N ALA K 261 " --> pdb=" O ASN K 258 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE K 263 " --> pdb=" O ALA K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 325 Processing helix chain 'K' and resid 337 through 344 removed outlier: 3.533A pdb=" N LEU K 341 " --> pdb=" O THR K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 389 Processing helix chain 'K' and resid 392 through 399 removed outlier: 3.623A pdb=" N ASN K 396 " --> pdb=" O PHE K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 469 removed outlier: 4.096A pdb=" N LEU K 464 " --> pdb=" O GLY K 460 " (cutoff:3.500A) Processing helix chain 'K' and resid 483 through 495 Processing helix chain 'K' and resid 502 through 506 removed outlier: 3.585A pdb=" N GLN K 506 " --> pdb=" O THR K 503 " (cutoff:3.500A) Processing helix chain 'K' and resid 508 through 513 removed outlier: 3.812A pdb=" N GLY K 513 " --> pdb=" O TRP K 509 " (cutoff:3.500A) Processing helix chain 'K' and resid 536 through 549 Processing helix chain 'K' and resid 574 through 579 removed outlier: 3.623A pdb=" N THR K 578 " --> pdb=" O ASN K 574 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR K 579 " --> pdb=" O PHE K 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 574 through 579' Processing helix chain 'K' and resid 587 through 592 removed outlier: 3.619A pdb=" N LYS K 592 " --> pdb=" O THR K 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 603 through 606 removed outlier: 3.761A pdb=" N SER K 606 " --> pdb=" O PRO K 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 603 through 606' Processing helix chain 'K' and resid 616 through 624 Processing helix chain 'K' and resid 639 through 657 removed outlier: 3.517A pdb=" N SER K 657 " --> pdb=" O LYS K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 665 through 669 Processing helix chain 'K' and resid 712 through 718 removed outlier: 4.402A pdb=" N PHE K 716 " --> pdb=" O GLY K 712 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN K 718 " --> pdb=" O ASP K 714 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 85 through 94 Processing helix chain 'L' and resid 174 through 180 Processing helix chain 'L' and resid 196 through 201 Processing helix chain 'L' and resid 210 through 218 removed outlier: 3.846A pdb=" N TYR L 218 " --> pdb=" O ILE L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 249 Processing helix chain 'L' and resid 258 through 263 removed outlier: 3.542A pdb=" N ALA L 261 " --> pdb=" O ASN L 258 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE L 263 " --> pdb=" O ALA L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 325 Processing helix chain 'L' and resid 337 through 344 removed outlier: 3.773A pdb=" N LEU L 341 " --> pdb=" O THR L 337 " (cutoff:3.500A) Processing helix chain 'L' and resid 380 through 389 Processing helix chain 'L' and resid 392 through 399 Processing helix chain 'L' and resid 460 through 469 removed outlier: 4.141A pdb=" N LEU L 464 " --> pdb=" O GLY L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 483 through 495 Processing helix chain 'L' and resid 502 through 506 Processing helix chain 'L' and resid 508 through 513 removed outlier: 3.853A pdb=" N GLY L 513 " --> pdb=" O TRP L 509 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 549 Processing helix chain 'L' and resid 574 through 579 removed outlier: 3.612A pdb=" N THR L 578 " --> pdb=" O ASN L 574 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TYR L 579 " --> pdb=" O PHE L 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 574 through 579' Processing helix chain 'L' and resid 603 through 606 removed outlier: 3.767A pdb=" N SER L 606 " --> pdb=" O PRO L 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 603 through 606' Processing helix chain 'L' and resid 616 through 624 Processing helix chain 'L' and resid 639 through 657 removed outlier: 3.722A pdb=" N SER L 657 " --> pdb=" O LYS L 653 " (cutoff:3.500A) Processing helix chain 'L' and resid 665 through 669 Processing helix chain 'L' and resid 712 through 718 removed outlier: 4.365A pdb=" N PHE L 716 " --> pdb=" O GLY L 712 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN L 718 " --> pdb=" O ASP L 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 15 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 18 through 20 current: chain 'A' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 62 through 68 current: chain 'A' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 90 through 92 current: chain 'A' and resid 117 through 131 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 117 through 131 current: chain 'A' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 177 through 178 current: chain 'A' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 213 through 227 current: chain 'A' and resid 256 through 270 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 15 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 20 current: chain 'B' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 64 through 68 current: chain 'B' and resid 117 through 131 removed outlier: 5.618A pdb=" N VAL B 124 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU B 143 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP B 128 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER B 130 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE B 137 " --> pdb=" O SER B 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 143 current: chain 'B' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 177 through 178 current: chain 'B' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 213 through 227 current: chain 'B' and resid 256 through 270 Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 39 Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 58 Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 15 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 20 current: chain 'C' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 90 through 92 current: chain 'C' and resid 117 through 131 removed outlier: 5.582A pdb=" N VAL C 124 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU C 143 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 126 " --> pdb=" O GLY C 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 143 current: chain 'C' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 177 through 178 current: chain 'C' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 213 through 227 current: chain 'C' and resid 256 through 270 removed outlier: 3.576A pdb=" N ILE C 281 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 29 removed outlier: 6.164A pdb=" N LEU C 25 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN C 68 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN C 27 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AB2, first strand: chain 'C' and resid 57 through 58 Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.679A pdb=" N ASN D 21 " --> pdb=" O ASN D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 48 through 53 current: chain 'D' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 197 through 202 current: chain 'F' and resid 193 through 194 Processing sheet with id=AB4, first strand: chain 'D' and resid 38 through 41 removed outlier: 3.661A pdb=" N LYS D 39 " --> pdb=" O ASP D 31 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP D 31 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N MET D 28 " --> pdb=" O GLY J 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 112 removed outlier: 3.505A pdb=" N LEU D 111 " --> pdb=" O TRP D 148 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SER D 143 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN D 149 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE D 141 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SER D 151 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 182 through 183 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 182 through 183 current: chain 'E' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 48 through 53 current: chain 'E' and resid 173 through 177 Processing sheet with id=AB7, first strand: chain 'E' and resid 28 through 32 Processing sheet with id=AB8, first strand: chain 'E' and resid 108 through 112 removed outlier: 3.557A pdb=" N SER E 151 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN E 140 " --> pdb=" O SER E 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 182 through 183 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 182 through 183 current: chain 'E' and resid 193 through 194 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 193 through 194 current: chain 'H' and resid 48 through 53 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 48 through 53 current: chain 'H' and resid 173 through 177 Processing sheet with id=AC1, first strand: chain 'F' and resid 79 through 81 removed outlier: 3.729A pdb=" N ASN F 25 " --> pdb=" O TYR F 47 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER F 53 " --> pdb=" O SER F 19 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER F 19 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL F 20 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 28 through 32 removed outlier: 8.334A pdb=" N LEU J 18 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU F 40 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR J 20 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS F 42 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N CYS J 22 " --> pdb=" O LYS F 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 38 through 42 current: chain 'J' and resid 77 through 82 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 77 through 82 current: chain 'J' and resid 128 through 129 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 128 through 129 current: chain 'J' and resid 152 through 154 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 152 through 154 current: chain 'K' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 659 through 664 current: chain 'K' and resid 690 through 698 removed outlier: 6.161A pdb=" N VAL K 707 " --> pdb=" O ASP K 694 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL K 696 " --> pdb=" O ASN K 705 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASN K 705 " --> pdb=" O VAL K 696 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 108 through 112 removed outlier: 6.873A pdb=" N VAL F 147 " --> pdb=" O SER F 143 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER F 143 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN F 149 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE F 141 " --> pdb=" O ASN F 149 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER F 151 " --> pdb=" O THR F 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 20 through 25 removed outlier: 3.842A pdb=" N ASN G 21 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN G 25 " --> pdb=" O TYR G 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 47 through 53 current: chain 'G' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 197 through 202 current: chain 'I' and resid 193 through 194 Processing sheet with id=AC5, first strand: chain 'G' and resid 38 through 41 removed outlier: 3.671A pdb=" N LYS G 39 " --> pdb=" O ASP G 31 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP G 31 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET G 28 " --> pdb=" O GLY L 150 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 108 through 112 removed outlier: 7.075A pdb=" N VAL G 147 " --> pdb=" O SER G 143 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER G 143 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASN G 149 " --> pdb=" O PHE G 141 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE G 141 " --> pdb=" O ASN G 149 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N SER G 151 " --> pdb=" O THR G 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.645A pdb=" N ASP H 31 " --> pdb=" O LYS H 39 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 39 " --> pdb=" O ASP H 31 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 108 through 112 removed outlier: 7.031A pdb=" N VAL H 147 " --> pdb=" O SER H 143 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER H 143 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASN H 149 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N PHE H 141 " --> pdb=" O ASN H 149 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER H 151 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 182 through 183 removed outlier: 3.643A pdb=" N PHE H 183 " --> pdb=" O ASP I 24 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER I 19 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER I 53 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN I 25 " --> pdb=" O TYR I 47 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP I 48 " --> pdb=" O GLU I 202 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU I 202 " --> pdb=" O TRP I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 28 through 32 removed outlier: 8.486A pdb=" N LEU L 18 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU I 40 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR L 20 " --> pdb=" O GLU I 40 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS I 42 " --> pdb=" O THR L 20 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N CYS L 22 " --> pdb=" O LYS I 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 38 through 42 current: chain 'L' and resid 128 through 129 Processing sheet with id=AD2, first strand: chain 'I' and resid 108 through 112 removed outlier: 3.561A pdb=" N SER I 151 " --> pdb=" O ASN I 140 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN I 140 " --> pdb=" O SER I 151 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 66 through 69 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 66 through 69 current: chain 'J' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 659 through 664 current: chain 'J' and resid 689 through 698 removed outlier: 6.182A pdb=" N VAL J 707 " --> pdb=" O ASP J 694 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL J 696 " --> pdb=" O ASN J 705 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN J 705 " --> pdb=" O VAL J 696 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 704 through 710 current: chain 'L' and resid 77 through 82 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 77 through 82 current: chain 'L' and resid 152 through 154 Processing sheet with id=AD4, first strand: chain 'J' and resid 226 through 228 Processing sheet with id=AD5, first strand: chain 'J' and resid 265 through 267 Processing sheet with id=AD6, first strand: chain 'J' and resid 270 through 274 removed outlier: 3.949A pdb=" N GLU J 436 " --> pdb=" O ASP J 306 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP J 306 " --> pdb=" O GLU J 436 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN J 438 " --> pdb=" O PHE J 304 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE J 304 " --> pdb=" O GLN J 438 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LYS J 440 " --> pdb=" O ASP J 302 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP J 302 " --> pdb=" O LYS J 440 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 276 through 282 removed outlier: 6.823A pdb=" N ALA J 295 " --> pdb=" O PRO J 277 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 550 through 551 removed outlier: 3.525A pdb=" N ALA J 551 " --> pdb=" O THR J 562 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 609 through 613 removed outlier: 6.168A pdb=" N SER J 595 " --> pdb=" O LEU J 630 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 785 through 788 removed outlier: 7.133A pdb=" N VAL J 817 " --> pdb=" O VAL J 772 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR J 774 " --> pdb=" O ARG J 815 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG J 815 " --> pdb=" O TYR J 774 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE J 776 " --> pdb=" O GLU J 813 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU J 813 " --> pdb=" O ILE J 776 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU J 829 " --> pdb=" O PHE J 812 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL J 827 " --> pdb=" O LEU J 814 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 19 through 25 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 40 through 42 current: chain 'K' and resid 128 through 129 Processing sheet with id=AE3, first strand: chain 'K' and resid 62 through 63 removed outlier: 3.677A pdb=" N SER K 62 " --> pdb=" O THR K 80 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 77 through 82 current: chain 'K' and resid 152 through 154 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 152 through 154 current: chain 'L' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 659 through 664 current: chain 'L' and resid 689 through 698 removed outlier: 6.440A pdb=" N VAL L 707 " --> pdb=" O ASP L 694 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL L 696 " --> pdb=" O ASN L 705 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN L 705 " --> pdb=" O VAL L 696 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 226 through 228 Processing sheet with id=AE5, first strand: chain 'K' and resid 265 through 267 Processing sheet with id=AE6, first strand: chain 'K' and resid 270 through 274 removed outlier: 3.514A pdb=" N GLU K 436 " --> pdb=" O LEU K 305 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY K 303 " --> pdb=" O GLN K 438 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 276 through 282 removed outlier: 6.868A pdb=" N ALA K 295 " --> pdb=" O PRO K 277 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE K 279 " --> pdb=" O VAL K 293 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 550 through 551 Processing sheet with id=AE9, first strand: chain 'K' and resid 609 through 613 removed outlier: 6.133A pdb=" N SER K 595 " --> pdb=" O LEU K 630 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 785 through 788 removed outlier: 3.583A pdb=" N TYR K 773 " --> pdb=" O VAL K 817 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 810 through 811 removed outlier: 3.513A pdb=" N VAL K 831 " --> pdb=" O ALA K 810 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 226 through 228 Processing sheet with id=AF4, first strand: chain 'L' and resid 265 through 267 Processing sheet with id=AF5, first strand: chain 'L' and resid 270 through 274 Processing sheet with id=AF6, first strand: chain 'L' and resid 276 through 282 removed outlier: 6.870A pdb=" N ALA L 295 " --> pdb=" O PRO L 277 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL L 290 " --> pdb=" O PHE L 421 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 550 through 551 Processing sheet with id=AF8, first strand: chain 'L' and resid 595 through 597 removed outlier: 6.162A pdb=" N SER L 595 " --> pdb=" O LEU L 630 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'L' and resid 600 through 601 Processing sheet with id=AG1, first strand: chain 'L' and resid 785 through 788 removed outlier: 3.754A pdb=" N ILE L 776 " --> pdb=" O TYR L 785 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL L 787 " --> pdb=" O TYR L 774 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU L 813 " --> pdb=" O ALA L 777 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL L 831 " --> pdb=" O ALA L 810 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1890 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: 7.23 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6146 1.31 - 1.44: 10279 1.44 - 1.56: 20698 1.56 - 1.69: 1 1.69 - 1.81: 123 Bond restraints: 37247 Sorted by residual: bond pdb=" CA ALA K 453 " pdb=" C ALA K 453 " ideal model delta sigma weight residual 1.522 1.448 0.074 9.30e-03 1.16e+04 6.37e+01 bond pdb=" CA ALA L 453 " pdb=" C ALA L 453 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.29e-02 6.01e+03 4.39e+01 bond pdb=" CA SER B 144 " pdb=" C SER B 144 " ideal model delta sigma weight residual 1.525 1.445 0.080 1.22e-02 6.72e+03 4.28e+01 bond pdb=" CA SER C 144 " pdb=" C SER C 144 " ideal model delta sigma weight residual 1.524 1.450 0.074 1.29e-02 6.01e+03 3.32e+01 bond pdb=" CA SER A 144 " pdb=" C SER A 144 " ideal model delta sigma weight residual 1.525 1.458 0.067 1.22e-02 6.72e+03 2.98e+01 ... (remaining 37242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 49063 2.53 - 5.06: 1281 5.06 - 7.58: 155 7.58 - 10.11: 40 10.11 - 12.64: 10 Bond angle restraints: 50549 Sorted by residual: angle pdb=" N SER C 144 " pdb=" CA SER C 144 " pdb=" C SER C 144 " ideal model delta sigma weight residual 112.41 123.39 -10.98 1.30e+00 5.92e-01 7.13e+01 angle pdb=" N SER A 144 " pdb=" CA SER A 144 " pdb=" C SER A 144 " ideal model delta sigma weight residual 112.30 122.26 -9.96 1.36e+00 5.41e-01 5.37e+01 angle pdb=" N ASP L 454 " pdb=" CA ASP L 454 " pdb=" C ASP L 454 " ideal model delta sigma weight residual 109.07 120.77 -11.70 1.61e+00 3.86e-01 5.28e+01 angle pdb=" N GLU J 760 " pdb=" CA GLU J 760 " pdb=" C GLU J 760 " ideal model delta sigma weight residual 111.54 101.68 9.86 1.36e+00 5.41e-01 5.26e+01 angle pdb=" N SER B 144 " pdb=" CA SER B 144 " pdb=" C SER B 144 " ideal model delta sigma weight residual 112.30 122.09 -9.79 1.36e+00 5.41e-01 5.18e+01 ... (remaining 50544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 20020 17.93 - 35.86: 1861 35.86 - 53.78: 283 53.78 - 71.71: 39 71.71 - 89.64: 17 Dihedral angle restraints: 22220 sinusoidal: 8933 harmonic: 13287 Sorted by residual: dihedral pdb=" N ASN L 758 " pdb=" C ASN L 758 " pdb=" CA ASN L 758 " pdb=" CB ASN L 758 " ideal model delta harmonic sigma weight residual 122.80 138.91 -16.11 0 2.50e+00 1.60e-01 4.15e+01 dihedral pdb=" C VAL L 120 " pdb=" N VAL L 120 " pdb=" CA VAL L 120 " pdb=" CB VAL L 120 " ideal model delta harmonic sigma weight residual -122.00 -137.80 15.80 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" N VAL L 120 " pdb=" C VAL L 120 " pdb=" CA VAL L 120 " pdb=" CB VAL L 120 " ideal model delta harmonic sigma weight residual 123.40 139.02 -15.62 0 2.50e+00 1.60e-01 3.90e+01 ... (remaining 22217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 5480 0.154 - 0.307: 39 0.307 - 0.461: 11 0.461 - 0.615: 7 0.615 - 0.768: 2 Chirality restraints: 5539 Sorted by residual: chirality pdb=" CA PRO K 122 " pdb=" N PRO K 122 " pdb=" C PRO K 122 " pdb=" CB PRO K 122 " both_signs ideal model delta sigma weight residual False 2.72 1.95 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA ASN L 758 " pdb=" N ASN L 758 " pdb=" C ASN L 758 " pdb=" CB ASN L 758 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA VAL L 120 " pdb=" N VAL L 120 " pdb=" C VAL L 120 " pdb=" CB VAL L 120 " both_signs ideal model delta sigma weight residual False 2.44 1.83 0.61 2.00e-01 2.50e+01 9.26e+00 ... (remaining 5536 not shown) Planarity restraints: 6566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP K 121 " 0.098 5.00e-02 4.00e+02 1.47e-01 3.43e+01 pdb=" N PRO K 122 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO K 122 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO K 122 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO K 119 " 0.028 2.00e-02 2.50e+03 5.64e-02 3.18e+01 pdb=" C PRO K 119 " -0.097 2.00e-02 2.50e+03 pdb=" O PRO K 119 " 0.037 2.00e-02 2.50e+03 pdb=" N VAL K 120 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN J 189 " 0.090 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO J 190 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO J 190 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO J 190 " 0.071 5.00e-02 4.00e+02 ... (remaining 6563 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 569 2.60 - 3.18: 33260 3.18 - 3.75: 54605 3.75 - 4.33: 79490 4.33 - 4.90: 131074 Nonbonded interactions: 298998 Sorted by model distance: nonbonded pdb=" O ASN K 553 " pdb=" ND2 ASN K 553 " model vdw 2.029 3.120 nonbonded pdb=" O VAL K 512 " pdb=" ND2 ASN K 528 " model vdw 2.195 3.120 nonbonded pdb=" NH2 ARG B 95 " pdb=" O ALA B 284 " model vdw 2.197 3.120 nonbonded pdb=" O ARG B 41 " pdb=" OG1 THR B 48 " model vdw 2.198 3.040 nonbonded pdb=" O PHE J 234 " pdb=" OH TYR J 245 " model vdw 2.199 3.040 ... (remaining 298993 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = (chain 'L' and (resid 1 through 746 or resid 759 through 833)) } 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 31.120 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.130 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 : 0.006 0.087 37247 Z= 0.315 Angle : 0.974 12.639 50549 Z= 0.570 Chirality : 0.059 0.768 5539 Planarity : 0.007 0.147 6566 Dihedral : 13.886 89.640 13728 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 1.82 % Allowed : 11.78 % Favored : 86.40 % Rotamer: Outliers : 0.32 % Allowed : 0.71 % Favored : 98.97 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % 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: -2.88 (0.12), residues: 4516 helix: -0.95 (0.20), residues: 604 sheet: -1.46 (0.16), residues: 1079 loop : -2.43 (0.11), residues: 2833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 30 TYR 0.027 0.002 TYR A 118 PHE 0.025 0.002 PHE K 548 TRP 0.069 0.003 TRP E 148 HIS 0.008 0.001 HIS K 66 Details of bonding type rmsd covalent geometry : bond 0.00568 (37247) covalent geometry : angle 0.97375 (50549) hydrogen bonds : bond 0.25216 ( 692) hydrogen bonds : angle 9.36357 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 780 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.8838 (m) cc_final: 0.8220 (m) REVERT: A 159 ILE cc_start: 0.8714 (mm) cc_final: 0.8488 (mm) REVERT: A 187 MET cc_start: 0.8430 (mpp) cc_final: 0.8199 (mpp) REVERT: B 167 TYR cc_start: 0.8556 (t80) cc_final: 0.8205 (t80) REVERT: D 12 TYR cc_start: 0.8799 (m-80) cc_final: 0.8480 (m-80) REVERT: E 71 GLU cc_start: 0.8627 (tp30) cc_final: 0.8324 (tp30) REVERT: E 118 THR cc_start: 0.7771 (p) cc_final: 0.7514 (p) REVERT: E 189 ASN cc_start: 0.7751 (m-40) cc_final: 0.7332 (m-40) REVERT: E 192 THR cc_start: 0.9257 (p) cc_final: 0.9022 (p) REVERT: E 202 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7373 (mt-10) REVERT: F 1 MET cc_start: 0.7902 (tmm) cc_final: 0.7600 (tmm) REVERT: F 113 THR cc_start: 0.8930 (p) cc_final: 0.8659 (p) REVERT: F 196 ILE cc_start: 0.8920 (mp) cc_final: 0.8516 (tt) REVERT: G 187 LEU cc_start: 0.8337 (tt) cc_final: 0.8041 (tt) REVERT: H 1 MET cc_start: 0.8115 (mtp) cc_final: 0.7760 (mmm) REVERT: H 178 MET cc_start: 0.9016 (mmm) cc_final: 0.8551 (mmt) REVERT: I 118 THR cc_start: 0.7649 (p) cc_final: 0.7382 (p) REVERT: I 196 ILE cc_start: 0.8737 (mp) cc_final: 0.8506 (tt) REVERT: J 181 LEU cc_start: 0.9045 (mm) cc_final: 0.8841 (mm) REVERT: J 486 LYS cc_start: 0.7110 (ttmt) cc_final: 0.6646 (tttt) REVERT: J 560 ARG cc_start: 0.8676 (mtp-110) cc_final: 0.8305 (mtp85) REVERT: J 818 ASP cc_start: 0.8172 (p0) cc_final: 0.7958 (p0) REVERT: K 172 TYR cc_start: 0.8443 (t80) cc_final: 0.8154 (t80) REVERT: K 451 ILE cc_start: 0.8989 (mt) cc_final: 0.8706 (pt) REVERT: K 455 LYS cc_start: 0.7929 (tptt) cc_final: 0.7655 (tptp) REVERT: K 458 LEU cc_start: 0.9006 (mt) cc_final: 0.8637 (mt) REVERT: K 505 TRP cc_start: 0.8578 (p90) cc_final: 0.8291 (p90) REVERT: K 518 LEU cc_start: 0.8250 (mm) cc_final: 0.7975 (tt) REVERT: K 798 MET cc_start: 0.7033 (pmm) cc_final: 0.6809 (pmm) REVERT: K 818 ASP cc_start: 0.7959 (p0) cc_final: 0.7344 (p0) REVERT: L 181 LEU cc_start: 0.9084 (mt) cc_final: 0.8845 (mp) REVERT: L 363 ASN cc_start: 0.8312 (m-40) cc_final: 0.7825 (m-40) REVERT: L 412 LEU cc_start: 0.8181 (mt) cc_final: 0.7609 (tp) REVERT: L 818 ASP cc_start: 0.8073 (p0) cc_final: 0.7684 (p0) outliers start: 13 outliers final: 5 residues processed: 788 average time/residue: 0.2002 time to fit residues: 265.7790 Evaluate side-chains 599 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 594 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 456 THR Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 122 PRO Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 458 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.0000 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 0.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 HIS C 35 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 104 GLN H 108 GLN I 104 GLN ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN J 506 GLN J 526 GLN J 540 ASN ** J 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 591 ASN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 540 ASN K 542 GLN K 735 ASN L 68 GLN L 108 GLN ** L 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 540 ASN ** L 721 GLN ** 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 = 0.3210 r_free = 0.3210 target = 0.114849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.099741 restraints weight = 54384.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101774 restraints weight = 31158.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.103131 restraints weight = 20890.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.104020 restraints weight = 15698.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.104473 restraints weight = 12908.346| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 37247 Z= 0.229 Angle : 0.801 11.697 50549 Z= 0.419 Chirality : 0.051 0.353 5539 Planarity : 0.007 0.157 6566 Dihedral : 6.667 49.776 5006 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 1.44 % Allowed : 11.38 % Favored : 87.18 % Rotamer: Outliers : 2.02 % Allowed : 9.85 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.88 (0.12), residues: 4516 helix: -0.98 (0.19), residues: 649 sheet: -1.52 (0.16), residues: 1100 loop : -2.42 (0.11), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 92 TYR 0.022 0.002 TYR L 656 PHE 0.029 0.002 PHE J 548 TRP 0.047 0.003 TRP E 148 HIS 0.006 0.001 HIS K 15 Details of bonding type rmsd covalent geometry : bond 0.00541 (37247) covalent geometry : angle 0.80135 (50549) hydrogen bonds : bond 0.05440 ( 692) hydrogen bonds : angle 6.56143 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 645 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.8951 (m) cc_final: 0.8222 (m) REVERT: A 187 MET cc_start: 0.8411 (mpp) cc_final: 0.8060 (mpp) REVERT: A 227 TYR cc_start: 0.9230 (m-80) cc_final: 0.8994 (m-10) REVERT: A 252 ASN cc_start: 0.8283 (t0) cc_final: 0.7969 (t0) REVERT: A 272 ASP cc_start: 0.7944 (m-30) cc_final: 0.7400 (p0) REVERT: D 12 TYR cc_start: 0.8818 (m-80) cc_final: 0.8503 (m-80) REVERT: D 40 GLU cc_start: 0.7628 (pt0) cc_final: 0.7285 (pt0) REVERT: D 175 THR cc_start: 0.9411 (p) cc_final: 0.9199 (p) REVERT: E 118 THR cc_start: 0.7762 (p) cc_final: 0.7498 (p) REVERT: F 196 ILE cc_start: 0.8943 (mp) cc_final: 0.8479 (tt) REVERT: I 118 THR cc_start: 0.7567 (p) cc_final: 0.7326 (p) REVERT: I 196 ILE cc_start: 0.8830 (mp) cc_final: 0.8547 (tt) REVERT: J 506 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.8996 (tp-100) REVERT: J 818 ASP cc_start: 0.7947 (p0) cc_final: 0.7664 (p0) REVERT: K 172 TYR cc_start: 0.8656 (t80) cc_final: 0.8362 (t80) REVERT: K 199 TYR cc_start: 0.8676 (m-80) cc_final: 0.8399 (m-10) REVERT: K 518 LEU cc_start: 0.8437 (mm) cc_final: 0.8213 (tp) REVERT: K 798 MET cc_start: 0.7056 (pmm) cc_final: 0.6657 (pmm) REVERT: K 812 PHE cc_start: 0.8043 (m-80) cc_final: 0.7654 (m-80) REVERT: K 818 ASP cc_start: 0.7942 (p0) cc_final: 0.7204 (p0) REVERT: L 412 LEU cc_start: 0.8046 (mt) cc_final: 0.7530 (tp) REVERT: L 414 THR cc_start: 0.8915 (m) cc_final: 0.8686 (p) REVERT: L 560 ARG cc_start: 0.8880 (mtp85) cc_final: 0.8275 (ttm110) REVERT: L 818 ASP cc_start: 0.8307 (p0) cc_final: 0.7698 (p0) outliers start: 82 outliers final: 56 residues processed: 683 average time/residue: 0.2193 time to fit residues: 253.2630 Evaluate side-chains 610 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 553 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 112 HIS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 189 ASN Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain I residue 28 MET Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 189 ASN Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 456 THR Chi-restraints excluded: chain J residue 506 GLN Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 763 TRP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 122 PRO Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 302 ASP Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain K residue 588 THR Chi-restraints excluded: chain K residue 763 TRP Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain L residue 588 THR Chi-restraints excluded: chain L residue 798 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 228 optimal weight: 0.0470 chunk 295 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 343 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN B 114 ASN D 104 GLN E 104 GLN F 85 GLN G 104 GLN H 104 GLN I 104 GLN ** J 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 506 GLN J 526 GLN J 553 ASN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 424 ASN K 553 ASN K 636 ASN K 735 ASN ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 735 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.102981 restraints weight = 53682.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.105014 restraints weight = 30823.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.106366 restraints weight = 20639.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107184 restraints weight = 15553.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.107785 restraints weight = 12870.189| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 37247 Z= 0.153 Angle : 0.721 11.743 50549 Z= 0.373 Chirality : 0.048 0.309 5539 Planarity : 0.006 0.151 6566 Dihedral : 6.223 48.495 5004 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 1.33 % Allowed : 10.56 % Favored : 88.11 % Rotamer: Outliers : 2.46 % Allowed : 13.82 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.71 (0.11), residues: 4516 helix: -0.56 (0.20), residues: 608 sheet: -1.41 (0.16), residues: 1087 loop : -2.36 (0.10), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 92 TYR 0.018 0.002 TYR B 118 PHE 0.024 0.002 PHE J 548 TRP 0.036 0.002 TRP E 148 HIS 0.006 0.001 HIS J 66 Details of bonding type rmsd covalent geometry : bond 0.00355 (37247) covalent geometry : angle 0.72080 (50549) hydrogen bonds : bond 0.04480 ( 692) hydrogen bonds : angle 6.01404 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 628 time to evaluate : 1.542 Fit side-chains revert: symmetry clash REVERT: A 122 CYS cc_start: 0.9061 (m) cc_final: 0.8245 (m) REVERT: A 187 MET cc_start: 0.8429 (mpp) cc_final: 0.7841 (mpp) REVERT: A 252 ASN cc_start: 0.8342 (t0) cc_final: 0.7997 (t0) REVERT: A 257 ILE cc_start: 0.9141 (mp) cc_final: 0.8785 (mt) REVERT: A 272 ASP cc_start: 0.7925 (m-30) cc_final: 0.7352 (p0) REVERT: A 294 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.5065 (t80) REVERT: B 167 TYR cc_start: 0.8627 (t80) cc_final: 0.8206 (t80) REVERT: C 294 PHE cc_start: 0.5134 (OUTLIER) cc_final: 0.4742 (t80) REVERT: D 12 TYR cc_start: 0.8854 (m-80) cc_final: 0.8581 (m-80) REVERT: D 40 GLU cc_start: 0.7631 (pt0) cc_final: 0.7310 (pt0) REVERT: D 175 THR cc_start: 0.9389 (p) cc_final: 0.9147 (p) REVERT: E 118 THR cc_start: 0.7746 (p) cc_final: 0.7527 (p) REVERT: F 196 ILE cc_start: 0.8933 (mp) cc_final: 0.8500 (tt) REVERT: G 1 MET cc_start: 0.8218 (mmm) cc_final: 0.7932 (mmm) REVERT: G 40 GLU cc_start: 0.7311 (pt0) cc_final: 0.7077 (pt0) REVERT: G 77 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: I 118 THR cc_start: 0.7644 (p) cc_final: 0.7421 (p) REVERT: J 181 LEU cc_start: 0.9133 (mm) cc_final: 0.8881 (mm) REVERT: J 418 ILE cc_start: 0.9166 (mt) cc_final: 0.8856 (mt) REVERT: J 656 TYR cc_start: 0.8477 (m-10) cc_final: 0.8185 (m-10) REVERT: K 140 ILE cc_start: 0.8971 (mm) cc_final: 0.8686 (mm) REVERT: K 174 ASP cc_start: 0.7720 (t0) cc_final: 0.7491 (m-30) REVERT: K 505 TRP cc_start: 0.8676 (p90) cc_final: 0.8037 (p90) REVERT: K 518 LEU cc_start: 0.8328 (mm) cc_final: 0.8127 (tp) REVERT: K 553 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7143 (p0) REVERT: K 579 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8558 (m-10) REVERT: K 798 MET cc_start: 0.7169 (pmm) cc_final: 0.6804 (pmm) REVERT: K 812 PHE cc_start: 0.8020 (m-80) cc_final: 0.7686 (m-80) REVERT: K 818 ASP cc_start: 0.7765 (p0) cc_final: 0.7116 (p0) REVERT: L 181 LEU cc_start: 0.9270 (mt) cc_final: 0.9063 (mp) REVERT: L 199 TYR cc_start: 0.8252 (m-10) cc_final: 0.7934 (m-10) REVERT: L 414 THR cc_start: 0.8789 (m) cc_final: 0.8431 (p) REVERT: L 448 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: L 514 TRP cc_start: 0.7792 (p90) cc_final: 0.7479 (p90) REVERT: L 656 TYR cc_start: 0.8319 (m-80) cc_final: 0.7814 (m-80) REVERT: L 818 ASP cc_start: 0.8300 (p0) cc_final: 0.7703 (p0) outliers start: 100 outliers final: 60 residues processed: 683 average time/residue: 0.2181 time to fit residues: 252.0585 Evaluate side-chains 613 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 547 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 112 HIS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 189 ASN Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 189 ASN Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 456 THR Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 526 GLN Chi-restraints excluded: chain J residue 763 TRP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 302 ASP Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain K residue 553 ASN Chi-restraints excluded: chain K residue 563 VAL Chi-restraints excluded: chain K residue 579 TYR Chi-restraints excluded: chain K residue 588 THR Chi-restraints excluded: chain K residue 590 ARG Chi-restraints excluded: chain K residue 735 ASN Chi-restraints excluded: chain K residue 763 TRP Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 228 GLN Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 448 ASP Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain L residue 588 THR Chi-restraints excluded: chain L residue 763 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 42 optimal weight: 8.9990 chunk 265 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 306 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 214 optimal weight: 0.1980 chunk 378 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 184 optimal weight: 8.9990 chunk 396 optimal weight: 5.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN B 56 ASN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 104 GLN I 104 GLN ** J 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 553 ASN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 735 ASN K 68 GLN ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 528 ASN K 553 ASN ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 521 ASN ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 734 ASN ** L 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 770 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.098506 restraints weight = 54248.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.100580 restraints weight = 30977.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101947 restraints weight = 20676.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.102844 restraints weight = 15532.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.103355 restraints weight = 12747.476| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 37247 Z= 0.218 Angle : 0.742 13.545 50549 Z= 0.383 Chirality : 0.049 0.288 5539 Planarity : 0.006 0.145 6566 Dihedral : 6.182 47.668 5001 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 1.28 % Allowed : 11.49 % Favored : 87.22 % Rotamer: Outliers : 2.86 % Allowed : 16.03 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.69 (0.12), residues: 4516 helix: -0.60 (0.20), residues: 615 sheet: -1.35 (0.15), residues: 1184 loop : -2.37 (0.11), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 815 TYR 0.020 0.002 TYR B 118 PHE 0.028 0.002 PHE J 548 TRP 0.035 0.002 TRP E 148 HIS 0.006 0.001 HIS K 66 Details of bonding type rmsd covalent geometry : bond 0.00516 (37247) covalent geometry : angle 0.74184 (50549) hydrogen bonds : bond 0.04479 ( 692) hydrogen bonds : angle 5.84120 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 581 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7927 (m-40) REVERT: A 122 CYS cc_start: 0.9097 (m) cc_final: 0.8283 (m) REVERT: A 187 MET cc_start: 0.8422 (mpp) cc_final: 0.7643 (mpp) REVERT: A 227 TYR cc_start: 0.9202 (m-10) cc_final: 0.8817 (m-10) REVERT: A 252 ASN cc_start: 0.8421 (t0) cc_final: 0.8117 (t0) REVERT: A 257 ILE cc_start: 0.9205 (mp) cc_final: 0.8861 (mt) REVERT: A 272 ASP cc_start: 0.7974 (m-30) cc_final: 0.7383 (p0) REVERT: A 294 PHE cc_start: 0.5806 (OUTLIER) cc_final: 0.5166 (t80) REVERT: B 167 TYR cc_start: 0.8653 (t80) cc_final: 0.8239 (t80) REVERT: C 294 PHE cc_start: 0.5460 (OUTLIER) cc_final: 0.4957 (t80) REVERT: D 12 TYR cc_start: 0.8919 (m-80) cc_final: 0.8641 (m-80) REVERT: D 40 GLU cc_start: 0.7662 (pt0) cc_final: 0.7335 (pt0) REVERT: D 175 THR cc_start: 0.9414 (p) cc_final: 0.9185 (p) REVERT: D 204 LEU cc_start: 0.9025 (pp) cc_final: 0.8682 (pp) REVERT: E 21 ASN cc_start: 0.8925 (t0) cc_final: 0.8412 (t0) REVERT: E 118 THR cc_start: 0.7744 (p) cc_final: 0.7511 (p) REVERT: F 24 ASP cc_start: 0.9000 (t0) cc_final: 0.8558 (t0) REVERT: F 196 ILE cc_start: 0.8958 (mp) cc_final: 0.8542 (tt) REVERT: G 1 MET cc_start: 0.8332 (mmm) cc_final: 0.7921 (mmm) REVERT: G 40 GLU cc_start: 0.7275 (pt0) cc_final: 0.7075 (pt0) REVERT: I 118 THR cc_start: 0.7833 (p) cc_final: 0.7578 (p) REVERT: J 181 LEU cc_start: 0.9142 (mm) cc_final: 0.8905 (mm) REVERT: J 228 GLN cc_start: 0.8380 (mt0) cc_final: 0.7999 (mp10) REVERT: J 247 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7683 (mp0) REVERT: J 418 ILE cc_start: 0.9124 (mt) cc_final: 0.8840 (mt) REVERT: J 428 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8061 (p) REVERT: J 656 TYR cc_start: 0.8526 (m-10) cc_final: 0.8307 (m-10) REVERT: K 140 ILE cc_start: 0.9144 (mm) cc_final: 0.8900 (mm) REVERT: K 428 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8316 (p) REVERT: K 505 TRP cc_start: 0.8687 (p90) cc_final: 0.8016 (p90) REVERT: K 518 LEU cc_start: 0.8304 (mm) cc_final: 0.8077 (tp) REVERT: K 553 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7860 (p0) REVERT: K 620 LYS cc_start: 0.8826 (ttpp) cc_final: 0.8530 (ttmm) REVERT: K 818 ASP cc_start: 0.7809 (p0) cc_final: 0.7202 (p0) REVERT: L 199 TYR cc_start: 0.8349 (m-10) cc_final: 0.8111 (m-10) REVERT: L 414 THR cc_start: 0.8926 (m) cc_final: 0.8515 (p) REVERT: L 656 TYR cc_start: 0.8424 (m-80) cc_final: 0.8038 (m-80) REVERT: L 818 ASP cc_start: 0.8456 (p0) cc_final: 0.7838 (p0) outliers start: 116 outliers final: 91 residues processed: 644 average time/residue: 0.2212 time to fit residues: 242.2105 Evaluate side-chains 637 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 540 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 112 HIS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 189 ASN Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 189 ASN Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 456 THR Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 763 TRP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 172 TYR Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 418 ILE Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain K residue 553 ASN Chi-restraints excluded: chain K residue 563 VAL Chi-restraints excluded: chain K residue 588 THR Chi-restraints excluded: chain K residue 590 ARG Chi-restraints excluded: chain K residue 614 PHE Chi-restraints excluded: chain K residue 667 LYS Chi-restraints excluded: chain K residue 763 TRP Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 228 GLN Chi-restraints excluded: chain L residue 230 LYS Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 512 VAL Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain L residue 579 TYR Chi-restraints excluded: chain L residue 588 THR Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 763 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 401 optimal weight: 10.0000 chunk 391 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 290 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 416 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN C 58 GLN C 161 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN G 104 GLN I 104 GLN J 372 HIS ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 526 GLN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 735 ASN K 68 GLN ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 553 ASN ** K 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.114963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.099601 restraints weight = 54015.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.101661 restraints weight = 30865.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.103028 restraints weight = 20622.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.103909 restraints weight = 15484.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.104523 restraints weight = 12710.089| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 37247 Z= 0.173 Angle : 0.708 13.364 50549 Z= 0.365 Chirality : 0.048 0.263 5539 Planarity : 0.005 0.142 6566 Dihedral : 6.052 46.202 5001 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 1.22 % Allowed : 11.05 % Favored : 87.73 % Rotamer: Outliers : 3.72 % Allowed : 16.87 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -2.64 (0.12), residues: 4516 helix: -0.53 (0.20), residues: 609 sheet: -1.36 (0.15), residues: 1192 loop : -2.32 (0.11), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 92 TYR 0.022 0.001 TYR B 118 PHE 0.025 0.002 PHE J 548 TRP 0.040 0.002 TRP L 505 HIS 0.007 0.001 HIS K 66 Details of bonding type rmsd covalent geometry : bond 0.00410 (37247) covalent geometry : angle 0.70794 (50549) hydrogen bonds : bond 0.04173 ( 692) hydrogen bonds : angle 5.72214 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 596 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.9109 (m) cc_final: 0.8280 (m) REVERT: A 147 PHE cc_start: 0.8537 (p90) cc_final: 0.8185 (p90) REVERT: A 187 MET cc_start: 0.8367 (mpp) cc_final: 0.7604 (mpp) REVERT: A 252 ASN cc_start: 0.8404 (t0) cc_final: 0.8079 (t0) REVERT: A 257 ILE cc_start: 0.9199 (mp) cc_final: 0.8866 (mt) REVERT: A 272 ASP cc_start: 0.7946 (m-30) cc_final: 0.7422 (p0) REVERT: A 294 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.5105 (t80) REVERT: B 27 ASN cc_start: 0.8525 (t0) cc_final: 0.8139 (t0) REVERT: B 167 TYR cc_start: 0.8639 (t80) cc_final: 0.8286 (t80) REVERT: B 218 MET cc_start: 0.8595 (ttm) cc_final: 0.8357 (ttm) REVERT: C 58 GLN cc_start: 0.8348 (mt0) cc_final: 0.8122 (mt0) REVERT: C 294 PHE cc_start: 0.5409 (OUTLIER) cc_final: 0.4989 (t80) REVERT: D 12 TYR cc_start: 0.8910 (m-80) cc_final: 0.8663 (m-80) REVERT: D 40 GLU cc_start: 0.7654 (pt0) cc_final: 0.7368 (pt0) REVERT: D 175 THR cc_start: 0.9420 (p) cc_final: 0.9167 (p) REVERT: E 21 ASN cc_start: 0.8910 (t0) cc_final: 0.8540 (t0) REVERT: E 118 THR cc_start: 0.7758 (p) cc_final: 0.7535 (p) REVERT: F 196 ILE cc_start: 0.8943 (mp) cc_final: 0.8536 (tt) REVERT: G 1 MET cc_start: 0.8193 (mmm) cc_final: 0.7695 (mmm) REVERT: G 40 GLU cc_start: 0.7257 (pt0) cc_final: 0.7011 (pt0) REVERT: H 204 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8193 (pp) REVERT: J 140 ILE cc_start: 0.9229 (mm) cc_final: 0.9000 (mm) REVERT: J 181 LEU cc_start: 0.9181 (mm) cc_final: 0.8938 (mm) REVERT: J 228 GLN cc_start: 0.8406 (mt0) cc_final: 0.8039 (mp10) REVERT: J 428 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8068 (p) REVERT: J 553 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.6788 (p0) REVERT: J 656 TYR cc_start: 0.8546 (m-10) cc_final: 0.8235 (m-10) REVERT: J 672 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7196 (mt-10) REVERT: K 44 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7952 (t80) REVERT: K 140 ILE cc_start: 0.9118 (mm) cc_final: 0.8905 (mm) REVERT: K 428 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8321 (p) REVERT: K 429 GLU cc_start: 0.7651 (mp0) cc_final: 0.7322 (mp0) REVERT: K 505 TRP cc_start: 0.8639 (p90) cc_final: 0.8048 (p90) REVERT: K 518 LEU cc_start: 0.8295 (mm) cc_final: 0.8067 (tp) REVERT: K 620 LYS cc_start: 0.8820 (ttpp) cc_final: 0.8503 (ttmm) REVERT: K 812 PHE cc_start: 0.8193 (m-80) cc_final: 0.7545 (m-10) REVERT: L 1 MET cc_start: 0.8079 (mmm) cc_final: 0.7646 (mmm) REVERT: L 199 TYR cc_start: 0.8319 (m-10) cc_final: 0.8047 (m-10) REVERT: L 505 TRP cc_start: 0.8564 (p-90) cc_final: 0.8355 (p-90) REVERT: L 656 TYR cc_start: 0.8406 (m-80) cc_final: 0.8112 (m-80) REVERT: L 818 ASP cc_start: 0.8443 (p0) cc_final: 0.7845 (p0) outliers start: 151 outliers final: 101 residues processed: 679 average time/residue: 0.2219 time to fit residues: 254.6300 Evaluate side-chains 658 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 550 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 112 HIS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 189 ASN Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 189 ASN Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 553 ASN Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 763 TRP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 44 TYR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 302 ASP Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 418 ILE Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 563 VAL Chi-restraints excluded: chain K residue 579 TYR Chi-restraints excluded: chain K residue 588 THR Chi-restraints excluded: chain K residue 590 ARG Chi-restraints excluded: chain K residue 614 PHE Chi-restraints excluded: chain K residue 677 ILE Chi-restraints excluded: chain K residue 763 TRP Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 228 GLN Chi-restraints excluded: chain L residue 230 LYS Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 512 VAL Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain L residue 579 TYR Chi-restraints excluded: chain L residue 588 THR Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 763 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 307 optimal weight: 0.7980 chunk 243 optimal weight: 10.0000 chunk 290 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 377 optimal weight: 3.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN G 104 GLN I 51 ASN I 104 GLN ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 526 GLN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 735 ASN K 68 GLN ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 553 ASN ** K 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.112765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097313 restraints weight = 54633.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.099387 restraints weight = 31149.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100740 restraints weight = 20763.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.101642 restraints weight = 15635.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.102219 restraints weight = 12822.672| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 37247 Z= 0.203 Angle : 0.722 14.321 50549 Z= 0.371 Chirality : 0.048 0.254 5539 Planarity : 0.005 0.142 6566 Dihedral : 5.999 33.606 5000 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 1.17 % Allowed : 11.54 % Favored : 87.29 % Rotamer: Outliers : 4.09 % Allowed : 17.29 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -2.65 (0.12), residues: 4516 helix: -0.64 (0.20), residues: 612 sheet: -1.33 (0.15), residues: 1173 loop : -2.32 (0.11), residues: 2731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 92 TYR 0.020 0.002 TYR G 193 PHE 0.025 0.002 PHE J 548 TRP 0.027 0.002 TRP E 148 HIS 0.005 0.001 HIS K 15 Details of bonding type rmsd covalent geometry : bond 0.00481 (37247) covalent geometry : angle 0.72159 (50549) hydrogen bonds : bond 0.04212 ( 692) hydrogen bonds : angle 5.68268 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 588 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.9109 (m) cc_final: 0.8311 (m) REVERT: A 187 MET cc_start: 0.8435 (mpp) cc_final: 0.7928 (mpp) REVERT: A 252 ASN cc_start: 0.8439 (t0) cc_final: 0.8232 (t0) REVERT: A 272 ASP cc_start: 0.7965 (m-30) cc_final: 0.7372 (p0) REVERT: A 294 PHE cc_start: 0.5353 (OUTLIER) cc_final: 0.5033 (t80) REVERT: B 27 ASN cc_start: 0.8620 (t0) cc_final: 0.8199 (t0) REVERT: B 167 TYR cc_start: 0.8647 (t80) cc_final: 0.8218 (t80) REVERT: C 294 PHE cc_start: 0.5268 (OUTLIER) cc_final: 0.4993 (t80) REVERT: D 12 TYR cc_start: 0.8951 (m-80) cc_final: 0.8723 (m-80) REVERT: D 40 GLU cc_start: 0.7774 (pt0) cc_final: 0.7407 (pt0) REVERT: D 175 THR cc_start: 0.9318 (p) cc_final: 0.9066 (p) REVERT: E 21 ASN cc_start: 0.8927 (t0) cc_final: 0.8418 (t0) REVERT: E 118 THR cc_start: 0.7852 (p) cc_final: 0.7617 (p) REVERT: F 24 ASP cc_start: 0.9039 (t0) cc_final: 0.8609 (t0) REVERT: F 196 ILE cc_start: 0.8941 (mp) cc_final: 0.8540 (tt) REVERT: G 1 MET cc_start: 0.8209 (mmm) cc_final: 0.7722 (mmm) REVERT: G 40 GLU cc_start: 0.7284 (pt0) cc_final: 0.7074 (pt0) REVERT: H 40 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7402 (mt-10) REVERT: H 204 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8220 (pp) REVERT: I 24 ASP cc_start: 0.8986 (t0) cc_final: 0.8772 (t0) REVERT: J 181 LEU cc_start: 0.9180 (mm) cc_final: 0.8941 (mm) REVERT: J 228 GLN cc_start: 0.8433 (mt0) cc_final: 0.8044 (mp10) REVERT: J 428 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8105 (p) REVERT: J 524 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8734 (tt) REVERT: J 553 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7273 (p0) REVERT: J 579 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.6465 (t80) REVERT: J 656 TYR cc_start: 0.8599 (m-10) cc_final: 0.8306 (m-10) REVERT: J 672 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7397 (mt-10) REVERT: K 44 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.8051 (t80) REVERT: K 46 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7748 (mtm110) REVERT: K 140 ILE cc_start: 0.9210 (mm) cc_final: 0.8984 (mm) REVERT: K 428 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8331 (p) REVERT: K 505 TRP cc_start: 0.8643 (p90) cc_final: 0.8085 (p90) REVERT: K 518 LEU cc_start: 0.8260 (mm) cc_final: 0.8005 (tp) REVERT: K 620 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8495 (ttmm) REVERT: K 636 ASN cc_start: 0.8564 (m-40) cc_final: 0.8143 (m-40) REVERT: K 812 PHE cc_start: 0.8316 (m-80) cc_final: 0.7870 (m-80) REVERT: L 199 TYR cc_start: 0.8341 (m-10) cc_final: 0.7959 (m-10) REVERT: L 372 HIS cc_start: 0.8662 (OUTLIER) cc_final: 0.7870 (m-70) REVERT: L 441 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6668 (mmmt) REVERT: L 592 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7999 (ptpt) REVERT: L 656 TYR cc_start: 0.8417 (m-80) cc_final: 0.8180 (m-80) REVERT: L 818 ASP cc_start: 0.8492 (p0) cc_final: 0.7882 (p0) outliers start: 166 outliers final: 114 residues processed: 684 average time/residue: 0.2150 time to fit residues: 249.2536 Evaluate side-chains 682 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 556 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 112 HIS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 189 ASN Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 189 ASN Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 553 ASN Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 763 TRP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 44 TYR Chi-restraints excluded: chain K residue 46 ARG Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 185 ASN Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 302 ASP Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 418 ILE Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 553 ASN Chi-restraints excluded: chain K residue 563 VAL Chi-restraints excluded: chain K residue 579 TYR Chi-restraints excluded: chain K residue 588 THR Chi-restraints excluded: chain K residue 614 PHE Chi-restraints excluded: chain K residue 677 ILE Chi-restraints excluded: chain K residue 763 TRP Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 798 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 228 GLN Chi-restraints excluded: chain L residue 230 LYS Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 318 ASP Chi-restraints excluded: chain L residue 372 HIS Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 512 VAL Chi-restraints excluded: chain L residue 536 SER Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain L residue 579 TYR Chi-restraints excluded: chain L residue 588 THR Chi-restraints excluded: chain L residue 592 LYS Chi-restraints excluded: chain L residue 717 ILE Chi-restraints excluded: chain L residue 763 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 356 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 388 optimal weight: 10.0000 chunk 372 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 414 optimal weight: 0.0870 chunk 296 optimal weight: 8.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN C 35 GLN C 161 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN G 104 GLN I 46 GLN I 104 GLN ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 ASN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 735 ASN ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 553 ASN ** K 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 459 ASN ** L 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 735 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.117103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.101715 restraints weight = 53782.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.103832 restraints weight = 30538.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.105212 restraints weight = 20247.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.106092 restraints weight = 15175.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.106671 restraints weight = 12447.843| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 37247 Z= 0.132 Angle : 0.679 13.096 50549 Z= 0.348 Chirality : 0.046 0.244 5539 Planarity : 0.005 0.142 6566 Dihedral : 5.761 33.573 5000 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 1.15 % Allowed : 10.47 % Favored : 88.37 % Rotamer: Outliers : 3.57 % Allowed : 18.52 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -2.55 (0.12), residues: 4516 helix: -0.39 (0.21), residues: 608 sheet: -1.37 (0.15), residues: 1177 loop : -2.24 (0.11), residues: 2731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 46 TYR 0.020 0.001 TYR G 193 PHE 0.022 0.001 PHE L 548 TRP 0.049 0.002 TRP L 505 HIS 0.007 0.001 HIS K 66 Details of bonding type rmsd covalent geometry : bond 0.00310 (37247) covalent geometry : angle 0.67862 (50549) hydrogen bonds : bond 0.03764 ( 692) hydrogen bonds : angle 5.57453 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 632 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.9081 (m) cc_final: 0.8178 (m) REVERT: A 294 PHE cc_start: 0.5314 (OUTLIER) cc_final: 0.4645 (p90) REVERT: B 27 ASN cc_start: 0.8521 (t0) cc_final: 0.8096 (t0) REVERT: B 167 TYR cc_start: 0.8620 (t80) cc_final: 0.8324 (t80) REVERT: D 12 TYR cc_start: 0.8883 (m-80) cc_final: 0.8672 (m-80) REVERT: D 40 GLU cc_start: 0.7763 (pt0) cc_final: 0.7413 (pt0) REVERT: D 175 THR cc_start: 0.9253 (p) cc_final: 0.8996 (p) REVERT: E 21 ASN cc_start: 0.8820 (t0) cc_final: 0.8270 (t0) REVERT: E 46 GLN cc_start: 0.9366 (tm-30) cc_final: 0.8510 (tm-30) REVERT: E 118 THR cc_start: 0.7773 (p) cc_final: 0.7533 (p) REVERT: F 96 LYS cc_start: 0.8007 (mptt) cc_final: 0.7762 (mptt) REVERT: F 196 ILE cc_start: 0.8930 (mp) cc_final: 0.8521 (tt) REVERT: G 1 MET cc_start: 0.7896 (mmm) cc_final: 0.7560 (mmm) REVERT: G 40 GLU cc_start: 0.7268 (pt0) cc_final: 0.7040 (pt0) REVERT: H 40 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7373 (mt-10) REVERT: H 204 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8179 (pp) REVERT: J 46 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7583 (ptt-90) REVERT: J 181 LEU cc_start: 0.9196 (mm) cc_final: 0.8972 (mm) REVERT: J 228 GLN cc_start: 0.8349 (mt0) cc_final: 0.8070 (mp10) REVERT: J 247 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7628 (mp0) REVERT: J 418 ILE cc_start: 0.8924 (mt) cc_final: 0.8678 (mt) REVERT: J 428 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8106 (p) REVERT: J 530 ILE cc_start: 0.9450 (mm) cc_final: 0.9206 (tp) REVERT: J 656 TYR cc_start: 0.8479 (m-10) cc_final: 0.8098 (m-10) REVERT: K 46 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7323 (mtm110) REVERT: K 428 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8360 (p) REVERT: K 429 GLU cc_start: 0.7691 (mp0) cc_final: 0.7460 (mp0) REVERT: K 505 TRP cc_start: 0.8590 (p90) cc_final: 0.7985 (p90) REVERT: K 518 LEU cc_start: 0.8250 (mm) cc_final: 0.8016 (tp) REVERT: K 553 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7383 (p0) REVERT: K 620 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8528 (ttmm) REVERT: K 812 PHE cc_start: 0.8276 (m-80) cc_final: 0.7756 (m-80) REVERT: L 1 MET cc_start: 0.7892 (mmm) cc_final: 0.7621 (mmm) REVERT: L 199 TYR cc_start: 0.8341 (m-10) cc_final: 0.7952 (m-10) REVERT: L 372 HIS cc_start: 0.8587 (OUTLIER) cc_final: 0.7898 (m-70) REVERT: L 441 LYS cc_start: 0.7065 (mmtt) cc_final: 0.6525 (mmmt) REVERT: L 514 TRP cc_start: 0.7731 (p90) cc_final: 0.7514 (p90) REVERT: L 591 ASN cc_start: 0.8387 (m-40) cc_final: 0.8071 (m-40) REVERT: L 592 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7937 (ptpt) REVERT: L 818 ASP cc_start: 0.8378 (p0) cc_final: 0.7727 (p0) outliers start: 145 outliers final: 102 residues processed: 722 average time/residue: 0.2191 time to fit residues: 266.3012 Evaluate side-chains 683 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 573 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 112 HIS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 189 ASN Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 189 ASN Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 536 SER Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 735 ASN Chi-restraints excluded: chain J residue 763 TRP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 46 ARG Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 185 ASN Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 302 ASP Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 418 ILE Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 553 ASN Chi-restraints excluded: chain K residue 563 VAL Chi-restraints excluded: chain K residue 579 TYR Chi-restraints excluded: chain K residue 614 PHE Chi-restraints excluded: chain K residue 763 TRP Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 798 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 228 GLN Chi-restraints excluded: chain L residue 230 LYS Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 372 HIS Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 536 SER Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain L residue 579 TYR Chi-restraints excluded: chain L residue 588 THR Chi-restraints excluded: chain L residue 592 LYS Chi-restraints excluded: chain L residue 763 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 192 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 369 optimal weight: 9.9990 chunk 293 optimal weight: 0.0570 chunk 359 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 139 optimal weight: 0.1980 overall best weight: 3.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN C 35 GLN C 161 GLN ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN G 104 GLN I 104 GLN ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 553 ASN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 735 ASN ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 553 ASN ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 HIS ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 735 ASN L 789 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.113610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.098178 restraints weight = 54333.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.100247 restraints weight = 31123.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.101611 restraints weight = 20833.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.102491 restraints weight = 15686.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.103063 restraints weight = 12891.537| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 37247 Z= 0.198 Angle : 0.721 14.190 50549 Z= 0.368 Chirality : 0.048 0.242 5539 Planarity : 0.005 0.142 6566 Dihedral : 5.836 33.879 5000 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 1.09 % Allowed : 11.45 % Favored : 87.47 % Rotamer: Outliers : 3.67 % Allowed : 19.61 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -2.59 (0.12), residues: 4516 helix: -0.59 (0.20), residues: 613 sheet: -1.37 (0.15), residues: 1173 loop : -2.23 (0.11), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 823 TYR 0.020 0.002 TYR G 193 PHE 0.024 0.002 PHE J 548 TRP 0.077 0.002 TRP L 505 HIS 0.007 0.001 HIS K 66 Details of bonding type rmsd covalent geometry : bond 0.00473 (37247) covalent geometry : angle 0.72098 (50549) hydrogen bonds : bond 0.04060 ( 692) hydrogen bonds : angle 5.56219 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 579 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.9091 (m) cc_final: 0.8254 (m) REVERT: A 294 PHE cc_start: 0.5431 (OUTLIER) cc_final: 0.5226 (t80) REVERT: B 27 ASN cc_start: 0.8664 (t0) cc_final: 0.8426 (t0) REVERT: B 167 TYR cc_start: 0.8645 (t80) cc_final: 0.8153 (t80) REVERT: C 52 ASP cc_start: 0.7980 (m-30) cc_final: 0.7743 (m-30) REVERT: D 12 TYR cc_start: 0.8941 (m-80) cc_final: 0.8732 (m-80) REVERT: D 40 GLU cc_start: 0.7727 (pt0) cc_final: 0.7380 (pt0) REVERT: D 175 THR cc_start: 0.9267 (p) cc_final: 0.9025 (p) REVERT: E 21 ASN cc_start: 0.8907 (t0) cc_final: 0.8397 (t0) REVERT: E 46 GLN cc_start: 0.9431 (tm-30) cc_final: 0.8794 (tm-30) REVERT: E 118 THR cc_start: 0.7872 (p) cc_final: 0.7652 (p) REVERT: F 24 ASP cc_start: 0.9056 (t0) cc_final: 0.8583 (t0) REVERT: F 196 ILE cc_start: 0.8932 (mp) cc_final: 0.8544 (tt) REVERT: G 1 MET cc_start: 0.8049 (mmm) cc_final: 0.7467 (tpt) REVERT: G 40 GLU cc_start: 0.7385 (pt0) cc_final: 0.7117 (pt0) REVERT: H 204 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8210 (pp) REVERT: J 181 LEU cc_start: 0.9201 (mm) cc_final: 0.8989 (mm) REVERT: J 228 GLN cc_start: 0.8414 (mt0) cc_final: 0.8078 (mp10) REVERT: J 247 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7654 (mp0) REVERT: J 428 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8124 (p) REVERT: J 524 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8691 (tt) REVERT: J 579 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.6501 (t80) REVERT: J 656 TYR cc_start: 0.8586 (m-10) cc_final: 0.8324 (m-10) REVERT: K 44 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.7787 (t80) REVERT: K 46 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7199 (mtm110) REVERT: K 428 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8284 (p) REVERT: K 429 GLU cc_start: 0.7665 (mp0) cc_final: 0.7419 (mp0) REVERT: K 505 TRP cc_start: 0.8625 (p90) cc_final: 0.8033 (p90) REVERT: K 518 LEU cc_start: 0.8267 (mm) cc_final: 0.8011 (tp) REVERT: K 553 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7536 (p0) REVERT: K 620 LYS cc_start: 0.8818 (ttpp) cc_final: 0.8542 (ttmm) REVERT: K 812 PHE cc_start: 0.8175 (m-80) cc_final: 0.7737 (m-80) REVERT: L 372 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.7859 (m-70) REVERT: L 441 LYS cc_start: 0.7387 (mmtt) cc_final: 0.6736 (mmmt) REVERT: L 592 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7882 (ptpt) REVERT: L 818 ASP cc_start: 0.8395 (p0) cc_final: 0.7837 (p0) outliers start: 149 outliers final: 119 residues processed: 672 average time/residue: 0.1952 time to fit residues: 221.5797 Evaluate side-chains 691 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 561 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 112 HIS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 189 ASN Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 189 ASN Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 735 ASN Chi-restraints excluded: chain J residue 763 TRP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 44 TYR Chi-restraints excluded: chain K residue 46 ARG Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 185 ASN Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 302 ASP Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 418 ILE Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 553 ASN Chi-restraints excluded: chain K residue 563 VAL Chi-restraints excluded: chain K residue 579 TYR Chi-restraints excluded: chain K residue 614 PHE Chi-restraints excluded: chain K residue 677 ILE Chi-restraints excluded: chain K residue 763 TRP Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 798 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 228 GLN Chi-restraints excluded: chain L residue 230 LYS Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 318 ASP Chi-restraints excluded: chain L residue 372 HIS Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain L residue 512 VAL Chi-restraints excluded: chain L residue 536 SER Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain L residue 579 TYR Chi-restraints excluded: chain L residue 588 THR Chi-restraints excluded: chain L residue 592 LYS Chi-restraints excluded: chain L residue 677 ILE Chi-restraints excluded: chain L residue 701 ASP Chi-restraints excluded: chain L residue 763 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 79 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 172 optimal weight: 0.6980 chunk 401 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 414 optimal weight: 5.9990 chunk 430 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 340 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN I 104 GLN ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 553 ASN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 735 ASN ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 GLN ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 506 GLN L 735 ASN L 781 HIS L 789 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.112509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097364 restraints weight = 54783.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.099361 restraints weight = 31702.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.100707 restraints weight = 21383.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.101589 restraints weight = 16124.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.102114 restraints weight = 13252.437| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 37247 Z= 0.220 Angle : 0.743 14.681 50549 Z= 0.379 Chirality : 0.049 0.238 5539 Planarity : 0.005 0.143 6566 Dihedral : 5.927 34.071 5000 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 1.09 % Allowed : 11.74 % Favored : 87.18 % Rotamer: Outliers : 3.89 % Allowed : 19.78 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -2.61 (0.12), residues: 4516 helix: -0.63 (0.20), residues: 613 sheet: -1.35 (0.15), residues: 1168 loop : -2.26 (0.11), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 823 TYR 0.022 0.002 TYR G 193 PHE 0.024 0.002 PHE J 548 TRP 0.064 0.002 TRP L 505 HIS 0.006 0.001 HIS K 66 Details of bonding type rmsd covalent geometry : bond 0.00525 (37247) covalent geometry : angle 0.74342 (50549) hydrogen bonds : bond 0.04185 ( 692) hydrogen bonds : angle 5.60513 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 574 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.9083 (m) cc_final: 0.8277 (m) REVERT: A 250 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8588 (mt) REVERT: A 294 PHE cc_start: 0.5303 (OUTLIER) cc_final: 0.4969 (t80) REVERT: B 27 ASN cc_start: 0.8716 (t0) cc_final: 0.8480 (t0) REVERT: B 167 TYR cc_start: 0.8566 (t80) cc_final: 0.7732 (t80) REVERT: C 133 LYS cc_start: 0.3564 (mptt) cc_final: 0.2494 (mmtm) REVERT: C 187 MET cc_start: 0.8633 (mmp) cc_final: 0.8377 (mpp) REVERT: D 40 GLU cc_start: 0.7715 (pt0) cc_final: 0.7417 (pt0) REVERT: D 175 THR cc_start: 0.9267 (p) cc_final: 0.9022 (p) REVERT: E 21 ASN cc_start: 0.8924 (t0) cc_final: 0.8449 (t0) REVERT: E 46 GLN cc_start: 0.9474 (tm-30) cc_final: 0.8555 (tm-30) REVERT: E 118 THR cc_start: 0.7917 (p) cc_final: 0.7678 (p) REVERT: F 24 ASP cc_start: 0.9088 (t0) cc_final: 0.8591 (t0) REVERT: F 196 ILE cc_start: 0.8910 (mp) cc_final: 0.8524 (tt) REVERT: G 1 MET cc_start: 0.8082 (mmm) cc_final: 0.7508 (tpt) REVERT: H 28 MET cc_start: 0.7789 (ptp) cc_final: 0.7573 (ptp) REVERT: H 204 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8228 (pp) REVERT: J 44 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8554 (t80) REVERT: J 181 LEU cc_start: 0.9220 (mm) cc_final: 0.9019 (mm) REVERT: J 228 GLN cc_start: 0.8401 (mt0) cc_final: 0.8104 (mp10) REVERT: J 428 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8135 (p) REVERT: J 524 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8697 (tt) REVERT: J 530 ILE cc_start: 0.9399 (mm) cc_final: 0.9177 (tt) REVERT: J 579 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.6568 (t80) REVERT: J 656 TYR cc_start: 0.8628 (m-10) cc_final: 0.8394 (m-10) REVERT: K 44 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.7947 (t80) REVERT: K 46 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7329 (mtm110) REVERT: K 428 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8317 (p) REVERT: K 505 TRP cc_start: 0.8629 (p90) cc_final: 0.8102 (p90) REVERT: K 518 LEU cc_start: 0.8252 (mm) cc_final: 0.7977 (tp) REVERT: K 553 ASN cc_start: 0.7928 (p0) cc_final: 0.7636 (p0) REVERT: K 620 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8551 (ttmm) REVERT: K 812 PHE cc_start: 0.8199 (m-80) cc_final: 0.7733 (m-80) REVERT: L 67 LYS cc_start: 0.8869 (tmtt) cc_final: 0.8619 (tptm) REVERT: L 372 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.7946 (m-70) REVERT: L 441 LYS cc_start: 0.7541 (mmtt) cc_final: 0.6864 (mmmt) REVERT: L 524 ILE cc_start: 0.8923 (mt) cc_final: 0.8708 (tt) REVERT: L 592 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7897 (ptpt) REVERT: L 818 ASP cc_start: 0.8386 (p0) cc_final: 0.7851 (p0) outliers start: 158 outliers final: 121 residues processed: 672 average time/residue: 0.2125 time to fit residues: 242.2316 Evaluate side-chains 690 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 557 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 112 HIS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 189 ASN Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 189 ASN Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 414 THR Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 536 SER Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 596 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 763 TRP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 44 TYR Chi-restraints excluded: chain K residue 46 ARG Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 151 THR Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 185 ASN Chi-restraints excluded: chain K residue 250 THR Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 302 ASP Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 418 ILE Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 563 VAL Chi-restraints excluded: chain K residue 579 TYR Chi-restraints excluded: chain K residue 588 THR Chi-restraints excluded: chain K residue 614 PHE Chi-restraints excluded: chain K residue 677 ILE Chi-restraints excluded: chain K residue 717 ILE Chi-restraints excluded: chain K residue 763 TRP Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 798 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 228 GLN Chi-restraints excluded: chain L residue 230 LYS Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 318 ASP Chi-restraints excluded: chain L residue 372 HIS Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain L residue 512 VAL Chi-restraints excluded: chain L residue 536 SER Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain L residue 579 TYR Chi-restraints excluded: chain L residue 588 THR Chi-restraints excluded: chain L residue 592 LYS Chi-restraints excluded: chain L residue 677 ILE Chi-restraints excluded: chain L residue 701 ASP Chi-restraints excluded: chain L residue 763 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 215 optimal weight: 1.9990 chunk 305 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 326 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 442 optimal weight: 2.9990 chunk 325 optimal weight: 9.9990 chunk 395 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN B 161 GLN C 35 GLN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 104 GLN I 104 GLN ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 553 ASN ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 735 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.098400 restraints weight = 54497.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.100492 restraints weight = 31011.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.101867 restraints weight = 20594.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.102785 restraints weight = 15456.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.103326 restraints weight = 12614.273| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 37247 Z= 0.175 Angle : 0.727 16.560 50549 Z= 0.370 Chirality : 0.048 0.234 5539 Planarity : 0.005 0.143 6566 Dihedral : 5.858 33.765 5000 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 1.02 % Allowed : 11.29 % Favored : 87.69 % Rotamer: Outliers : 3.50 % Allowed : 20.32 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -2.58 (0.12), residues: 4516 helix: -0.49 (0.20), residues: 611 sheet: -1.34 (0.16), residues: 1101 loop : -2.25 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 46 TYR 0.022 0.001 TYR G 193 PHE 0.023 0.002 PHE J 548 TRP 0.111 0.002 TRP L 505 HIS 0.007 0.001 HIS K 66 Details of bonding type rmsd covalent geometry : bond 0.00417 (37247) covalent geometry : angle 0.72685 (50549) hydrogen bonds : bond 0.03995 ( 692) hydrogen bonds : angle 5.57849 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 602 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.9055 (m) cc_final: 0.8204 (m) REVERT: A 250 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8520 (mt) REVERT: B 27 ASN cc_start: 0.8654 (t0) cc_final: 0.8425 (t0) REVERT: B 167 TYR cc_start: 0.8475 (t80) cc_final: 0.7523 (t80) REVERT: C 133 LYS cc_start: 0.3990 (mptt) cc_final: 0.2641 (mmtm) REVERT: C 187 MET cc_start: 0.8590 (mmp) cc_final: 0.8361 (mpp) REVERT: D 40 GLU cc_start: 0.7698 (pt0) cc_final: 0.7397 (pt0) REVERT: D 175 THR cc_start: 0.9245 (p) cc_final: 0.8998 (p) REVERT: E 21 ASN cc_start: 0.8882 (t0) cc_final: 0.8380 (t0) REVERT: E 46 GLN cc_start: 0.9431 (tm-30) cc_final: 0.8431 (tm-30) REVERT: E 118 THR cc_start: 0.7879 (p) cc_final: 0.7645 (p) REVERT: F 24 ASP cc_start: 0.9032 (t0) cc_final: 0.8540 (t0) REVERT: F 196 ILE cc_start: 0.8909 (mp) cc_final: 0.8517 (tt) REVERT: G 1 MET cc_start: 0.8040 (mmm) cc_final: 0.7522 (tpt) REVERT: G 30 ARG cc_start: 0.8989 (mtm110) cc_final: 0.8570 (mtm110) REVERT: G 40 GLU cc_start: 0.7496 (pt0) cc_final: 0.7257 (pt0) REVERT: H 28 MET cc_start: 0.7789 (ptp) cc_final: 0.7589 (ptp) REVERT: H 204 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8197 (pp) REVERT: I 21 ASN cc_start: 0.8745 (t0) cc_final: 0.8383 (t0) REVERT: J 44 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8465 (t80) REVERT: J 181 LEU cc_start: 0.9194 (mm) cc_final: 0.8987 (mm) REVERT: J 228 GLN cc_start: 0.8344 (mt0) cc_final: 0.8137 (mp10) REVERT: J 247 GLU cc_start: 0.8028 (mp0) cc_final: 0.7531 (mp0) REVERT: J 428 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8098 (p) REVERT: J 524 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8720 (tt) REVERT: J 530 ILE cc_start: 0.9311 (mm) cc_final: 0.9053 (tt) REVERT: J 579 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.6540 (t80) REVERT: J 656 TYR cc_start: 0.8573 (m-10) cc_final: 0.8331 (m-10) REVERT: J 724 ASN cc_start: 0.7741 (t0) cc_final: 0.7512 (t0) REVERT: K 44 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.7926 (t80) REVERT: K 46 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7275 (mtm110) REVERT: K 428 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8323 (p) REVERT: K 505 TRP cc_start: 0.8541 (p90) cc_final: 0.8063 (p90) REVERT: K 518 LEU cc_start: 0.8175 (mm) cc_final: 0.7915 (tp) REVERT: K 553 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7488 (p0) REVERT: K 620 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8568 (ttmm) REVERT: K 812 PHE cc_start: 0.8055 (m-80) cc_final: 0.7680 (m-80) REVERT: L 372 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.7926 (m-70) REVERT: L 441 LYS cc_start: 0.7550 (mmtt) cc_final: 0.6846 (mmmt) REVERT: L 524 ILE cc_start: 0.8924 (mt) cc_final: 0.8706 (tt) REVERT: L 592 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7887 (ptpt) REVERT: L 656 TYR cc_start: 0.8409 (m-80) cc_final: 0.8083 (m-80) REVERT: L 818 ASP cc_start: 0.8377 (p0) cc_final: 0.7777 (p0) outliers start: 142 outliers final: 120 residues processed: 687 average time/residue: 0.2059 time to fit residues: 240.2050 Evaluate side-chains 714 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 582 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 112 HIS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 189 ASN Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 104 GLN Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 189 ASN Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 414 THR Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 524 ILE Chi-restraints excluded: chain J residue 536 SER Chi-restraints excluded: chain J residue 579 TYR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 596 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 763 TRP Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 44 TYR Chi-restraints excluded: chain K residue 46 ARG Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 185 ASN Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 302 ASP Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 418 ILE Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 524 ILE Chi-restraints excluded: chain K residue 536 SER Chi-restraints excluded: chain K residue 553 ASN Chi-restraints excluded: chain K residue 563 VAL Chi-restraints excluded: chain K residue 579 TYR Chi-restraints excluded: chain K residue 588 THR Chi-restraints excluded: chain K residue 614 PHE Chi-restraints excluded: chain K residue 677 ILE Chi-restraints excluded: chain K residue 763 TRP Chi-restraints excluded: chain K residue 768 THR Chi-restraints excluded: chain K residue 798 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain L residue 228 GLN Chi-restraints excluded: chain L residue 230 LYS Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 318 ASP Chi-restraints excluded: chain L residue 372 HIS Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 536 SER Chi-restraints excluded: chain L residue 555 LEU Chi-restraints excluded: chain L residue 576 LEU Chi-restraints excluded: chain L residue 579 TYR Chi-restraints excluded: chain L residue 588 THR Chi-restraints excluded: chain L residue 592 LYS Chi-restraints excluded: chain L residue 677 ILE Chi-restraints excluded: chain L residue 701 ASP Chi-restraints excluded: chain L residue 763 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 123 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 137 optimal weight: 8.9990 chunk 247 optimal weight: 0.9990 chunk 405 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 339 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 140 optimal weight: 0.4980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN I 104 GLN ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 735 ASN ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 735 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.114272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.099101 restraints weight = 54180.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.101122 restraints weight = 30665.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.102468 restraints weight = 20493.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.103359 restraints weight = 15374.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.103977 restraints weight = 12601.102| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.245 37247 Z= 0.254 Angle : 0.867 59.199 50549 Z= 0.483 Chirality : 0.048 0.372 5539 Planarity : 0.006 0.144 6566 Dihedral : 5.852 33.770 5000 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 1.02 % Allowed : 11.29 % Favored : 87.69 % Rotamer: Outliers : 3.57 % Allowed : 20.57 % Favored : 75.86 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -2.58 (0.12), residues: 4516 helix: -0.49 (0.20), residues: 611 sheet: -1.34 (0.16), residues: 1101 loop : -2.26 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 46 TYR 0.018 0.001 TYR A 227 PHE 0.023 0.002 PHE J 548 TRP 0.102 0.003 TRP J 505 HIS 0.006 0.001 HIS K 66 Details of bonding type rmsd covalent geometry : bond 0.00529 (37247) covalent geometry : angle 0.86701 (50549) hydrogen bonds : bond 0.03990 ( 692) hydrogen bonds : angle 5.58112 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5988.57 seconds wall clock time: 105 minutes 12.09 seconds (6312.09 seconds total)