Starting phenix.real_space_refine on Sun Jun 29 18:36:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mrd_9196/06_2025/6mrd_9196.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mrd_9196/06_2025/6mrd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6mrd_9196/06_2025/6mrd_9196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mrd_9196/06_2025/6mrd_9196.map" model { file = "/net/cci-nas-00/data/ceres_data/6mrd_9196/06_2025/6mrd_9196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mrd_9196/06_2025/6mrd_9196.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.075 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): 1.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.44, per 1000 atoms: 0.56 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: 8.50 Conformation dependent library (CDL) restraints added in 4.2 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: 4.56 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: 13.53 Time building geometry restraints manager: 10.05 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: 0.04 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.920 Extract box with map and model: 1.310 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 75.950 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.370 ------------------------------------------------------------------------------- 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 : 43.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (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 TRP 0.009 0.002 TRP D 44 HIS 0.002 0.001 HIS E 243 PHE 0.017 0.002 PHE B 104 TYR 0.012 0.002 TYR U 88 ARG 0.007 0.001 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.14016 ( 1828) hydrogen bonds : angle 6.49426 ( 5259) covalent geometry : bond 0.00832 (33348) covalent geometry : angle 0.87804 (44989) *********************** 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 : 3.554 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: 0.4739 time to fit residues: 219.8352 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 : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 5.9990 chunk 328 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 340 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 253 optimal weight: 0.0040 chunk 394 optimal weight: 0.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.038975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.031149 restraints weight = 276815.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.032306 restraints weight = 147434.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.033128 restraints weight = 93454.182| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33348 Z= 0.133 Angle : 0.636 20.155 44989 Z= 0.320 Chirality : 0.073 1.634 5425 Planarity : 0.003 0.030 5761 Dihedral : 10.393 178.129 4669 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 52.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.31 % Favored : 91.53 % Rotamer: Outliers : 0.42 % Allowed : 5.40 % Favored : 94.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4368 helix: 0.96 (0.12), residues: 2079 sheet: -2.79 (0.19), residues: 560 loop : -2.67 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 44 HIS 0.001 0.001 HIS D 316 PHE 0.008 0.001 PHE R 6 TYR 0.014 0.001 TYR O 88 ARG 0.004 0.000 ARG B 171 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 1828) hydrogen bonds : angle 4.95555 ( 5259) covalent geometry : bond 0.00270 (33348) covalent geometry : angle 0.63605 (44989) *********************** 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 186 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 4.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.8312 (mtp) cc_final: 0.7918 (mmm) REVERT: A 453 MET cc_start: 0.9018 (ttm) cc_final: 0.8111 (tpp) REVERT: U 32 MET cc_start: 0.8968 (ttp) cc_final: 0.8141 (tpp) REVERT: T 32 MET cc_start: 0.8542 (ptm) cc_final: 0.8184 (ptt) REVERT: T 84 ASP cc_start: 0.7758 (m-30) cc_final: 0.7385 (t0) REVERT: T 85 ASP cc_start: 0.9079 (m-30) cc_final: 0.8720 (m-30) REVERT: G 453 MET cc_start: 0.9037 (ttm) cc_final: 0.8058 (tpp) REVERT: F 292 MET cc_start: 0.9319 (mtm) cc_final: 0.8575 (mtt) REVERT: F 332 MET cc_start: 0.8607 (mtp) cc_final: 0.7929 (mmm) REVERT: F 453 MET cc_start: 0.8538 (mmt) cc_final: 0.8228 (mmm) REVERT: E 332 MET cc_start: 0.8552 (mtp) cc_final: 0.8243 (mmm) REVERT: E 453 MET cc_start: 0.8972 (ttm) cc_final: 0.8334 (tmm) REVERT: D 453 MET cc_start: 0.8985 (ttm) cc_final: 0.8080 (tpp) REVERT: C 292 MET cc_start: 0.9453 (mtp) cc_final: 0.9181 (mtm) REVERT: C 453 MET cc_start: 0.9001 (ttm) cc_final: 0.8149 (tmm) REVERT: C 471 MET cc_start: 0.8843 (mmm) cc_final: 0.8616 (mmm) REVERT: B 31 MET cc_start: 0.8076 (ttm) cc_final: 0.7780 (ttm) REVERT: B 453 MET cc_start: 0.8943 (ttm) cc_final: 0.8152 (tmm) outliers start: 15 outliers final: 5 residues processed: 180 average time/residue: 0.4257 time to fit residues: 132.4733 Evaluate side-chains 158 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 3.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain P residue 17 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 86 optimal weight: 20.0000 chunk 165 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 382 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 361 optimal weight: 9.9990 chunk 102 optimal weight: 0.0470 overall best weight: 2.0682 ------------------------------------------------------------------------------- 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 ** U 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** ** G 211 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** ** C 284 ASN ** 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 = 0.3064 r_free = 0.3064 target = 0.038811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031003 restraints weight = 276801.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.032124 restraints weight = 149609.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.032909 restraints weight = 94642.527| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33348 Z= 0.139 Angle : 0.599 20.312 44989 Z= 0.299 Chirality : 0.073 1.636 5425 Planarity : 0.003 0.034 5761 Dihedral : 9.277 168.154 4669 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 50.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.68 % Favored : 91.25 % Rotamer: Outliers : 0.59 % Allowed : 5.74 % Favored : 93.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4368 helix: 1.59 (0.12), residues: 2079 sheet: -2.44 (0.19), residues: 588 loop : -2.54 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 44 HIS 0.001 0.000 HIS G 316 PHE 0.010 0.001 PHE B 195 TYR 0.012 0.001 TYR P 88 ARG 0.004 0.000 ARG P 20 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 1828) hydrogen bonds : angle 4.59682 ( 5259) covalent geometry : bond 0.00279 (33348) covalent geometry : angle 0.59942 (44989) *********************** 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 181 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 3.714 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: 0.8863 (mmm) cc_final: 0.8619 (tmm) REVERT: A 332 MET cc_start: 0.8313 (mtp) cc_final: 0.7976 (tmm) REVERT: O 32 MET cc_start: 0.8767 (ttp) cc_final: 0.8210 (ttp) REVERT: U 4 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7487 (tm-30) REVERT: U 32 MET cc_start: 0.8878 (ttp) cc_final: 0.8294 (ptt) REVERT: U 84 ASP cc_start: 0.7873 (m-30) cc_final: 0.7651 (t0) REVERT: T 76 TYR cc_start: 0.9068 (m-10) cc_final: 0.8836 (m-10) REVERT: T 84 ASP cc_start: 0.7616 (m-30) cc_final: 0.7235 (t0) REVERT: T 85 ASP cc_start: 0.9060 (m-30) cc_final: 0.8708 (m-30) REVERT: Q 32 MET cc_start: 0.8408 (ptt) cc_final: 0.8126 (ppp) REVERT: G 453 MET cc_start: 0.8976 (ttm) cc_final: 0.8050 (tpp) REVERT: F 81 THR cc_start: 0.9294 (m) cc_final: 0.9092 (p) REVERT: F 332 MET cc_start: 0.8457 (mtp) cc_final: 0.7834 (mmm) REVERT: F 453 MET cc_start: 0.8564 (mmt) cc_final: 0.8246 (mmm) REVERT: E 332 MET cc_start: 0.8469 (mtp) cc_final: 0.8143 (mmm) REVERT: E 453 MET cc_start: 0.8970 (ttm) cc_final: 0.8316 (tmm) REVERT: D 281 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8055 (m-10) REVERT: D 453 MET cc_start: 0.8953 (ttm) cc_final: 0.8286 (tpp) REVERT: C 453 MET cc_start: 0.9029 (ttm) cc_final: 0.8116 (tpp) REVERT: C 489 MET cc_start: 0.8988 (mmt) cc_final: 0.8746 (mmt) REVERT: B 453 MET cc_start: 0.8933 (ttm) cc_final: 0.8384 (tpp) outliers start: 21 outliers final: 11 residues processed: 173 average time/residue: 0.4351 time to fit residues: 130.7708 Evaluate side-chains 161 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain B residue 332 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 370 optimal weight: 9.9990 chunk 300 optimal weight: 5.9990 chunk 321 optimal weight: 0.2980 chunk 44 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 chunk 353 optimal weight: 0.8980 chunk 429 optimal weight: 0.0270 chunk 402 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 363 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 GLN 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** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.039902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.032063 restraints weight = 268842.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.033232 restraints weight = 142242.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.034029 restraints weight = 89068.743| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2408 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= 0.079 Angle : 0.548 20.254 44989 Z= 0.267 Chirality : 0.073 1.657 5425 Planarity : 0.003 0.036 5761 Dihedral : 7.880 148.174 4669 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 48.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.53 % Allowed : 6.44 % Favored : 93.03 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4368 helix: 2.19 (0.12), residues: 2093 sheet: -1.87 (0.21), residues: 539 loop : -2.33 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 44 HIS 0.001 0.001 HIS C 316 PHE 0.007 0.001 PHE D 195 TYR 0.009 0.001 TYR B 66 ARG 0.002 0.000 ARG U 20 Details of bonding type rmsd hydrogen bonds : bond 0.02741 ( 1828) hydrogen bonds : angle 4.14605 ( 5259) covalent geometry : bond 0.00156 (33348) covalent geometry : angle 0.54796 (44989) *********************** 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 188 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 3.722 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: 0.8944 (mmm) cc_final: 0.8604 (tmm) REVERT: A 332 MET cc_start: 0.8360 (mtp) cc_final: 0.7982 (tmm) REVERT: A 453 MET cc_start: 0.8653 (mmm) cc_final: 0.8234 (mmm) REVERT: O 32 MET cc_start: 0.8715 (ttp) cc_final: 0.8092 (ttp) REVERT: U 32 MET cc_start: 0.8729 (ttp) cc_final: 0.8303 (ptt) REVERT: U 84 ASP cc_start: 0.7916 (m-30) cc_final: 0.7706 (t0) REVERT: T 84 ASP cc_start: 0.7855 (m-30) cc_final: 0.7485 (t0) REVERT: T 85 ASP cc_start: 0.9103 (m-30) cc_final: 0.8704 (m-30) REVERT: R 32 MET cc_start: 0.8770 (ptt) cc_final: 0.8387 (ppp) REVERT: Q 32 MET cc_start: 0.8405 (ptt) cc_final: 0.8161 (ppp) REVERT: Q 85 ASP cc_start: 0.9035 (m-30) cc_final: 0.8813 (m-30) REVERT: G 453 MET cc_start: 0.8960 (ttm) cc_final: 0.7997 (tpp) REVERT: F 81 THR cc_start: 0.9302 (m) cc_final: 0.9092 (p) REVERT: F 292 MET cc_start: 0.9312 (mtm) cc_final: 0.8636 (mtt) REVERT: F 453 MET cc_start: 0.8545 (mmt) cc_final: 0.8235 (mmm) REVERT: E 332 MET cc_start: 0.8515 (mtp) cc_final: 0.8251 (mtm) REVERT: E 453 MET cc_start: 0.8923 (ttm) cc_final: 0.8105 (tpp) REVERT: D 292 MET cc_start: 0.9427 (mtm) cc_final: 0.8724 (mtt) REVERT: D 453 MET cc_start: 0.8925 (ttm) cc_final: 0.8293 (tpp) REVERT: C 453 MET cc_start: 0.9018 (ttm) cc_final: 0.8057 (tpp) REVERT: B 453 MET cc_start: 0.8891 (ttm) cc_final: 0.8331 (tpp) outliers start: 19 outliers final: 9 residues processed: 180 average time/residue: 0.4227 time to fit residues: 132.6550 Evaluate side-chains 152 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 3.774 ------------------------------------------------------------------------------- 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 G residue 269 VAL Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain C residue 500 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 41 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 394 optimal weight: 7.9990 chunk 235 optimal weight: 0.8980 chunk 25 optimal weight: 0.0470 chunk 285 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 300 optimal weight: 0.0870 chunk 352 optimal weight: 8.9990 chunk 307 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 overall best weight: 1.0058 ------------------------------------------------------------------------------- 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** ** U 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** ** 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** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.039663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.031772 restraints weight = 272638.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.032956 restraints weight = 144629.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.033768 restraints weight = 89787.782| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33348 Z= 0.089 Angle : 0.544 20.246 44989 Z= 0.264 Chirality : 0.072 1.623 5425 Planarity : 0.003 0.037 5761 Dihedral : 7.315 164.956 4669 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 48.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.90 % Allowed : 6.55 % Favored : 92.55 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 4368 helix: 2.50 (0.12), residues: 2086 sheet: -1.62 (0.21), residues: 574 loop : -2.31 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 44 HIS 0.001 0.000 HIS G 316 PHE 0.009 0.001 PHE A 281 TYR 0.027 0.001 TYR U 76 ARG 0.002 0.000 ARG U 20 Details of bonding type rmsd hydrogen bonds : bond 0.02639 ( 1828) hydrogen bonds : angle 4.06832 ( 5259) covalent geometry : bond 0.00178 (33348) covalent geometry : angle 0.54416 (44989) *********************** 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: 32 poor density : 146 time to evaluate : 5.169 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 166 MET cc_start: 0.8958 (mmm) cc_final: 0.8610 (tmm) REVERT: A 332 MET cc_start: 0.8300 (mtp) cc_final: 0.7930 (tmm) REVERT: A 453 MET cc_start: 0.8623 (mmm) cc_final: 0.8133 (mmm) REVERT: O 32 MET cc_start: 0.8720 (ttp) cc_final: 0.8154 (ttp) REVERT: U 32 MET cc_start: 0.8671 (ttp) cc_final: 0.8291 (ptt) REVERT: U 75 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7750 (tm-30) REVERT: T 84 ASP cc_start: 0.7764 (m-30) cc_final: 0.7355 (t0) REVERT: T 85 ASP cc_start: 0.9079 (m-30) cc_final: 0.8671 (m-30) REVERT: R 32 MET cc_start: 0.8995 (ptt) cc_final: 0.8465 (ppp) REVERT: Q 32 MET cc_start: 0.8779 (ptt) cc_final: 0.8553 (ptt) REVERT: Q 85 ASP cc_start: 0.9082 (m-30) cc_final: 0.8836 (m-30) REVERT: G 453 MET cc_start: 0.8987 (ttm) cc_final: 0.8026 (tpp) REVERT: F 81 THR cc_start: 0.9314 (m) cc_final: 0.9104 (p) REVERT: F 332 MET cc_start: 0.8600 (mtm) cc_final: 0.8199 (mmm) REVERT: F 453 MET cc_start: 0.8554 (mmt) cc_final: 0.8244 (mmm) REVERT: E 31 MET cc_start: 0.8131 (ttm) cc_final: 0.7893 (ttm) REVERT: E 453 MET cc_start: 0.8970 (ttm) cc_final: 0.8208 (tpp) REVERT: D 31 MET cc_start: 0.8222 (ttm) cc_final: 0.7940 (ttm) REVERT: D 292 MET cc_start: 0.9442 (mtm) cc_final: 0.8747 (mtt) REVERT: D 453 MET cc_start: 0.8953 (ttm) cc_final: 0.8305 (tpp) REVERT: C 453 MET cc_start: 0.9035 (ttm) cc_final: 0.8426 (tpp) REVERT: B 453 MET cc_start: 0.8915 (ttm) cc_final: 0.8385 (tpp) outliers start: 32 outliers final: 20 residues processed: 171 average time/residue: 0.4457 time to fit residues: 133.9057 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 : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 292 MET 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 500 VAL 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 500 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 257 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 292 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 428 optimal weight: 5.9990 chunk 4 optimal weight: 0.0870 chunk 416 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 376 optimal weight: 1.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- 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** U 61 GLN ** G 134 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** ** 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** ** C 284 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.039647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.031643 restraints weight = 272670.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.032820 restraints weight = 145303.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.033638 restraints weight = 90549.884| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33348 Z= 0.097 Angle : 0.538 20.260 44989 Z= 0.262 Chirality : 0.072 1.632 5425 Planarity : 0.002 0.036 5761 Dihedral : 7.043 179.869 4669 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 48.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.70 % Allowed : 6.64 % Favored : 92.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 4368 helix: 2.72 (0.12), residues: 2086 sheet: -1.43 (0.22), residues: 581 loop : -2.24 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 44 HIS 0.001 0.000 HIS G 316 PHE 0.024 0.001 PHE D 281 TYR 0.009 0.001 TYR B 66 ARG 0.002 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.02566 ( 1828) hydrogen bonds : angle 3.96744 ( 5259) covalent geometry : bond 0.00194 (33348) covalent geometry : angle 0.53798 (44989) *********************** 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 169 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 3.903 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 166 MET cc_start: 0.8950 (mmm) cc_final: 0.8583 (tmm) REVERT: A 453 MET cc_start: 0.8653 (mmm) cc_final: 0.8243 (mmm) REVERT: U 32 MET cc_start: 0.8525 (ttp) cc_final: 0.8251 (ptt) REVERT: T 84 ASP cc_start: 0.7685 (m-30) cc_final: 0.7283 (t0) REVERT: T 85 ASP cc_start: 0.9080 (m-30) cc_final: 0.8619 (m-30) REVERT: R 32 MET cc_start: 0.9111 (ptt) cc_final: 0.8513 (ppp) REVERT: Q 32 MET cc_start: 0.8817 (ptt) cc_final: 0.8561 (ptt) REVERT: Q 85 ASP cc_start: 0.9057 (m-30) cc_final: 0.8816 (m-30) REVERT: G 453 MET cc_start: 0.8998 (ttm) cc_final: 0.8165 (tpp) REVERT: F 81 THR cc_start: 0.9312 (m) cc_final: 0.9109 (p) REVERT: F 332 MET cc_start: 0.8364 (mtm) cc_final: 0.8018 (mmm) REVERT: F 453 MET cc_start: 0.8549 (mmt) cc_final: 0.8273 (mmm) REVERT: E 332 MET cc_start: 0.8452 (mtp) cc_final: 0.7937 (mmm) REVERT: E 453 MET cc_start: 0.8951 (ttm) cc_final: 0.8217 (tpp) REVERT: D 292 MET cc_start: 0.9415 (mtm) cc_final: 0.8727 (mtt) REVERT: D 453 MET cc_start: 0.8974 (ttm) cc_final: 0.8486 (tpp) REVERT: C 453 MET cc_start: 0.9007 (ttm) cc_final: 0.8455 (tpp) REVERT: B 453 MET cc_start: 0.8917 (ttm) cc_final: 0.8420 (tpp) outliers start: 25 outliers final: 16 residues processed: 161 average time/residue: 0.4277 time to fit residues: 120.8986 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 : 3.593 ------------------------------------------------------------------------------- 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 17 LEU Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain G residue 292 MET 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 500 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain D 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 500 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 365 optimal weight: 8.9990 chunk 390 optimal weight: 10.0000 chunk 210 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 346 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 219 optimal weight: 0.0980 chunk 78 optimal weight: 8.9990 chunk 135 optimal weight: 40.0000 chunk 169 optimal weight: 7.9990 chunk 356 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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** ** R 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** ** 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** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.038832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.030980 restraints weight = 275207.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.032103 restraints weight = 147187.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032901 restraints weight = 92272.697| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33348 Z= 0.145 Angle : 0.578 20.174 44989 Z= 0.282 Chirality : 0.072 1.620 5425 Planarity : 0.003 0.035 5761 Dihedral : 6.840 166.599 4669 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 50.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.87 % Allowed : 7.06 % Favored : 92.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 4368 helix: 2.67 (0.12), residues: 2086 sheet: -1.32 (0.20), residues: 623 loop : -2.34 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 44 HIS 0.001 0.000 HIS G 316 PHE 0.020 0.001 PHE D 281 TYR 0.014 0.001 TYR U 76 ARG 0.002 0.000 ARG R 20 Details of bonding type rmsd hydrogen bonds : bond 0.02754 ( 1828) hydrogen bonds : angle 4.10343 ( 5259) covalent geometry : bond 0.00294 (33348) covalent geometry : angle 0.57759 (44989) *********************** 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 172 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 4.322 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 166 MET cc_start: 0.8896 (mmm) cc_final: 0.8592 (tmm) REVERT: U 32 MET cc_start: 0.8468 (ttp) cc_final: 0.8238 (ptt) REVERT: T 84 ASP cc_start: 0.7615 (m-30) cc_final: 0.7261 (t0) REVERT: T 85 ASP cc_start: 0.9087 (m-30) cc_final: 0.8683 (m-30) REVERT: R 32 MET cc_start: 0.9059 (ptt) cc_final: 0.8480 (ppp) REVERT: Q 32 MET cc_start: 0.8847 (ptt) cc_final: 0.8546 (ptt) REVERT: Q 85 ASP cc_start: 0.9045 (m-30) cc_final: 0.8788 (m-30) REVERT: G 453 MET cc_start: 0.8978 (ttm) cc_final: 0.8703 (tpp) REVERT: F 81 THR cc_start: 0.9306 (m) cc_final: 0.9102 (p) REVERT: F 453 MET cc_start: 0.8487 (mmt) cc_final: 0.8257 (mmm) REVERT: E 332 MET cc_start: 0.8356 (mtp) cc_final: 0.7899 (mmm) REVERT: E 453 MET cc_start: 0.8926 (ttm) cc_final: 0.8351 (tpp) REVERT: D 292 MET cc_start: 0.9432 (mtm) cc_final: 0.8691 (mtt) REVERT: D 453 MET cc_start: 0.8990 (ttm) cc_final: 0.8562 (tpp) REVERT: C 453 MET cc_start: 0.8959 (ttm) cc_final: 0.8488 (tpp) REVERT: B 453 MET cc_start: 0.8942 (ttm) cc_final: 0.8513 (tpp) outliers start: 31 outliers final: 26 residues processed: 161 average time/residue: 0.4335 time to fit residues: 123.3528 Evaluate side-chains 164 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 3.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain U residue 17 LEU 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 292 MET 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 500 VAL 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 500 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 86 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 296 optimal weight: 0.0470 chunk 144 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 428 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 219 optimal weight: 0.0030 chunk 393 optimal weight: 0.8980 overall best weight: 1.5892 ------------------------------------------------------------------------------- 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** R 61 GLN ** G 134 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** ** 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** ** C 284 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.039237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.031354 restraints weight = 271732.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.032492 restraints weight = 144936.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.033281 restraints weight = 91113.256| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33348 Z= 0.105 Angle : 0.542 20.354 44989 Z= 0.264 Chirality : 0.072 1.638 5425 Planarity : 0.002 0.036 5761 Dihedral : 6.577 141.325 4669 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 49.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.84 % Allowed : 7.17 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 4368 helix: 2.78 (0.12), residues: 2093 sheet: -1.18 (0.20), residues: 623 loop : -2.31 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 44 HIS 0.001 0.000 HIS E 316 PHE 0.009 0.001 PHE D 195 TYR 0.009 0.001 TYR U 76 ARG 0.002 0.000 ARG P 20 Details of bonding type rmsd hydrogen bonds : bond 0.02587 ( 1828) hydrogen bonds : angle 3.94947 ( 5259) covalent geometry : bond 0.00213 (33348) covalent geometry : angle 0.54158 (44989) *********************** 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 171 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 3.701 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 166 MET cc_start: 0.8899 (mmm) cc_final: 0.8576 (tmm) REVERT: A 453 MET cc_start: 0.8715 (mmm) cc_final: 0.8198 (mmm) REVERT: O 32 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8295 (ptt) REVERT: T 84 ASP cc_start: 0.7617 (m-30) cc_final: 0.7259 (t0) REVERT: T 85 ASP cc_start: 0.9072 (m-30) cc_final: 0.8586 (m-30) REVERT: S 32 MET cc_start: 0.9161 (ptt) cc_final: 0.8554 (ppp) REVERT: R 32 MET cc_start: 0.9092 (ptt) cc_final: 0.8519 (ppp) REVERT: Q 32 MET cc_start: 0.8818 (ptt) cc_final: 0.8518 (ptt) REVERT: G 453 MET cc_start: 0.8955 (ttm) cc_final: 0.8684 (tpp) REVERT: F 81 THR cc_start: 0.9319 (m) cc_final: 0.9105 (p) REVERT: F 332 MET cc_start: 0.8391 (mtm) cc_final: 0.7968 (mmm) REVERT: F 453 MET cc_start: 0.8486 (mmt) cc_final: 0.8244 (mmm) REVERT: E 332 MET cc_start: 0.8401 (mtp) cc_final: 0.7900 (mmm) REVERT: E 453 MET cc_start: 0.8910 (ttm) cc_final: 0.8410 (tpp) REVERT: D 292 MET cc_start: 0.9437 (mtm) cc_final: 0.8707 (mtt) REVERT: D 453 MET cc_start: 0.8992 (ttm) cc_final: 0.8565 (tpp) REVERT: C 453 MET cc_start: 0.8958 (ttm) cc_final: 0.8492 (tpp) REVERT: B 453 MET cc_start: 0.8939 (ttm) cc_final: 0.8606 (tpp) outliers start: 30 outliers final: 25 residues processed: 161 average time/residue: 0.4232 time to fit residues: 118.8280 Evaluate side-chains 162 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL 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 17 LEU Chi-restraints excluded: chain U 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 G residue 281 PHE Chi-restraints excluded: chain G residue 292 MET 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 500 VAL Chi-restraints excluded: chain E residue 325 ILE 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 500 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 238 optimal weight: 5.9990 chunk 84 optimal weight: 0.0770 chunk 202 optimal weight: 4.9990 chunk 290 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 361 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 276 optimal weight: 0.9990 chunk 239 optimal weight: 10.0000 chunk 160 optimal weight: 0.3980 chunk 196 optimal weight: 10.0000 overall best weight: 2.2944 ------------------------------------------------------------------------------- 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** ** T 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** ** E 134 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** D 367 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.038723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.030866 restraints weight = 273709.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.031999 restraints weight = 145690.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032782 restraints weight = 91140.546| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33348 Z= 0.139 Angle : 0.575 20.319 44989 Z= 0.280 Chirality : 0.072 1.618 5425 Planarity : 0.003 0.035 5761 Dihedral : 6.461 125.473 4669 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 51.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.82 % Allowed : 7.34 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 4368 helix: 2.72 (0.12), residues: 2093 sheet: -1.11 (0.20), residues: 623 loop : -2.31 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 44 HIS 0.001 0.000 HIS E 316 PHE 0.020 0.001 PHE E 281 TYR 0.008 0.001 TYR U 76 ARG 0.002 0.000 ARG E 369 Details of bonding type rmsd hydrogen bonds : bond 0.02729 ( 1828) hydrogen bonds : angle 4.05869 ( 5259) covalent geometry : bond 0.00282 (33348) covalent geometry : angle 0.57535 (44989) *********************** 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 166 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 3.699 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 166 MET cc_start: 0.8903 (mmm) cc_final: 0.8620 (mmp) REVERT: A 453 MET cc_start: 0.8643 (mmm) cc_final: 0.8134 (mmm) REVERT: T 84 ASP cc_start: 0.7691 (m-30) cc_final: 0.7316 (t0) REVERT: T 85 ASP cc_start: 0.9073 (m-30) cc_final: 0.8640 (m-30) REVERT: S 32 MET cc_start: 0.9132 (ptt) cc_final: 0.8602 (ppp) REVERT: R 32 MET cc_start: 0.9109 (ptt) cc_final: 0.8504 (ppp) REVERT: Q 32 MET cc_start: 0.8752 (ptt) cc_final: 0.8476 (ptt) REVERT: P 32 MET cc_start: 0.9147 (ptm) cc_final: 0.8938 (ptt) REVERT: G 453 MET cc_start: 0.8933 (ttm) cc_final: 0.8686 (tpp) REVERT: F 81 THR cc_start: 0.9312 (m) cc_final: 0.9101 (p) REVERT: F 166 MET cc_start: 0.8885 (tpp) cc_final: 0.8443 (tmm) REVERT: F 332 MET cc_start: 0.8280 (mtm) cc_final: 0.7949 (mmm) REVERT: F 453 MET cc_start: 0.8483 (mmt) cc_final: 0.8242 (mmm) REVERT: E 332 MET cc_start: 0.8364 (mtp) cc_final: 0.7901 (mmm) REVERT: E 453 MET cc_start: 0.8903 (ttm) cc_final: 0.8582 (tpp) REVERT: D 453 MET cc_start: 0.8963 (ttm) cc_final: 0.8591 (tpp) REVERT: C 453 MET cc_start: 0.8940 (ttm) cc_final: 0.8508 (tpp) REVERT: B 453 MET cc_start: 0.8905 (ttm) cc_final: 0.8593 (tpp) outliers start: 29 outliers final: 27 residues processed: 155 average time/residue: 0.4131 time to fit residues: 112.1974 Evaluate side-chains 162 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain U residue 17 LEU 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 R residue 53 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 292 MET 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 500 VAL Chi-restraints excluded: chain E residue 325 ILE 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 500 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 284 optimal weight: 7.9990 chunk 372 optimal weight: 0.5980 chunk 364 optimal weight: 7.9990 chunk 259 optimal weight: 0.9980 chunk 421 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 385 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 ** T 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** ** 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** ** C 284 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.038738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.030804 restraints weight = 276969.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.031934 restraints weight = 148135.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.032725 restraints weight = 92840.227| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33348 Z= 0.137 Angle : 0.568 20.236 44989 Z= 0.277 Chirality : 0.072 1.635 5425 Planarity : 0.003 0.035 5761 Dihedral : 6.364 125.552 4669 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 52.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.79 % Allowed : 7.45 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 4368 helix: 2.72 (0.11), residues: 2100 sheet: -1.02 (0.21), residues: 609 loop : -2.22 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 44 HIS 0.001 0.000 HIS E 316 PHE 0.014 0.001 PHE E 281 TYR 0.008 0.001 TYR U 76 ARG 0.002 0.000 ARG T 20 Details of bonding type rmsd hydrogen bonds : bond 0.02711 ( 1828) hydrogen bonds : angle 4.04623 ( 5259) covalent geometry : bond 0.00277 (33348) covalent geometry : angle 0.56817 (44989) ********************** 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 165 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 3.606 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 166 MET cc_start: 0.8911 (mmm) cc_final: 0.8542 (tmm) REVERT: A 453 MET cc_start: 0.8687 (mmm) cc_final: 0.8150 (mmm) REVERT: O 4 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8021 (pm20) REVERT: O 32 MET cc_start: 0.8935 (ptt) cc_final: 0.8330 (ppp) REVERT: T 84 ASP cc_start: 0.7752 (m-30) cc_final: 0.7343 (t0) REVERT: T 85 ASP cc_start: 0.9134 (m-30) cc_final: 0.8720 (m-30) REVERT: R 32 MET cc_start: 0.9123 (ptt) cc_final: 0.8564 (ppp) REVERT: P 32 MET cc_start: 0.9142 (ptm) cc_final: 0.8921 (ptt) REVERT: G 453 MET cc_start: 0.8971 (ttm) cc_final: 0.8721 (tpp) REVERT: F 166 MET cc_start: 0.8805 (tpp) cc_final: 0.8367 (tmm) REVERT: F 332 MET cc_start: 0.8313 (mtm) cc_final: 0.7929 (mmm) REVERT: F 453 MET cc_start: 0.8538 (mmt) cc_final: 0.8268 (mmm) REVERT: E 332 MET cc_start: 0.8407 (mtp) cc_final: 0.7890 (mmm) REVERT: E 453 MET cc_start: 0.8938 (ttm) cc_final: 0.8624 (tpp) REVERT: D 292 MET cc_start: 0.9440 (mtm) cc_final: 0.8701 (mtt) REVERT: D 453 MET cc_start: 0.8995 (ttm) cc_final: 0.8602 (tpp) REVERT: C 453 MET cc_start: 0.9005 (ttm) cc_final: 0.8559 (tpp) REVERT: B 453 MET cc_start: 0.8935 (ttm) cc_final: 0.8641 (tpp) REVERT: B 523 THR cc_start: 0.9663 (OUTLIER) cc_final: 0.9346 (t) outliers start: 28 outliers final: 24 residues processed: 155 average time/residue: 0.4092 time to fit residues: 111.3727 Evaluate side-chains 160 residues out of total 3556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U 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 281 PHE Chi-restraints excluded: chain G residue 292 MET 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 500 VAL Chi-restraints excluded: chain E residue 325 ILE 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 500 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 126 optimal weight: 0.2980 chunk 84 optimal weight: 0.0870 chunk 187 optimal weight: 30.0000 chunk 392 optimal weight: 8.9990 chunk 415 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 204 optimal weight: 0.0030 chunk 285 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 overall best weight: 0.6772 ------------------------------------------------------------------------------- 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** ** G 134 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 265 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.039635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.031587 restraints weight = 272369.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.032748 restraints weight = 144994.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.033556 restraints weight = 90854.298| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33348 Z= 0.078 Angle : 0.531 20.494 44989 Z= 0.257 Chirality : 0.072 1.635 5425 Planarity : 0.002 0.036 5761 Dihedral : 6.209 126.021 4669 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 49.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.65 % Allowed : 7.56 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.14), residues: 4368 helix: 2.90 (0.12), residues: 2114 sheet: -1.03 (0.21), residues: 623 loop : -2.13 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 44 HIS 0.001 0.001 HIS E 316 PHE 0.014 0.001 PHE E 281 TYR 0.009 0.001 TYR U 76 ARG 0.002 0.000 ARG U 20 Details of bonding type rmsd hydrogen bonds : bond 0.02493 ( 1828) hydrogen bonds : angle 3.82759 ( 5259) covalent geometry : bond 0.00158 (33348) covalent geometry : angle 0.53141 (44989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8217.38 seconds wall clock time: 145 minutes 54.96 seconds (8754.96 seconds total)