Starting phenix.real_space_refine (version: dev) on Mon May 16 22:00:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrd_9196/05_2022/6mrd_9196_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrd_9196/05_2022/6mrd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrd_9196/05_2022/6mrd_9196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrd_9196/05_2022/6mrd_9196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrd_9196/05_2022/6mrd_9196_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrd_9196/05_2022/6mrd_9196_updated.pdb" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 18.61, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 15.92 Conformation dependent library (CDL) restraints added in 4.9 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... running ksdssp... Secondary structure from input PDB file: 133 helices and 56 sheets defined 43.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 9 through 25 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.843A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 105 removed outlier: 3.615A pdb=" N GLU A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 133 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 230 through 243 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 283 through 296 Processing helix chain 'A' and resid 340 through 356 Processing helix chain 'A' and resid 362 through 374 Processing helix chain 'A' and resid 387 through 409 removed outlier: 3.896A pdb=" N GLU A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 435 through 459 removed outlier: 4.086A pdb=" N LYS A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 489 through 492 No H-bonds generated for 'chain 'A' and resid 489 through 492' 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 93 through 95 No H-bonds generated for 'chain 'O' and resid 93 through 95' Processing helix chain 'U' and resid 93 through 95 No H-bonds generated for 'chain 'U' and resid 93 through 95' Processing helix chain 'T' and resid 93 through 95 No H-bonds generated for 'chain 'T' and resid 93 through 95' Processing helix chain 'S' and resid 93 through 95 No H-bonds generated for 'chain 'S' and resid 93 through 95' Processing helix chain 'R' and resid 93 through 95 No H-bonds generated for 'chain 'R' and resid 93 through 95' Processing helix chain 'Q' and resid 93 through 95 No H-bonds generated for 'chain 'Q' and resid 93 through 95' Processing helix chain 'P' and resid 93 through 95 No H-bonds generated for 'chain 'P' and resid 93 through 95' Processing helix chain 'G' and resid 9 through 25 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 65 through 85 removed outlier: 3.789A pdb=" N VAL G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 105 removed outlier: 3.653A pdb=" N GLU G 105 " --> pdb=" O LYS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 133 Processing helix chain 'G' and resid 141 through 151 Processing helix chain 'G' and resid 156 through 169 Processing helix chain 'G' and resid 230 through 243 Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 256 through 267 Processing helix chain 'G' and resid 283 through 296 Processing helix chain 'G' and resid 340 through 356 Processing helix chain 'G' and resid 362 through 374 Processing helix chain 'G' and resid 387 through 409 removed outlier: 3.804A pdb=" N GLU G 409 " --> pdb=" O ARG G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 429 Proline residue: G 425 - end of helix Processing helix chain 'G' and resid 435 through 459 removed outlier: 4.105A pdb=" N LYS G 449 " --> pdb=" O LYS G 445 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE G 450 " --> pdb=" O ARG G 446 " (cutoff:3.500A) Proline residue: G 451 - end of helix Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 489 through 492 No H-bonds generated for 'chain 'G' and resid 489 through 492' 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 25 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 65 through 85 removed outlier: 3.754A pdb=" N VAL F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 105 removed outlier: 3.647A pdb=" N GLU F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 133 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 156 through 169 Processing helix chain 'F' and resid 230 through 243 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 256 through 267 Processing helix chain 'F' and resid 283 through 296 removed outlier: 3.678A pdb=" N ASN F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 356 Processing helix chain 'F' and resid 362 through 374 Processing helix chain 'F' and resid 387 through 409 removed outlier: 3.829A pdb=" N GLU F 409 " --> pdb=" O ARG F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 429 Proline residue: F 425 - end of helix Processing helix chain 'F' and resid 435 through 459 removed outlier: 4.123A pdb=" N LYS F 449 " --> pdb=" O LYS F 445 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE F 450 " --> pdb=" O ARG F 446 " (cutoff:3.500A) Proline residue: F 451 - end of helix Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 489 through 492 No H-bonds generated for 'chain 'F' and resid 489 through 492' 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 25 Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 65 through 85 removed outlier: 3.811A pdb=" N VAL E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 105 removed outlier: 3.682A pdb=" N GLU E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 134 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 156 through 169 Processing helix chain 'E' and resid 230 through 243 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 256 through 267 Processing helix chain 'E' and resid 283 through 296 removed outlier: 3.665A pdb=" N ASN E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 356 Processing helix chain 'E' and resid 362 through 374 Processing helix chain 'E' and resid 387 through 409 removed outlier: 3.883A pdb=" N GLU E 409 " --> pdb=" O ARG E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 429 Proline residue: E 425 - end of helix Processing helix chain 'E' and resid 435 through 459 removed outlier: 4.094A pdb=" N LYS E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE E 450 " --> pdb=" O ARG E 446 " (cutoff:3.500A) Proline residue: E 451 - end of helix Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 489 through 492 No H-bonds generated for 'chain 'E' and resid 489 through 492' 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 25 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 65 through 85 removed outlier: 3.698A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 105 removed outlier: 3.635A pdb=" N GLU D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 133 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 230 through 243 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 256 through 267 Processing helix chain 'D' and resid 283 through 296 Processing helix chain 'D' and resid 340 through 356 Processing helix chain 'D' and resid 362 through 374 Processing helix chain 'D' and resid 387 through 409 removed outlier: 3.872A pdb=" N GLU D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 429 Proline residue: D 425 - end of helix Processing helix chain 'D' and resid 435 through 459 removed outlier: 4.114A pdb=" N LYS D 449 " --> pdb=" O LYS D 445 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 489 through 492 No H-bonds generated for 'chain 'D' and resid 489 through 492' 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 25 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 65 through 85 removed outlier: 3.769A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 105 removed outlier: 3.660A pdb=" N GLU C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 133 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 230 through 243 Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 256 through 267 Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 340 through 356 Processing helix chain 'C' and resid 362 through 374 Processing helix chain 'C' and resid 387 through 409 removed outlier: 3.855A pdb=" N GLU C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 429 Proline residue: C 425 - end of helix Processing helix chain 'C' and resid 435 through 459 removed outlier: 4.085A pdb=" N LYS C 449 " --> pdb=" O LYS C 445 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Proline residue: C 451 - end of helix Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 489 through 492 No H-bonds generated for 'chain 'C' and resid 489 through 492' 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 25 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 65 through 85 removed outlier: 3.772A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 105 removed outlier: 3.610A pdb=" N GLU B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 133 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 230 through 243 Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 283 through 296 removed outlier: 4.193A pdb=" N LYS B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 356 Processing helix chain 'B' and resid 362 through 374 Processing helix chain 'B' and resid 387 through 409 removed outlier: 3.811A pdb=" N GLU B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 429 Proline residue: B 425 - end of helix Processing helix chain 'B' and resid 435 through 459 removed outlier: 4.042A pdb=" N LYS B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 489 through 492 No H-bonds generated for 'chain 'B' and resid 489 through 492' 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= A, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'A' and resid 188 through 190 Processing sheet with id= D, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= E, first strand: chain 'A' and resid 219 through 222 Processing sheet with id= F, first strand: chain 'A' and resid 412 through 414 Processing sheet with id= G, first strand: chain 'A' and resid 477 through 480 Processing sheet with id= H, 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: 6.431A pdb=" N GLU O 19 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL O 46 " --> pdb=" O GLU O 19 " (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= I, first strand: chain 'U' and resid 79 through 83 removed outlier: 9.342A pdb=" N ASP U 87 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ARG U 20 " --> pdb=" O ASP U 87 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU U 19 " --> pdb=" O VAL U 46 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL U 46 " --> pdb=" O GLU U 19 " (cutoff:3.500A) Processing sheet with id= J, 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: 6.449A pdb=" N GLU T 19 " --> pdb=" O VAL T 46 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL T 46 " --> pdb=" O GLU T 19 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 79 through 83 removed outlier: 9.313A pdb=" N ASP S 87 " --> pdb=" O ARG S 20 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG S 20 " --> pdb=" O ASP S 87 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU S 19 " --> pdb=" O VAL S 46 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL S 46 " --> pdb=" O GLU S 19 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'R' and resid 79 through 83 removed outlier: 9.336A pdb=" N ASP R 87 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ARG R 20 " --> pdb=" O ASP R 87 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU R 19 " --> pdb=" O VAL R 46 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL R 46 " --> pdb=" O GLU R 19 " (cutoff:3.500A) Processing sheet with id= M, 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: 6.419A pdb=" N GLU Q 19 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL Q 46 " --> pdb=" O GLU Q 19 " (cutoff:3.500A) Processing sheet with id= N, 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: 6.441A pdb=" N GLU P 19 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL P 46 " --> pdb=" O GLU P 19 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= P, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= Q, first strand: chain 'G' and resid 175 through 178 removed outlier: 6.008A pdb=" N ALA G 378 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS G 178 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU G 380 " --> pdb=" O LYS G 178 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 193 through 195 Processing sheet with id= S, first strand: chain 'G' and resid 219 through 223 Processing sheet with id= T, first strand: chain 'G' and resid 412 through 414 Processing sheet with id= U, first strand: chain 'G' and resid 477 through 480 Processing sheet with id= V, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= W, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= X, first strand: chain 'F' and resid 174 through 176 Processing sheet with id= Y, first strand: chain 'F' and resid 193 through 195 Processing sheet with id= Z, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= AA, first strand: chain 'F' and resid 412 through 414 Processing sheet with id= AB, first strand: chain 'F' and resid 477 through 480 Processing sheet with id= AC, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= AD, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= AE, first strand: chain 'E' and resid 188 through 190 Processing sheet with id= AF, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= AG, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= AH, first strand: chain 'E' and resid 412 through 414 Processing sheet with id= AI, first strand: chain 'E' and resid 477 through 480 Processing sheet with id= AJ, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= AK, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= AL, first strand: chain 'D' and resid 188 through 190 Processing sheet with id= AM, first strand: chain 'D' and resid 193 through 195 Processing sheet with id= AN, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= AO, first strand: chain 'D' and resid 412 through 414 Processing sheet with id= AP, first strand: chain 'D' and resid 477 through 480 Processing sheet with id= AQ, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= AR, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= AS, first strand: chain 'C' and resid 188 through 190 Processing sheet with id= AT, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= AU, first strand: chain 'C' and resid 219 through 222 Processing sheet with id= AV, first strand: chain 'C' and resid 412 through 414 Processing sheet with id= AW, first strand: chain 'C' and resid 477 through 480 Processing sheet with id= AX, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= AY, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= AZ, first strand: chain 'B' and resid 188 through 190 Processing sheet with id= BA, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= BB, first strand: chain 'B' and resid 219 through 222 Processing sheet with id= BC, first strand: chain 'B' and resid 412 through 414 Processing sheet with id= BD, first strand: chain 'B' and resid 477 through 480 1631 hydrogen bonds defined for protein. 4677 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: 12.64 Time building geometry restraints manager: 16.83 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: 66.86 - 81.62: 28 81.62 - 96.38: 17 96.38 - 111.13: 17667 111.13 - 125.89: 30452 125.89 - 140.64: 234 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: 20769 34.15 - 68.29: 62 68.29 - 102.44: 22 102.44 - 136.58: 2 136.58 - 170.73: 12 Dihedral angle restraints: 20867 sinusoidal: 8456 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 20864 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: 222 2.16 - 2.77: 12289 2.77 - 3.38: 49498 3.38 - 3.99: 70592 3.99 - 4.60: 104212 Nonbonded interactions: 236813 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 236808 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 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. 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.860 Extract box with map and model: 12.660 Check model and map are aligned: 0.470 Convert atoms to be neutral: 0.290 Process input model: 86.430 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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= 0.545 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 4.164 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 outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.4590 time to fit residues: 212.3816 Evaluate side-chains 155 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 3.947 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3224 ------------------------------------------------------------------------------- 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: 1.9990 chunk 328 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 340 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 chunk 394 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 A 367 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 284 ASN G 367 ASN F 80 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 284 ASN D 367 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN C 367 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN B 367 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1245 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= 0.178 Angle : 0.605 20.229 44989 Z= 0.303 Chirality : 0.072 1.628 5425 Planarity : 0.003 0.033 5761 Dihedral : 10.323 179.694 4669 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 56.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.97 % Favored : 91.87 % Rotamer Outliers : 0.56 % 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: -1.44 (0.12), residues: 4368 helix: 0.86 (0.11), residues: 2065 sheet: -2.63 (0.18), residues: 588 loop : -2.64 (0.13), residues: 1715 *********************** 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 187 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 4.404 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 outliers start: 20 outliers final: 7 residues processed: 179 average time/residue: 0.4554 time to fit residues: 139.8870 Evaluate side-chains 161 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 4.234 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3643 time to fit residues: 10.0049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 328 optimal weight: 3.9990 chunk 268 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 394 optimal weight: 6.9990 chunk 426 optimal weight: 4.9990 chunk 351 optimal weight: 9.9990 chunk 391 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 316 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** U 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 33348 Z= 0.270 Angle : 0.652 20.336 44989 Z= 0.324 Chirality : 0.072 1.615 5425 Planarity : 0.003 0.032 5761 Dihedral : 8.781 174.962 4669 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 60.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.21 % Favored : 89.63 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.07 (0.13), residues: 4368 helix: 1.24 (0.12), residues: 2044 sheet: -2.35 (0.19), residues: 574 loop : -2.57 (0.14), residues: 1750 *********************** 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 186 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 4.065 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 outliers start: 24 outliers final: 8 residues processed: 180 average time/residue: 0.4326 time to fit residues: 134.5133 Evaluate side-chains 156 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 4.074 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3122 time to fit residues: 10.1934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 390 optimal weight: 8.9990 chunk 296 optimal weight: 9.9990 chunk 204 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 396 optimal weight: 1.9990 chunk 419 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 375 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** O 4 GLN ** U 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 33348 Z= 0.229 Angle : 0.610 20.467 44989 Z= 0.303 Chirality : 0.073 1.631 5425 Planarity : 0.003 0.032 5761 Dihedral : 8.005 163.258 4669 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 59.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.04 % Favored : 90.80 % Rotamer Outliers : 0.45 % 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: -0.72 (0.13), residues: 4368 helix: 1.61 (0.12), residues: 2037 sheet: -2.12 (0.20), residues: 574 loop : -2.50 (0.14), residues: 1757 *********************** 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 173 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 4.167 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 outliers start: 16 outliers final: 6 residues processed: 166 average time/residue: 0.4354 time to fit residues: 126.3768 Evaluate side-chains 155 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 4.106 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3301 time to fit residues: 9.4989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 312 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 357 optimal weight: 6.9990 chunk 289 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 214 optimal weight: 0.6980 chunk 376 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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** O 4 GLN ** U 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 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** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 33348 Z= 0.279 Angle : 0.640 20.398 44989 Z= 0.318 Chirality : 0.073 1.629 5425 Planarity : 0.003 0.026 5761 Dihedral : 7.890 152.757 4669 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 61.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.53 % Favored : 89.31 % Rotamer Outliers : 0.45 % 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: -0.75 (0.13), residues: 4368 helix: 1.52 (0.12), residues: 2044 sheet: -2.04 (0.19), residues: 609 loop : -2.48 (0.14), residues: 1715 *********************** 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 166 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 4.333 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 outliers start: 16 outliers final: 6 residues processed: 157 average time/residue: 0.4320 time to fit residues: 117.8183 Evaluate side-chains 152 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 4.029 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3641 time to fit residues: 9.2436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 9.9990 chunk 377 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 419 optimal weight: 8.9990 chunk 348 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 HIS ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 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** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 33348 Z= 0.219 Angle : 0.595 20.415 44989 Z= 0.295 Chirality : 0.072 1.634 5425 Planarity : 0.002 0.025 5761 Dihedral : 7.592 172.022 4669 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 59.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.39 % Favored : 90.48 % Rotamer Outliers : 0.17 % 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: -0.46 (0.13), residues: 4368 helix: 1.77 (0.12), residues: 2058 sheet: -1.86 (0.20), residues: 609 loop : -2.41 (0.14), residues: 1701 *********************** 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 157 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 3.848 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 outliers start: 6 outliers final: 4 residues processed: 154 average time/residue: 0.4470 time to fit residues: 120.5340 Evaluate side-chains 149 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 4.054 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3444 time to fit residues: 8.0468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 404 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 237 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 418 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 255 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 HIS ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 33348 Z= 0.217 Angle : 0.592 20.370 44989 Z= 0.292 Chirality : 0.072 1.618 5425 Planarity : 0.002 0.026 5761 Dihedral : 7.328 178.309 4669 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 60.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.73 % Favored : 90.13 % Rotamer Outliers : 0.20 % 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: -0.33 (0.13), residues: 4368 helix: 1.88 (0.12), residues: 2058 sheet: -1.91 (0.20), residues: 567 loop : -2.31 (0.14), residues: 1743 *********************** 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 157 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 4.438 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 outliers start: 7 outliers final: 5 residues processed: 154 average time/residue: 0.4595 time to fit residues: 121.9741 Evaluate side-chains 149 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 3.701 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5516 time to fit residues: 9.5882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 258 optimal weight: 0.0050 chunk 167 optimal weight: 0.8980 chunk 249 optimal weight: 0.0870 chunk 126 optimal weight: 0.2980 chunk 82 optimal weight: 0.0010 chunk 81 optimal weight: 0.0170 chunk 265 optimal weight: 3.9990 chunk 284 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 328 optimal weight: 0.9980 overall best weight: 0.0816 ------------------------------------------------------------------------------- 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 243 HIS ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 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** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 33348 Z= 0.106 Angle : 0.536 20.462 44989 Z= 0.260 Chirality : 0.072 1.631 5425 Planarity : 0.002 0.023 5761 Dihedral : 6.931 168.841 4669 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 54.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 0.22 % 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: 0.38 (0.14), residues: 4368 helix: 2.51 (0.12), residues: 2079 sheet: -1.43 (0.22), residues: 567 loop : -2.13 (0.14), residues: 1722 *********************** 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 159 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 4.167 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 outliers start: 8 outliers final: 6 residues processed: 153 average time/residue: 0.4433 time to fit residues: 119.1880 Evaluate side-chains 148 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 4.209 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3209 time to fit residues: 9.2880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 380 optimal weight: 1.9990 chunk 400 optimal weight: 0.3980 chunk 365 optimal weight: 9.9990 chunk 389 optimal weight: 3.9990 chunk 234 optimal weight: 0.1980 chunk 169 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 368 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 243 HIS ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 33348 Z= 0.162 Angle : 0.553 20.349 44989 Z= 0.270 Chirality : 0.071 1.605 5425 Planarity : 0.002 0.023 5761 Dihedral : 6.727 154.110 4669 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 57.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer Outliers : 0.08 % 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: 0.42 (0.14), residues: 4368 helix: 2.48 (0.12), residues: 2086 sheet: -1.28 (0.22), residues: 567 loop : -2.09 (0.15), residues: 1715 *********************** 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 147 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 4.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 144 average time/residue: 0.4440 time to fit residues: 111.5416 Evaluate side-chains 145 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 4.061 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3266 time to fit residues: 6.6195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 255 optimal weight: 0.9990 chunk 412 optimal weight: 0.8980 chunk 251 optimal weight: 20.0000 chunk 195 optimal weight: 0.6980 chunk 286 optimal weight: 3.9990 chunk 432 optimal weight: 0.9980 chunk 397 optimal weight: 0.5980 chunk 344 optimal weight: 0.0000 chunk 35 optimal weight: 0.7980 chunk 265 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 243 HIS A 265 ASN S 61 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 33348 Z= 0.103 Angle : 0.528 20.406 44989 Z= 0.255 Chirality : 0.072 1.634 5425 Planarity : 0.002 0.025 5761 Dihedral : 6.415 124.601 4669 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 54.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer Outliers : 0.00 % 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: 0.68 (0.14), residues: 4368 helix: 2.82 (0.12), residues: 2079 sheet: -1.01 (0.21), residues: 637 loop : -2.20 (0.15), residues: 1652 ********************** 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 151 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.4569 time to fit residues: 119.3479 Evaluate side-chains 144 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 4.220 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 273 optimal weight: 6.9990 chunk 366 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 317 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 344 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 354 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 243 HIS ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 367 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 HIS ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.037576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.029703 restraints weight = 284456.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030774 restraints weight = 153041.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.031543 restraints weight = 96972.573| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 33348 Z= 0.359 Angle : 0.692 20.007 44989 Z= 0.343 Chirality : 0.072 1.598 5425 Planarity : 0.003 0.024 5761 Dihedral : 6.673 118.961 4669 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 64.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.05 % Favored : 89.86 % Rotamer Outliers : 0.17 % 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: -0.02 (0.13), residues: 4368 helix: 1.95 (0.12), residues: 2086 sheet: -1.39 (0.22), residues: 525 loop : -2.10 (0.14), residues: 1757 =============================================================================== Job complete usr+sys time: 4457.76 seconds wall clock time: 85 minutes 40.83 seconds (5140.83 seconds total)