Starting phenix.real_space_refine on Fri Mar 6 21:31:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mrd_9196/03_2026/6mrd_9196.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mrd_9196/03_2026/6mrd_9196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mrd_9196/03_2026/6mrd_9196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mrd_9196/03_2026/6mrd_9196.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mrd_9196/03_2026/6mrd_9196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mrd_9196/03_2026/6mrd_9196.map" } resolution = 3.82 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= 0.001 sd= 0.075 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: 7 Type Number sf(0) Gaussians P 14 5.49 5 Mg 7 5.21 5 S 105 5.16 5 C 20741 2.51 5 N 5628 2.21 5 O 6545 1.98 5 H 1477 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34517 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "O" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "R" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "Q" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "P" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "G" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "F" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "E" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "D" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "C" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "B" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4147 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.83, per 1000 atoms: 0.23 Number of scatterers: 34517 At special positions: 0 Unit cell: (153.01, 156.22, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 105 16.00 P 14 15.00 Mg 7 11.99 O 6545 8.00 N 5628 7.00 C 20741 6.00 H 1477 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.3 seconds 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7938 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 50 sheets defined 48.4% alpha, 12.4% 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 9 through 26 Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 64 through 86 removed outlier: 3.843A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 104 Processing helix chain 'A' and resid 112 through 134 Processing helix chain 'A' and resid 140 through 152 removed outlier: 3.766A pdb=" N ILE A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 170 removed outlier: 3.781A pdb=" N GLY A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 244 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.507A pdb=" N LYS A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 339 through 357 Processing helix chain 'A' and resid 361 through 375 Processing helix chain 'A' and resid 386 through 410 removed outlier: 3.896A pdb=" N GLU A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.684A pdb=" N LEU A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 434 through 449 removed outlier: 4.086A pdb=" N LYS A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 460 Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 498 through 517 removed outlier: 3.773A pdb=" N THR A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'U' and resid 94 through 96 No H-bonds generated for 'chain 'U' and resid 94 through 96' Processing helix chain 'T' and resid 94 through 96 No H-bonds generated for 'chain 'T' and resid 94 through 96' Processing helix chain 'S' and resid 94 through 96 No H-bonds generated for 'chain 'S' and resid 94 through 96' Processing helix chain 'R' and resid 94 through 96 No H-bonds generated for 'chain 'R' and resid 94 through 96' Processing helix chain 'Q' and resid 94 through 96 No H-bonds generated for 'chain 'Q' and resid 94 through 96' Processing helix chain 'P' and resid 94 through 96 No H-bonds generated for 'chain 'P' and resid 94 through 96' Processing helix chain 'G' and resid 9 through 26 Processing helix chain 'G' and resid 54 through 60 Processing helix chain 'G' and resid 64 through 86 removed outlier: 3.789A pdb=" N VAL G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 104 Processing helix chain 'G' and resid 112 through 134 Processing helix chain 'G' and resid 140 through 152 removed outlier: 3.774A pdb=" N ILE G 144 " --> pdb=" O THR G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.854A pdb=" N GLY G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 244 Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 255 through 268 Processing helix chain 'G' and resid 282 through 297 removed outlier: 3.606A pdb=" N LYS G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 357 Processing helix chain 'G' and resid 361 through 375 removed outlier: 3.848A pdb=" N LYS G 365 " --> pdb=" O TYR G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 410 removed outlier: 3.804A pdb=" N GLU G 409 " --> pdb=" O ARG G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 430 removed outlier: 3.633A pdb=" N LEU G 421 " --> pdb=" O GLY G 417 " (cutoff:3.500A) Proline residue: G 425 - end of helix Processing helix chain 'G' and resid 434 through 449 removed outlier: 4.105A pdb=" N LYS G 449 " --> pdb=" O LYS G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 460 Processing helix chain 'G' and resid 462 through 473 Processing helix chain 'G' and resid 489 through 493 Processing helix chain 'G' and resid 498 through 517 removed outlier: 3.797A pdb=" N THR G 517 " --> pdb=" O SER G 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 26 Processing helix chain 'F' and resid 54 through 60 removed outlier: 3.531A pdb=" N ILE F 60 " --> pdb=" O VAL F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 removed outlier: 3.754A pdb=" N VAL F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 104 Processing helix chain 'F' and resid 112 through 134 Processing helix chain 'F' and resid 140 through 152 removed outlier: 3.754A pdb=" N ILE F 144 " --> pdb=" O THR F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 170 removed outlier: 3.823A pdb=" N GLY F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 244 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.511A pdb=" N LYS F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 297 removed outlier: 4.047A pdb=" N LYS F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 357 Processing helix chain 'F' and resid 361 through 375 removed outlier: 3.771A pdb=" N LYS F 365 " --> pdb=" O TYR F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 410 removed outlier: 3.829A pdb=" N GLU F 409 " --> pdb=" O ARG F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 430 removed outlier: 3.676A pdb=" N LEU F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) Proline residue: F 425 - end of helix Processing helix chain 'F' and resid 434 through 449 removed outlier: 4.123A pdb=" N LYS F 449 " --> pdb=" O LYS F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 460 Processing helix chain 'F' and resid 462 through 473 Processing helix chain 'F' and resid 489 through 493 Processing helix chain 'F' and resid 498 through 517 removed outlier: 3.765A pdb=" N THR F 517 " --> pdb=" O SER F 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 Processing helix chain 'E' and resid 54 through 60 Processing helix chain 'E' and resid 64 through 86 removed outlier: 3.811A pdb=" N VAL E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 104 Processing helix chain 'E' and resid 112 through 134 Processing helix chain 'E' and resid 140 through 152 removed outlier: 3.758A pdb=" N ILE E 144 " --> pdb=" O THR E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 170 removed outlier: 3.791A pdb=" N GLY E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 255 through 268 Processing helix chain 'E' and resid 282 through 297 removed outlier: 3.898A pdb=" N LYS E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 357 Processing helix chain 'E' and resid 361 through 375 Processing helix chain 'E' and resid 386 through 410 removed outlier: 3.883A pdb=" N GLU E 409 " --> pdb=" O ARG E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 430 removed outlier: 3.702A pdb=" N LEU E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Proline residue: E 425 - end of helix Processing helix chain 'E' and resid 434 through 449 removed outlier: 4.094A pdb=" N LYS E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 460 Processing helix chain 'E' and resid 462 through 473 Processing helix chain 'E' and resid 489 through 493 Processing helix chain 'E' and resid 498 through 517 removed outlier: 3.738A pdb=" N THR E 517 " --> pdb=" O SER E 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 26 Processing helix chain 'D' and resid 54 through 60 Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.698A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 104 Processing helix chain 'D' and resid 112 through 134 Processing helix chain 'D' and resid 140 through 152 removed outlier: 3.771A pdb=" N ILE D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.850A pdb=" N GLY D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 244 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 339 through 357 Processing helix chain 'D' and resid 361 through 375 Processing helix chain 'D' and resid 386 through 410 removed outlier: 3.872A pdb=" N GLU D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 430 removed outlier: 3.654A pdb=" N LEU D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) Proline residue: D 425 - end of helix Processing helix chain 'D' and resid 434 through 449 removed outlier: 4.114A pdb=" N LYS D 449 " --> pdb=" O LYS D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 460 Processing helix chain 'D' and resid 462 through 473 Processing helix chain 'D' and resid 489 through 493 Processing helix chain 'D' and resid 498 through 517 removed outlier: 3.846A pdb=" N THR D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 104 Processing helix chain 'C' and resid 112 through 134 Processing helix chain 'C' and resid 140 through 152 removed outlier: 3.746A pdb=" N ILE C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.863A pdb=" N GLY C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 244 Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 255 through 268 Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 339 through 357 Processing helix chain 'C' and resid 361 through 375 Processing helix chain 'C' and resid 386 through 410 removed outlier: 3.855A pdb=" N GLU C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 430 removed outlier: 3.619A pdb=" N LEU C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) Proline residue: C 425 - end of helix Processing helix chain 'C' and resid 434 through 449 removed outlier: 4.085A pdb=" N LYS C 449 " --> pdb=" O LYS C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 460 Processing helix chain 'C' and resid 462 through 473 Processing helix chain 'C' and resid 489 through 493 Processing helix chain 'C' and resid 498 through 517 removed outlier: 3.800A pdb=" N THR C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 64 through 86 removed outlier: 3.772A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 104 Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 140 through 152 removed outlier: 3.793A pdb=" N ILE B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.874A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 244 Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.531A pdb=" N LYS B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 removed outlier: 4.193A pdb=" N LYS B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 357 Processing helix chain 'B' and resid 361 through 375 Processing helix chain 'B' and resid 386 through 410 removed outlier: 3.811A pdb=" N GLU B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.662A pdb=" N LEU B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Proline residue: B 425 - end of helix Processing helix chain 'B' and resid 434 through 449 removed outlier: 4.042A pdb=" N LYS B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 460 Processing helix chain 'B' and resid 462 through 473 Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 498 through 517 removed outlier: 3.770A pdb=" N THR B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 5.741A pdb=" N THR B 37 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 520 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 7.329A pdb=" N THR A 37 " --> pdb=" O VAL G 520 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N VAL G 522 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 39 " --> pdb=" O VAL G 522 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N GLU G 524 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 276 removed outlier: 6.625A pdb=" N LEU A 247 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR A 219 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE A 250 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA7, first strand: chain 'A' and resid 477 through 480 Processing sheet with id=AA8, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.570A pdb=" N GLY U 98 " --> pdb=" O LEU U 72 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU U 17 " --> pdb=" O VAL U 47 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL U 49 " --> pdb=" O ARG U 15 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG U 15 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ARG U 20 " --> pdb=" O ASP U 87 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ASP U 87 " --> pdb=" O ARG U 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 79 through 83 removed outlier: 9.397A pdb=" N ASP O 87 " --> pdb=" O ARG O 20 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ARG O 20 " --> pdb=" O ASP O 87 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG O 15 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL O 49 " --> pdb=" O ARG O 15 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU O 17 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS O 70 " --> pdb=" O TYR O 100 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY O 98 " --> pdb=" O LEU O 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 10 through 11 removed outlier: 7.091A pdb=" N LEU S 17 " --> pdb=" O VAL S 47 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL S 49 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ARG S 15 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG S 20 " --> pdb=" O ASP S 87 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ASP S 87 " --> pdb=" O ARG S 20 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 79 through 83 removed outlier: 9.338A pdb=" N ASP T 87 " --> pdb=" O ARG T 20 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ARG T 20 " --> pdb=" O ASP T 87 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG T 15 " --> pdb=" O VAL T 49 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL T 49 " --> pdb=" O ARG T 15 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU T 17 " --> pdb=" O VAL T 47 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY T 98 " --> pdb=" O LEU T 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 11 removed outlier: 3.514A pdb=" N GLY R 98 " --> pdb=" O LEU R 72 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU R 17 " --> pdb=" O VAL R 47 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL R 49 " --> pdb=" O ARG R 15 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG R 15 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ARG R 20 " --> pdb=" O ASP R 87 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N ASP R 87 " --> pdb=" O ARG R 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 52 through 53 Processing sheet with id=AB5, first strand: chain 'Q' and resid 79 through 83 removed outlier: 9.382A pdb=" N ASP Q 87 " --> pdb=" O ARG Q 20 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ARG Q 20 " --> pdb=" O ASP Q 87 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG Q 15 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL Q 49 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU Q 17 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY Q 98 " --> pdb=" O LEU Q 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 79 through 83 removed outlier: 9.347A pdb=" N ASP P 87 " --> pdb=" O ARG P 20 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG P 20 " --> pdb=" O ASP P 87 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG P 15 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL P 49 " --> pdb=" O ARG P 15 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU P 17 " --> pdb=" O VAL P 47 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY P 98 " --> pdb=" O LEU P 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 48 through 50 removed outlier: 7.379A pdb=" N THR G 37 " --> pdb=" O VAL F 520 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N VAL F 522 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE G 39 " --> pdb=" O VAL F 522 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N GLU F 524 " --> pdb=" O ILE G 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 175 through 178 Processing sheet with id=AB9, first strand: chain 'G' and resid 193 through 195 Processing sheet with id=AC1, first strand: chain 'G' and resid 273 through 276 removed outlier: 6.561A pdb=" N LEU G 247 " --> pdb=" O VAL G 274 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR G 219 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ILE G 250 " --> pdb=" O TYR G 219 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 412 through 414 Processing sheet with id=AC3, first strand: chain 'G' and resid 477 through 480 Processing sheet with id=AC4, first strand: chain 'F' and resid 48 through 50 removed outlier: 7.371A pdb=" N THR F 37 " --> pdb=" O VAL E 520 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N VAL E 522 " --> pdb=" O THR F 37 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE F 39 " --> pdb=" O VAL E 522 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLU E 524 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 174 through 176 Processing sheet with id=AC6, first strand: chain 'F' and resid 193 through 195 Processing sheet with id=AC7, first strand: chain 'F' and resid 273 through 276 removed outlier: 6.602A pdb=" N LEU F 247 " --> pdb=" O VAL F 274 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR F 219 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE F 250 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AC9, first strand: chain 'F' and resid 477 through 480 Processing sheet with id=AD1, first strand: chain 'E' and resid 48 through 50 removed outlier: 7.528A pdb=" N THR E 37 " --> pdb=" O VAL D 520 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N VAL D 522 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE E 39 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N GLU D 524 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 175 through 176 Processing sheet with id=AD3, first strand: chain 'E' and resid 193 through 195 removed outlier: 3.769A pdb=" N ASP E 330 " --> pdb=" O THR E 327 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 273 through 276 removed outlier: 6.624A pdb=" N LEU E 247 " --> pdb=" O VAL E 274 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR E 219 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE E 250 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AD6, first strand: chain 'E' and resid 477 through 480 Processing sheet with id=AD7, first strand: chain 'D' and resid 48 through 50 removed outlier: 7.394A pdb=" N THR D 37 " --> pdb=" O VAL C 520 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N VAL C 522 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE D 39 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N GLU C 524 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 175 through 176 Processing sheet with id=AD9, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.777A pdb=" N ASP D 330 " --> pdb=" O THR D 327 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 273 through 276 removed outlier: 6.633A pdb=" N LEU D 247 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR D 219 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE D 250 " --> pdb=" O TYR D 219 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AE3, first strand: chain 'D' and resid 477 through 480 Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 50 removed outlier: 7.546A pdb=" N THR C 37 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N VAL B 522 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE C 39 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N GLU B 524 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 175 through 176 Processing sheet with id=AE6, first strand: chain 'C' and resid 193 through 195 Processing sheet with id=AE7, first strand: chain 'C' and resid 273 through 276 removed outlier: 6.627A pdb=" N LEU C 247 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR C 219 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE C 250 " --> pdb=" O TYR C 219 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AE9, first strand: chain 'C' and resid 477 through 480 Processing sheet with id=AF1, first strand: chain 'B' and resid 175 through 176 Processing sheet with id=AF2, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AF3, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.617A pdb=" N LEU B 247 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR B 219 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE B 250 " --> pdb=" O TYR B 219 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AF5, first strand: chain 'B' and resid 477 through 480 1828 hydrogen bonds defined for protein. 5259 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: 6.98 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1477 1.03 - 1.22: 0 1.22 - 1.42: 12473 1.42 - 1.61: 20665 1.61 - 1.81: 210 Bond restraints: 34825 Sorted by residual: bond pdb=" C1' ADP F 601 " pdb=" C2' ADP F 601 " ideal model delta sigma weight residual 1.524 1.295 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1' ADP G 601 " pdb=" C2' ADP G 601 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1' ADP E 601 " pdb=" C2' ADP E 601 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1' ADP C 601 " pdb=" C2' ADP C 601 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1' ADP A 601 " pdb=" C2' ADP A 601 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.27e+02 ... (remaining 34820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.12: 48312 10.12 - 20.23: 39 20.23 - 30.35: 30 30.35 - 40.46: 14 40.46 - 50.58: 3 Bond angle restraints: 48398 Sorted by residual: angle pdb=" C ASP F 52 " pdb=" N GLY F 53 " pdb=" H GLY F 53 " ideal model delta sigma weight residual 124.45 73.87 50.58 3.00e+00 1.11e-01 2.84e+02 angle pdb=" CA GLY F 53 " pdb=" N GLY F 53 " pdb=" H GLY F 53 " ideal model delta sigma weight residual 114.15 66.86 47.28 3.00e+00 1.11e-01 2.48e+02 angle pdb=" N ILE F 150 " pdb=" CA ILE F 150 " pdb=" HA ILE F 150 " ideal model delta sigma weight residual 110.00 68.28 41.72 3.00e+00 1.11e-01 1.93e+02 angle pdb=" N THR F 91 " pdb=" CA THR F 91 " pdb=" HA THR F 91 " ideal model delta sigma weight residual 110.00 71.55 38.45 3.00e+00 1.11e-01 1.64e+02 angle pdb=" N VAL F 54 " pdb=" CA VAL F 54 " pdb=" HA VAL F 54 " ideal model delta sigma weight residual 110.00 71.84 38.16 3.00e+00 1.11e-01 1.62e+02 ... (remaining 48393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 20948 34.15 - 68.29: 107 68.29 - 102.44: 22 102.44 - 136.58: 2 136.58 - 170.73: 12 Dihedral angle restraints: 21091 sinusoidal: 8680 harmonic: 12411 Sorted by residual: dihedral pdb=" CA LYS D 268 " pdb=" C LYS D 268 " pdb=" N VAL D 269 " pdb=" CA VAL D 269 " ideal model delta harmonic sigma weight residual -180.00 -136.62 -43.38 0 5.00e+00 4.00e-02 7.53e+01 dihedral pdb=" CA LYS A 268 " pdb=" C LYS A 268 " pdb=" N VAL A 269 " pdb=" CA VAL A 269 " ideal model delta harmonic sigma weight residual -180.00 -136.82 -43.18 0 5.00e+00 4.00e-02 7.46e+01 dihedral pdb=" CA LYS F 268 " pdb=" C LYS F 268 " pdb=" N VAL F 269 " pdb=" CA VAL F 269 " ideal model delta harmonic sigma weight residual -180.00 -136.83 -43.17 0 5.00e+00 4.00e-02 7.45e+01 ... (remaining 21088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.312: 5415 0.312 - 0.624: 2 0.624 - 0.937: 0 0.937 - 1.249: 0 1.249 - 1.561: 8 Chirality restraints: 5425 Sorted by residual: chirality pdb=" CB ILE C 494 " pdb=" CA ILE C 494 " pdb=" CG1 ILE C 494 " pdb=" CG2 ILE C 494 " both_signs ideal model delta sigma weight residual False 2.64 1.08 1.56 2.00e-01 2.50e+01 6.09e+01 chirality pdb=" CB ILE A 494 " pdb=" CA ILE A 494 " pdb=" CG1 ILE A 494 " pdb=" CG2 ILE A 494 " both_signs ideal model delta sigma weight residual False 2.64 1.10 1.55 2.00e-01 2.50e+01 6.00e+01 chirality pdb=" CB ILE E 494 " pdb=" CA ILE E 494 " pdb=" CG1 ILE E 494 " pdb=" CG2 ILE E 494 " both_signs ideal model delta sigma weight residual False 2.64 1.10 1.55 2.00e-01 2.50e+01 5.97e+01 ... (remaining 5422 not shown) Planarity restraints: 5887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 278 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 279 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 279 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 279 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 196 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C ASP D 196 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP D 196 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG D 197 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 525 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.01e+00 pdb=" N PRO D 526 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 526 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 526 " -0.024 5.00e-02 4.00e+02 ... (remaining 5884 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 221 2.16 - 2.77: 12212 2.77 - 3.38: 49333 3.38 - 3.99: 70305 3.99 - 4.60: 103960 Nonbonded interactions: 236031 Sorted by model distance: nonbonded pdb=" H GLY F 53 " pdb=" HA2 GLY F 53 " model vdw 1.548 1.816 nonbonded pdb=" H VAL F 54 " pdb=" HA VAL F 54 " model vdw 1.561 1.816 nonbonded pdb=" H ILE F 494 " pdb=" HA ILE F 494 " model vdw 1.602 1.816 nonbonded pdb=" HA ILE F 150 " pdb=" HB ILE F 150 " model vdw 1.659 1.952 nonbonded pdb=" HA THR F 91 " pdb=" HB THR F 91 " model vdw 1.684 1.952 ... (remaining 236026 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 2.820 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: 0.310 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.490 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.008 0.229 33348 Z= 0.403 Angle : 0.878 19.234 44989 Z= 0.451 Chirality : 0.073 1.561 5425 Planarity : 0.004 0.053 5761 Dihedral : 10.503 170.727 12684 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 43.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.71 % Favored : 90.11 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.11), residues: 4368 helix: -0.68 (0.10), residues: 2058 sheet: -3.13 (0.16), residues: 609 loop : -2.98 (0.13), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 13 TYR 0.012 0.002 TYR U 88 PHE 0.017 0.002 PHE B 104 TRP 0.009 0.002 TRP D 44 HIS 0.002 0.001 HIS E 243 Details of bonding type rmsd covalent geometry : bond 0.00832 (33348) covalent geometry : angle 0.87804 (44989) hydrogen bonds : bond 0.14016 ( 1828) hydrogen bonds : angle 6.49426 ( 5259) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 MET cc_start: 0.8995 (ttm) cc_final: 0.8474 (tmm) REVERT: O 32 MET cc_start: 0.8933 (ttp) cc_final: 0.8590 (ttp) REVERT: U 32 MET cc_start: 0.8927 (ttp) cc_final: 0.8699 (ptp) REVERT: S 17 LEU cc_start: 0.9531 (tp) cc_final: 0.9303 (tp) REVERT: G 219 TYR cc_start: 0.8882 (m-80) cc_final: 0.8451 (m-80) REVERT: G 292 MET cc_start: 0.9525 (mtp) cc_final: 0.9281 (mtm) REVERT: G 453 MET cc_start: 0.9029 (ttm) cc_final: 0.8208 (tmm) REVERT: E 453 MET cc_start: 0.9052 (ttm) cc_final: 0.8389 (tmm) REVERT: D 453 MET cc_start: 0.9125 (ttm) cc_final: 0.8863 (mmt) REVERT: C 219 TYR cc_start: 0.8716 (m-80) cc_final: 0.8343 (m-80) REVERT: C 292 MET cc_start: 0.9498 (mtp) cc_final: 0.9030 (mtm) REVERT: C 453 MET cc_start: 0.9045 (ttm) cc_final: 0.8276 (tmm) REVERT: B 292 MET cc_start: 0.9445 (mtp) cc_final: 0.9187 (mtm) REVERT: B 453 MET cc_start: 0.8995 (ttm) cc_final: 0.8149 (tmm) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2279 time to fit residues: 105.0333 Evaluate side-chains 156 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.0040 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 7.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 HIS G 284 ASN G 367 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 ASN F 367 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN E 367 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN D 367 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN C 367 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.031614 restraints weight = 274633.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032773 restraints weight = 146422.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.033613 restraints weight = 92678.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.034216 restraints weight = 63918.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.034649 restraints weight = 46931.660| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33348 Z= 0.116 Angle : 0.620 20.256 44989 Z= 0.311 Chirality : 0.073 1.639 5425 Planarity : 0.003 0.031 5761 Dihedral : 10.350 177.448 4669 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 50.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.85 % Favored : 91.99 % Rotamer: Outliers : 0.39 % Allowed : 5.29 % Favored : 94.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 4368 helix: 0.98 (0.12), residues: 2100 sheet: -2.75 (0.19), residues: 560 loop : -2.60 (0.13), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 171 TYR 0.011 0.001 TYR O 88 PHE 0.007 0.001 PHE R 6 TRP 0.011 0.002 TRP B 44 HIS 0.001 0.001 HIS G 243 Details of bonding type rmsd covalent geometry : bond 0.00222 (33348) covalent geometry : angle 0.62018 (44989) hydrogen bonds : bond 0.03655 ( 1828) hydrogen bonds : angle 4.84224 ( 5259) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.8363 (mtp) cc_final: 0.7906 (mmm) REVERT: A 453 MET cc_start: 0.8969 (ttm) cc_final: 0.8095 (tpp) REVERT: U 32 MET cc_start: 0.8930 (ttp) cc_final: 0.8115 (tpp) REVERT: U 84 ASP cc_start: 0.7936 (m-30) cc_final: 0.7653 (t0) REVERT: T 32 MET cc_start: 0.8489 (ptm) cc_final: 0.8137 (ptt) REVERT: T 84 ASP cc_start: 0.7676 (m-30) cc_final: 0.7363 (t0) REVERT: T 85 ASP cc_start: 0.9020 (m-30) cc_final: 0.8656 (m-30) REVERT: G 453 MET cc_start: 0.8958 (ttm) cc_final: 0.8036 (tpp) REVERT: F 292 MET cc_start: 0.9349 (mtm) cc_final: 0.8610 (mtt) REVERT: F 332 MET cc_start: 0.8677 (mtp) cc_final: 0.7920 (mmm) REVERT: F 453 MET cc_start: 0.8474 (mmt) cc_final: 0.8132 (mmm) REVERT: E 332 MET cc_start: 0.8602 (mtp) cc_final: 0.8284 (tpp) REVERT: E 453 MET cc_start: 0.8902 (ttm) cc_final: 0.8147 (tpt) REVERT: D 453 MET cc_start: 0.8870 (ttm) cc_final: 0.7965 (tpp) REVERT: C 292 MET cc_start: 0.9447 (mtp) cc_final: 0.9171 (mtm) REVERT: C 453 MET cc_start: 0.8964 (ttm) cc_final: 0.8574 (mmm) REVERT: C 471 MET cc_start: 0.8795 (mmm) cc_final: 0.8565 (mmm) REVERT: B 221 LEU cc_start: 0.9423 (tp) cc_final: 0.9144 (tt) REVERT: B 453 MET cc_start: 0.8894 (ttm) cc_final: 0.8138 (tmm) outliers start: 14 outliers final: 1 residues processed: 191 average time/residue: 0.2028 time to fit residues: 67.3710 Evaluate side-chains 151 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 13 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 286 optimal weight: 6.9990 chunk 373 optimal weight: 6.9990 chunk 424 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** U 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.038189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.030368 restraints weight = 278700.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.031478 restraints weight = 151032.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.032258 restraints weight = 95662.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.032821 restraints weight = 66841.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.033226 restraints weight = 49823.784| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33348 Z= 0.204 Angle : 0.659 20.222 44989 Z= 0.330 Chirality : 0.073 1.629 5425 Planarity : 0.003 0.033 5761 Dihedral : 9.334 170.161 4669 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 53.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.50 % Favored : 90.34 % Rotamer: Outliers : 0.65 % Allowed : 5.88 % Favored : 93.48 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 4368 helix: 1.43 (0.12), residues: 2065 sheet: -2.33 (0.19), residues: 567 loop : -2.62 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 20 TYR 0.014 0.001 TYR P 88 PHE 0.011 0.001 PHE B 195 TRP 0.009 0.002 TRP B 44 HIS 0.001 0.001 HIS G 316 Details of bonding type rmsd covalent geometry : bond 0.00414 (33348) covalent geometry : angle 0.65912 (44989) hydrogen bonds : bond 0.03571 ( 1828) hydrogen bonds : angle 4.81558 ( 5259) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.8999 (tpp) cc_final: 0.8641 (tmm) REVERT: A 332 MET cc_start: 0.8287 (mtp) cc_final: 0.7906 (tmm) REVERT: A 453 MET cc_start: 0.8973 (ttm) cc_final: 0.8108 (tpp) REVERT: O 32 MET cc_start: 0.8824 (ttp) cc_final: 0.8213 (ttp) REVERT: U 32 MET cc_start: 0.8872 (ttp) cc_final: 0.8122 (tpp) REVERT: U 84 ASP cc_start: 0.7868 (m-30) cc_final: 0.7635 (t0) REVERT: T 76 TYR cc_start: 0.9094 (m-10) cc_final: 0.8832 (m-10) REVERT: T 84 ASP cc_start: 0.7617 (m-30) cc_final: 0.7234 (t0) REVERT: T 85 ASP cc_start: 0.9063 (m-30) cc_final: 0.8712 (m-30) REVERT: Q 32 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8174 (ppp) REVERT: G 453 MET cc_start: 0.9007 (ttm) cc_final: 0.8083 (tpp) REVERT: F 332 MET cc_start: 0.8502 (mtp) cc_final: 0.7849 (mmm) REVERT: F 453 MET cc_start: 0.8558 (mmt) cc_final: 0.8249 (mmm) REVERT: E 31 MET cc_start: 0.8414 (ttm) cc_final: 0.8207 (ttm) REVERT: E 332 MET cc_start: 0.8494 (mtp) cc_final: 0.8141 (mmm) REVERT: E 453 MET cc_start: 0.8998 (ttm) cc_final: 0.8403 (tmm) REVERT: D 31 MET cc_start: 0.8338 (ttm) cc_final: 0.8012 (ttm) REVERT: D 453 MET cc_start: 0.9001 (ttm) cc_final: 0.8336 (tpp) REVERT: C 292 MET cc_start: 0.9476 (mtp) cc_final: 0.9221 (mtm) REVERT: C 453 MET cc_start: 0.9050 (ttm) cc_final: 0.8473 (tpp) REVERT: C 489 MET cc_start: 0.9013 (mmt) cc_final: 0.8771 (mmt) REVERT: B 453 MET cc_start: 0.8968 (ttm) cc_final: 0.8393 (tpp) outliers start: 23 outliers final: 15 residues processed: 165 average time/residue: 0.1951 time to fit residues: 56.6607 Evaluate side-chains 160 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain Q residue 32 MET Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 390 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 165 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 307 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 431 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** T 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 HIS ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.029206 restraints weight = 285717.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.030268 restraints weight = 154537.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.031019 restraints weight = 98082.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031548 restraints weight = 68748.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.031943 restraints weight = 51875.276| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 33348 Z= 0.296 Angle : 0.769 19.980 44989 Z= 0.382 Chirality : 0.074 1.623 5425 Planarity : 0.004 0.036 5761 Dihedral : 7.939 152.843 4669 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 61.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.61 % Favored : 88.23 % Rotamer: Outliers : 1.15 % Allowed : 6.89 % Favored : 91.96 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -1.25 (0.13), residues: 4368 helix: 1.04 (0.11), residues: 2100 sheet: -2.50 (0.18), residues: 581 loop : -2.68 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 369 TYR 0.008 0.001 TYR G 479 PHE 0.017 0.002 PHE D 195 TRP 0.011 0.002 TRP G 44 HIS 0.002 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00605 (33348) covalent geometry : angle 0.76911 (44989) hydrogen bonds : bond 0.03826 ( 1828) hydrogen bonds : angle 5.13685 ( 5259) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.8989 (tpp) cc_final: 0.8622 (tmm) REVERT: A 332 MET cc_start: 0.8386 (mtp) cc_final: 0.8053 (tmm) REVERT: A 453 MET cc_start: 0.8970 (ttm) cc_final: 0.8379 (tpp) REVERT: U 32 MET cc_start: 0.8881 (ttp) cc_final: 0.8257 (ptt) REVERT: T 85 ASP cc_start: 0.9106 (m-30) cc_final: 0.8879 (m-30) REVERT: G 453 MET cc_start: 0.9030 (ttm) cc_final: 0.8675 (tpp) REVERT: F 292 MET cc_start: 0.9313 (mtm) cc_final: 0.8499 (mtm) REVERT: F 427 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9216 (tp) REVERT: F 453 MET cc_start: 0.8635 (mmt) cc_final: 0.8341 (mmm) REVERT: E 332 MET cc_start: 0.8378 (mtp) cc_final: 0.8070 (mmm) REVERT: E 453 MET cc_start: 0.9014 (ttm) cc_final: 0.8511 (tmm) REVERT: D 453 MET cc_start: 0.9049 (ttm) cc_final: 0.8657 (tpp) REVERT: C 292 MET cc_start: 0.9492 (mtp) cc_final: 0.9149 (mtt) REVERT: C 489 MET cc_start: 0.9195 (mmt) cc_final: 0.8925 (mmt) REVERT: B 453 MET cc_start: 0.8990 (ttm) cc_final: 0.8481 (tmm) outliers start: 41 outliers final: 22 residues processed: 173 average time/residue: 0.1970 time to fit residues: 59.3229 Evaluate side-chains 159 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 32 MET Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 390 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 134 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 327 optimal weight: 0.9980 chunk 367 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 171 optimal weight: 0.1980 chunk 303 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 GLN F 284 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.038107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.030222 restraints weight = 279012.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.031335 restraints weight = 148549.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.032112 restraints weight = 93555.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.032677 restraints weight = 65198.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.033079 restraints weight = 48766.716| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33348 Z= 0.103 Angle : 0.568 20.403 44989 Z= 0.282 Chirality : 0.073 1.639 5425 Planarity : 0.003 0.036 5761 Dihedral : 7.585 161.937 4669 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 52.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.87 % Allowed : 7.17 % Favored : 91.96 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -0.32 (0.13), residues: 4368 helix: 1.88 (0.12), residues: 2100 sheet: -1.99 (0.22), residues: 525 loop : -2.38 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 369 TYR 0.009 0.001 TYR B 66 PHE 0.010 0.001 PHE D 195 TRP 0.013 0.002 TRP D 44 HIS 0.001 0.000 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00209 (33348) covalent geometry : angle 0.56779 (44989) hydrogen bonds : bond 0.03075 ( 1828) hydrogen bonds : angle 4.39709 ( 5259) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.8989 (tpp) cc_final: 0.8600 (tmm) REVERT: A 292 MET cc_start: 0.9153 (mtm) cc_final: 0.8501 (mtt) REVERT: A 332 MET cc_start: 0.8443 (mtp) cc_final: 0.8071 (tmm) REVERT: A 453 MET cc_start: 0.8945 (ttm) cc_final: 0.8279 (tpp) REVERT: O 76 TYR cc_start: 0.8852 (m-10) cc_final: 0.8651 (m-10) REVERT: U 32 MET cc_start: 0.8815 (ttp) cc_final: 0.8359 (ptt) REVERT: T 76 TYR cc_start: 0.9094 (m-10) cc_final: 0.8862 (m-10) REVERT: T 84 ASP cc_start: 0.7605 (m-30) cc_final: 0.7184 (t0) REVERT: T 85 ASP cc_start: 0.9099 (m-30) cc_final: 0.8740 (m-30) REVERT: Q 32 MET cc_start: 0.8974 (ptt) cc_final: 0.8166 (ppp) REVERT: Q 85 ASP cc_start: 0.9043 (m-30) cc_final: 0.8813 (m-30) REVERT: G 453 MET cc_start: 0.8952 (ttm) cc_final: 0.8700 (tpp) REVERT: F 292 MET cc_start: 0.9310 (mtm) cc_final: 0.8630 (mtt) REVERT: F 332 MET cc_start: 0.8549 (mtm) cc_final: 0.8228 (mmm) REVERT: F 453 MET cc_start: 0.8534 (mmt) cc_final: 0.8242 (mmm) REVERT: E 31 MET cc_start: 0.8138 (ttm) cc_final: 0.7929 (ttm) REVERT: E 332 MET cc_start: 0.8498 (mtp) cc_final: 0.8163 (mmm) REVERT: E 453 MET cc_start: 0.8969 (ttm) cc_final: 0.8509 (tmm) REVERT: D 453 MET cc_start: 0.8997 (ttm) cc_final: 0.8571 (tpp) REVERT: C 453 MET cc_start: 0.8479 (mmm) cc_final: 0.7986 (mmm) REVERT: B 453 MET cc_start: 0.8956 (ttm) cc_final: 0.8594 (tpp) outliers start: 31 outliers final: 16 residues processed: 169 average time/residue: 0.1961 time to fit residues: 57.7795 Evaluate side-chains 155 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 32 MET Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 390 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 362 optimal weight: 4.9990 chunk 411 optimal weight: 8.9990 chunk 392 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 399 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 306 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 HIS ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.036983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.029250 restraints weight = 284534.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.030312 restraints weight = 153213.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.031079 restraints weight = 96748.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.031590 restraints weight = 67696.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.031988 restraints weight = 51089.927| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 33348 Z= 0.278 Angle : 0.725 20.007 44989 Z= 0.359 Chirality : 0.073 1.621 5425 Planarity : 0.003 0.033 5761 Dihedral : 7.599 174.922 4669 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 60.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.38 % Favored : 88.60 % Rotamer: Outliers : 1.07 % Allowed : 7.90 % Favored : 91.03 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -0.78 (0.13), residues: 4368 helix: 1.48 (0.12), residues: 2100 sheet: -2.20 (0.19), residues: 560 loop : -2.56 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 396 TYR 0.007 0.001 TYR E 479 PHE 0.017 0.002 PHE D 195 TRP 0.013 0.002 TRP G 44 HIS 0.002 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00569 (33348) covalent geometry : angle 0.72489 (44989) hydrogen bonds : bond 0.03502 ( 1828) hydrogen bonds : angle 4.87522 ( 5259) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.9212 (mtm) cc_final: 0.8856 (mtm) REVERT: A 332 MET cc_start: 0.8323 (mtp) cc_final: 0.8041 (tmm) REVERT: A 453 MET cc_start: 0.8979 (ttm) cc_final: 0.8366 (tpp) REVERT: T 85 ASP cc_start: 0.9112 (m-30) cc_final: 0.8875 (m-30) REVERT: Q 85 ASP cc_start: 0.9069 (m-30) cc_final: 0.8852 (m-30) REVERT: G 453 MET cc_start: 0.9038 (ttm) cc_final: 0.8753 (tpp) REVERT: F 292 MET cc_start: 0.9316 (mtm) cc_final: 0.8683 (mtt) REVERT: F 332 MET cc_start: 0.8492 (mtm) cc_final: 0.8092 (mmm) REVERT: F 453 MET cc_start: 0.8505 (mmt) cc_final: 0.8125 (mmm) REVERT: E 31 MET cc_start: 0.8217 (ttm) cc_final: 0.8015 (ttm) REVERT: E 332 MET cc_start: 0.8423 (mtp) cc_final: 0.8141 (mmm) REVERT: E 453 MET cc_start: 0.9015 (ttm) cc_final: 0.8548 (tmm) REVERT: D 453 MET cc_start: 0.9043 (ttm) cc_final: 0.8662 (tpp) REVERT: B 453 MET cc_start: 0.8986 (ttm) cc_final: 0.8547 (tmm) outliers start: 38 outliers final: 26 residues processed: 163 average time/residue: 0.2000 time to fit residues: 56.7644 Evaluate side-chains 160 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 390 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 73 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 370 optimal weight: 0.0870 chunk 367 optimal weight: 8.9990 chunk 208 optimal weight: 0.9990 chunk 376 optimal weight: 0.9990 chunk 352 optimal weight: 0.0270 chunk 251 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 400 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.038395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030526 restraints weight = 276882.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.031660 restraints weight = 146520.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.032444 restraints weight = 91443.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.032996 restraints weight = 63614.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.033406 restraints weight = 47300.514| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33348 Z= 0.084 Angle : 0.549 20.416 44989 Z= 0.270 Chirality : 0.073 1.640 5425 Planarity : 0.003 0.036 5761 Dihedral : 7.225 178.768 4669 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 52.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.65 % Allowed : 8.21 % Favored : 91.14 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: 0.04 (0.13), residues: 4368 helix: 2.27 (0.12), residues: 2086 sheet: -1.71 (0.22), residues: 525 loop : -2.32 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 369 TYR 0.009 0.001 TYR B 66 PHE 0.009 0.001 PHE D 195 TRP 0.013 0.002 TRP G 44 HIS 0.001 0.000 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00170 (33348) covalent geometry : angle 0.54931 (44989) hydrogen bonds : bond 0.02868 ( 1828) hydrogen bonds : angle 4.18707 ( 5259) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.9126 (mtm) cc_final: 0.8489 (mtt) REVERT: A 332 MET cc_start: 0.8380 (mtp) cc_final: 0.8077 (tmm) REVERT: A 453 MET cc_start: 0.8931 (ttm) cc_final: 0.8271 (tpp) REVERT: O 76 TYR cc_start: 0.8790 (m-10) cc_final: 0.8557 (m-10) REVERT: U 32 MET cc_start: 0.8583 (ptm) cc_final: 0.8175 (ptt) REVERT: T 76 TYR cc_start: 0.9038 (m-10) cc_final: 0.8813 (m-10) REVERT: T 85 ASP cc_start: 0.9123 (m-30) cc_final: 0.8886 (m-30) REVERT: R 32 MET cc_start: 0.9189 (ptt) cc_final: 0.8572 (ppp) REVERT: Q 85 ASP cc_start: 0.9056 (m-30) cc_final: 0.8843 (m-30) REVERT: P 32 MET cc_start: 0.9176 (ptm) cc_final: 0.8909 (ptt) REVERT: G 453 MET cc_start: 0.8971 (ttm) cc_final: 0.8575 (tpp) REVERT: F 292 MET cc_start: 0.9337 (mtm) cc_final: 0.8707 (mtt) REVERT: F 332 MET cc_start: 0.8517 (mtm) cc_final: 0.8117 (mmm) REVERT: F 453 MET cc_start: 0.8493 (mmt) cc_final: 0.8203 (mmm) REVERT: E 332 MET cc_start: 0.8496 (mtp) cc_final: 0.8173 (mmm) REVERT: E 453 MET cc_start: 0.8952 (ttm) cc_final: 0.8655 (tmm) REVERT: D 292 MET cc_start: 0.9447 (mtm) cc_final: 0.8710 (mtt) REVERT: D 453 MET cc_start: 0.8993 (ttm) cc_final: 0.8566 (tpp) REVERT: B 453 MET cc_start: 0.8953 (ttm) cc_final: 0.8693 (tpp) outliers start: 23 outliers final: 17 residues processed: 159 average time/residue: 0.1856 time to fit residues: 51.7880 Evaluate side-chains 152 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain C residue 500 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 183 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 316 optimal weight: 9.9990 chunk 371 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 0.0470 chunk 277 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.037990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.030157 restraints weight = 278877.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.031248 restraints weight = 148847.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.032020 restraints weight = 93843.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.032584 restraints weight = 65406.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.032965 restraints weight = 48827.396| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33348 Z= 0.135 Angle : 0.574 20.393 44989 Z= 0.282 Chirality : 0.072 1.620 5425 Planarity : 0.003 0.036 5761 Dihedral : 7.035 169.001 4669 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 54.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.76 % Allowed : 8.61 % Favored : 90.64 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: 0.10 (0.13), residues: 4368 helix: 2.31 (0.12), residues: 2100 sheet: -1.55 (0.20), residues: 602 loop : -2.39 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 20 TYR 0.007 0.001 TYR B 66 PHE 0.026 0.001 PHE B 281 TRP 0.015 0.002 TRP G 44 HIS 0.002 0.000 HIS G 243 Details of bonding type rmsd covalent geometry : bond 0.00274 (33348) covalent geometry : angle 0.57409 (44989) hydrogen bonds : bond 0.02862 ( 1828) hydrogen bonds : angle 4.22039 ( 5259) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.9134 (mtm) cc_final: 0.8502 (mtm) REVERT: A 332 MET cc_start: 0.8291 (mtp) cc_final: 0.8009 (tmm) REVERT: A 453 MET cc_start: 0.8957 (ttm) cc_final: 0.8335 (tpp) REVERT: O 76 TYR cc_start: 0.8777 (m-10) cc_final: 0.8517 (m-10) REVERT: U 32 MET cc_start: 0.8546 (ptm) cc_final: 0.8161 (ptt) REVERT: T 85 ASP cc_start: 0.9120 (m-30) cc_final: 0.8880 (m-30) REVERT: R 32 MET cc_start: 0.9177 (ptt) cc_final: 0.8583 (ppp) REVERT: Q 85 ASP cc_start: 0.9037 (m-30) cc_final: 0.8813 (m-30) REVERT: P 32 MET cc_start: 0.9156 (ptm) cc_final: 0.8889 (ptt) REVERT: G 453 MET cc_start: 0.8991 (ttm) cc_final: 0.8684 (tpp) REVERT: F 225 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8559 (mmtp) REVERT: F 332 MET cc_start: 0.8406 (mtm) cc_final: 0.8009 (mmm) REVERT: F 453 MET cc_start: 0.8524 (mmt) cc_final: 0.8252 (mmm) REVERT: E 332 MET cc_start: 0.8419 (mtp) cc_final: 0.8112 (mmm) REVERT: E 453 MET cc_start: 0.8969 (ttm) cc_final: 0.8659 (tmm) REVERT: D 453 MET cc_start: 0.9005 (ttm) cc_final: 0.8615 (tpp) REVERT: B 453 MET cc_start: 0.8967 (ttm) cc_final: 0.8710 (tpp) outliers start: 27 outliers final: 21 residues processed: 153 average time/residue: 0.1820 time to fit residues: 48.2771 Evaluate side-chains 156 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 500 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 64 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 334 optimal weight: 0.2980 chunk 118 optimal weight: 0.9990 chunk 337 optimal weight: 0.2980 chunk 326 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.038887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.031003 restraints weight = 274330.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.032124 restraints weight = 146467.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.032916 restraints weight = 92474.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.033495 restraints weight = 64331.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.033881 restraints weight = 47705.652| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33348 Z= 0.079 Angle : 0.537 20.526 44989 Z= 0.262 Chirality : 0.072 1.640 5425 Planarity : 0.003 0.037 5761 Dihedral : 6.680 144.450 4669 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 51.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.56 % Allowed : 8.75 % Favored : 90.69 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: 0.50 (0.14), residues: 4368 helix: 2.64 (0.12), residues: 2100 sheet: -1.40 (0.22), residues: 539 loop : -2.17 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 266 TYR 0.008 0.001 TYR B 66 PHE 0.011 0.001 PHE B 195 TRP 0.015 0.002 TRP G 44 HIS 0.001 0.000 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00160 (33348) covalent geometry : angle 0.53679 (44989) hydrogen bonds : bond 0.02616 ( 1828) hydrogen bonds : angle 3.94341 ( 5259) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8986 (mtm) cc_final: 0.8573 (mtt) REVERT: A 332 MET cc_start: 0.8297 (mtp) cc_final: 0.7976 (tmm) REVERT: A 453 MET cc_start: 0.8965 (ttm) cc_final: 0.8295 (tpp) REVERT: O 76 TYR cc_start: 0.8777 (m-10) cc_final: 0.8549 (m-10) REVERT: U 32 MET cc_start: 0.8497 (ptm) cc_final: 0.8094 (ptt) REVERT: U 84 ASP cc_start: 0.7950 (m-30) cc_final: 0.7463 (t0) REVERT: T 32 MET cc_start: 0.9026 (ptm) cc_final: 0.8791 (ptt) REVERT: T 85 ASP cc_start: 0.9086 (m-30) cc_final: 0.8830 (m-30) REVERT: R 32 MET cc_start: 0.9188 (ptt) cc_final: 0.8602 (ppp) REVERT: Q 32 MET cc_start: 0.8981 (ptt) cc_final: 0.8721 (ptt) REVERT: P 32 MET cc_start: 0.9165 (ptm) cc_final: 0.8910 (ptt) REVERT: G 453 MET cc_start: 0.8941 (ttm) cc_final: 0.8589 (tpp) REVERT: F 332 MET cc_start: 0.8404 (mtm) cc_final: 0.8011 (mmm) REVERT: F 453 MET cc_start: 0.8511 (mmt) cc_final: 0.8219 (mmm) REVERT: E 332 MET cc_start: 0.8449 (mtp) cc_final: 0.8111 (mmm) REVERT: E 453 MET cc_start: 0.8926 (ttm) cc_final: 0.8473 (tmm) REVERT: D 453 MET cc_start: 0.8980 (ttm) cc_final: 0.8569 (tpp) REVERT: B 453 MET cc_start: 0.8944 (ttm) cc_final: 0.8708 (tpp) outliers start: 20 outliers final: 17 residues processed: 154 average time/residue: 0.1966 time to fit residues: 53.2832 Evaluate side-chains 154 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 426 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 324 optimal weight: 2.9990 chunk 307 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 326 optimal weight: 3.9990 chunk 430 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.038608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030657 restraints weight = 278564.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.031770 restraints weight = 148810.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.032544 restraints weight = 93825.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.033127 restraints weight = 65365.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033515 restraints weight = 48776.431| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 33348 Z= 0.114 Angle : 0.553 20.434 44989 Z= 0.269 Chirality : 0.072 1.624 5425 Planarity : 0.003 0.037 5761 Dihedral : 6.528 125.178 4669 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 53.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.62 % Allowed : 8.72 % Favored : 90.66 % 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 are not related in a simple way. whole: 0.51 (0.14), residues: 4368 helix: 2.65 (0.12), residues: 2100 sheet: -1.27 (0.21), residues: 609 loop : -2.23 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 20 TYR 0.008 0.001 TYR Q 76 PHE 0.009 0.001 PHE D 195 TRP 0.016 0.002 TRP G 44 HIS 0.001 0.000 HIS G 243 Details of bonding type rmsd covalent geometry : bond 0.00232 (33348) covalent geometry : angle 0.55322 (44989) hydrogen bonds : bond 0.02644 ( 1828) hydrogen bonds : angle 3.99102 ( 5259) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.9300 (mtm) cc_final: 0.8577 (mtt) REVERT: A 332 MET cc_start: 0.8220 (mtp) cc_final: 0.7948 (tmm) REVERT: A 453 MET cc_start: 0.8947 (ttm) cc_final: 0.8330 (tpp) REVERT: O 32 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8533 (ptt) REVERT: O 76 TYR cc_start: 0.8779 (m-10) cc_final: 0.8548 (m-10) REVERT: U 32 MET cc_start: 0.8529 (ptm) cc_final: 0.8153 (ptt) REVERT: U 84 ASP cc_start: 0.7895 (m-30) cc_final: 0.7427 (t0) REVERT: T 32 MET cc_start: 0.9035 (ptm) cc_final: 0.8822 (ptt) REVERT: T 85 ASP cc_start: 0.9084 (m-30) cc_final: 0.8857 (m-30) REVERT: R 32 MET cc_start: 0.9158 (ptt) cc_final: 0.8578 (ppp) REVERT: Q 32 MET cc_start: 0.8961 (ptt) cc_final: 0.8720 (ptt) REVERT: P 32 MET cc_start: 0.9130 (ptm) cc_final: 0.8875 (ptt) REVERT: G 453 MET cc_start: 0.8947 (ttm) cc_final: 0.8665 (tpp) REVERT: F 225 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8382 (mmtp) REVERT: F 453 MET cc_start: 0.8488 (mmt) cc_final: 0.8214 (mmm) REVERT: E 332 MET cc_start: 0.8423 (mtp) cc_final: 0.8084 (mmm) REVERT: E 453 MET cc_start: 0.8925 (ttm) cc_final: 0.8639 (tmm) REVERT: D 292 MET cc_start: 0.9310 (mtm) cc_final: 0.8730 (mtt) REVERT: D 453 MET cc_start: 0.8972 (ttm) cc_final: 0.8596 (tpp) REVERT: B 453 MET cc_start: 0.8936 (ttm) cc_final: 0.8722 (tpp) outliers start: 22 outliers final: 19 residues processed: 150 average time/residue: 0.1972 time to fit residues: 51.4375 Evaluate side-chains 156 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 337 optimal weight: 2.9990 chunk 257 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 411 optimal weight: 10.0000 chunk 307 optimal weight: 9.9990 chunk 341 optimal weight: 7.9990 chunk 414 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 302 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 367 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 HIS E 367 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.037191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.029371 restraints weight = 285599.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.030440 restraints weight = 152997.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.031211 restraints weight = 96962.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.031729 restraints weight = 67627.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.032138 restraints weight = 50987.977| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 33348 Z= 0.270 Angle : 0.721 20.065 44989 Z= 0.354 Chirality : 0.073 1.614 5425 Planarity : 0.003 0.034 5761 Dihedral : 6.837 123.371 4669 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 60.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 0.70 % Allowed : 9.06 % Favored : 90.24 % 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 are not related in a simple way. whole: -0.12 (0.13), residues: 4368 helix: 1.98 (0.11), residues: 2100 sheet: -1.60 (0.20), residues: 567 loop : -2.29 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 197 TYR 0.009 0.001 TYR T 88 PHE 0.014 0.002 PHE D 195 TRP 0.015 0.002 TRP B 44 HIS 0.003 0.001 HIS G 243 Details of bonding type rmsd covalent geometry : bond 0.00554 (33348) covalent geometry : angle 0.72060 (44989) hydrogen bonds : bond 0.03394 ( 1828) hydrogen bonds : angle 4.68761 ( 5259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4233.19 seconds wall clock time: 75 minutes 41.24 seconds (4541.24 seconds total)