Starting phenix.real_space_refine on Thu Feb 22 15:18:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrd_9196/02_2024/6mrd_9196_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrd_9196/02_2024/6mrd_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_9196/02_2024/6mrd_9196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrd_9196/02_2024/6mrd_9196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrd_9196/02_2024/6mrd_9196_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrd_9196/02_2024/6mrd_9196_updated.pdb" } 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 Residue "A ARG 422": "NH1" <-> "NH2" Residue "O ARG 15": "NH1" <-> "NH2" Residue "O ARG 92": "NH1" <-> "NH2" Residue "U ARG 15": "NH1" <-> "NH2" Residue "U ARG 92": "NH1" <-> "NH2" Residue "T ARG 15": "NH1" <-> "NH2" Residue "T ARG 92": "NH1" <-> "NH2" Residue "S ARG 15": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "R ARG 15": "NH1" <-> "NH2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "Q ARG 15": "NH1" <-> "NH2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "P ARG 15": "NH1" <-> "NH2" Residue "P ARG 92": "NH1" <-> "NH2" Residue "G ARG 422": "NH1" <-> "NH2" Residue "F ARG 422": "NH1" <-> "NH2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 422": "NH1" <-> "NH2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "B ARG 422": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 17.50, per 1000 atoms: 0.51 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: 14.71 Conformation dependent library (CDL) restraints added in 5.9 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: 6.72 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: 13.05 Time building geometry restraints manager: 15.79 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: 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: 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 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: 2.240 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: 0.830 Extract box with map and model: 11.130 Check model and map are aligned: 0.500 Set scattering table: 0.330 Process input model: 90.410 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.300 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: 0.020 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.240 ------------------------------------------------------------------------------- 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= 0.545 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 % 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 *********************** 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 : 3.671 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: 0.4793 time to fit residues: 220.1348 Evaluate side-chains 156 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 4.086 ------------------------------------------------------------------------------- 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 243 HIS G 284 ASN G 367 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 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: 0.8618 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33348 Z= 0.177 Angle : 0.601 20.222 44989 Z= 0.301 Chirality : 0.073 1.634 5425 Planarity : 0.003 0.033 5761 Dihedral : 10.206 178.956 4669 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 56.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.94 % Favored : 91.90 % Rotamer: Outliers : 0.53 % Allowed : 5.40 % Favored : 94.07 % 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: -1.37 (0.13), residues: 4368 helix: 0.93 (0.12), residues: 2065 sheet: -2.62 (0.18), residues: 588 loop : -2.62 (0.13), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 44 HIS 0.001 0.000 HIS G 243 PHE 0.008 0.001 PHE D 195 TYR 0.011 0.001 TYR U 76 ARG 0.003 0.000 ARG Q 7 *********************** 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 190 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 3.921 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 292 MET cc_start: 0.8998 (mtm) cc_final: 0.8441 (mtt) REVERT: A 332 MET cc_start: 0.8293 (mtp) cc_final: 0.7933 (mmm) REVERT: A 453 MET cc_start: 0.8979 (ttm) cc_final: 0.8532 (tmm) REVERT: U 4 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7510 (tm-30) REVERT: U 84 ASP cc_start: 0.7839 (m-30) cc_final: 0.7617 (t0) REVERT: T 32 MET cc_start: 0.8556 (ptm) cc_final: 0.8298 (ptt) REVERT: T 84 ASP cc_start: 0.7762 (m-30) cc_final: 0.7399 (t0) REVERT: T 85 ASP cc_start: 0.9053 (m-30) cc_final: 0.8701 (m-30) REVERT: G 166 MET cc_start: 0.7968 (tmm) cc_final: 0.7646 (tmm) REVERT: G 219 TYR cc_start: 0.8568 (m-80) cc_final: 0.8295 (m-80) REVERT: G 453 MET cc_start: 0.9001 (ttm) cc_final: 0.8115 (tpp) REVERT: F 166 MET cc_start: 0.8094 (tmm) cc_final: 0.7863 (tmm) REVERT: F 332 MET cc_start: 0.8498 (mtp) cc_final: 0.7913 (mmm) REVERT: F 453 MET cc_start: 0.8537 (mmt) cc_final: 0.8278 (mmm) REVERT: E 166 MET cc_start: 0.7997 (tmm) cc_final: 0.7676 (tmm) REVERT: E 332 MET cc_start: 0.8522 (mtp) cc_final: 0.8278 (mmm) REVERT: E 453 MET cc_start: 0.9010 (ttm) cc_final: 0.8450 (tmm) REVERT: C 292 MET cc_start: 0.9400 (mtp) cc_final: 0.9014 (mtt) REVERT: C 453 MET cc_start: 0.9022 (ttm) cc_final: 0.8099 (tmm) REVERT: B 31 MET cc_start: 0.8253 (ttm) cc_final: 0.7959 (ttm) REVERT: B 221 LEU cc_start: 0.9535 (tp) cc_final: 0.9256 (tt) REVERT: B 453 MET cc_start: 0.8919 (ttm) cc_final: 0.8108 (tmm) outliers start: 19 outliers final: 6 residues processed: 183 average time/residue: 0.4492 time to fit residues: 141.4550 Evaluate side-chains 166 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 3.558 ------------------------------------------------------------------------------- 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 53 SER Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain C residue 133 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 328 optimal weight: 2.9990 chunk 268 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 394 optimal weight: 7.9990 chunk 426 optimal weight: 0.9980 chunk 351 optimal weight: 10.0000 chunk 391 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 316 optimal weight: 10.0000 overall best weight: 2.6784 ------------------------------------------------------------------------------- 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** ** 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** ** 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: 0.8642 moved from start: 0.1678 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= 0.222 Angle : 0.611 20.308 44989 Z= 0.302 Chirality : 0.072 1.615 5425 Planarity : 0.003 0.031 5761 Dihedral : 8.608 173.633 4669 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 56.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.20 % Favored : 90.64 % Rotamer: Outliers : 0.76 % Allowed : 5.37 % Favored : 93.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.88 (0.13), residues: 4368 helix: 1.41 (0.12), residues: 2058 sheet: -2.27 (0.19), residues: 574 loop : -2.53 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 44 HIS 0.001 0.000 HIS G 243 PHE 0.011 0.001 PHE D 195 TYR 0.009 0.001 TYR U 76 ARG 0.002 0.000 ARG P 20 *********************** 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 188 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 4.205 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: 0.8836 (mmm) cc_final: 0.8480 (tmm) REVERT: A 292 MET cc_start: 0.9085 (mtm) cc_final: 0.8747 (mtm) REVERT: A 332 MET cc_start: 0.8233 (mtp) cc_final: 0.7949 (tmm) REVERT: A 453 MET cc_start: 0.9000 (ttm) cc_final: 0.8149 (tpp) REVERT: O 32 MET cc_start: 0.8549 (ttp) cc_final: 0.8236 (ptt) REVERT: U 84 ASP cc_start: 0.7880 (m-30) cc_final: 0.7626 (t0) REVERT: T 84 ASP cc_start: 0.7647 (m-30) cc_final: 0.7232 (t0) REVERT: T 85 ASP cc_start: 0.9070 (m-30) cc_final: 0.8722 (m-30) REVERT: Q 32 MET cc_start: 0.8544 (ptt) cc_final: 0.8306 (ppp) REVERT: G 166 MET cc_start: 0.8014 (tmm) cc_final: 0.7696 (tmm) REVERT: G 219 TYR cc_start: 0.8435 (m-80) cc_final: 0.8209 (m-80) REVERT: G 453 MET cc_start: 0.8985 (ttm) cc_final: 0.8163 (tpp) REVERT: F 166 MET cc_start: 0.8136 (tmm) cc_final: 0.7917 (tmm) REVERT: F 292 MET cc_start: 0.9307 (mtm) cc_final: 0.8610 (mtt) REVERT: E 31 MET cc_start: 0.8461 (ttm) cc_final: 0.8244 (ttm) REVERT: E 166 MET cc_start: 0.8036 (tmm) cc_final: 0.7797 (tmm) REVERT: E 332 MET cc_start: 0.8413 (mtp) cc_final: 0.8176 (mmm) REVERT: E 453 MET cc_start: 0.9031 (ttm) cc_final: 0.8355 (tpp) REVERT: C 292 MET cc_start: 0.9436 (mtp) cc_final: 0.9206 (mtm) REVERT: C 453 MET cc_start: 0.9054 (ttm) cc_final: 0.8251 (tmm) REVERT: B 453 MET cc_start: 0.9004 (ttm) cc_final: 0.8236 (tmm) outliers start: 27 outliers final: 13 residues processed: 181 average time/residue: 0.4308 time to fit residues: 134.4372 Evaluate side-chains 165 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain B residue 193 MET 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 390 optimal weight: 7.9990 chunk 296 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 188 optimal weight: 0.4980 chunk 265 optimal weight: 7.9990 chunk 396 optimal weight: 0.0870 chunk 419 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 375 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 S 61 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 ASN ** 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** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2023 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= 0.111 Angle : 0.539 20.420 44989 Z= 0.264 Chirality : 0.072 1.634 5425 Planarity : 0.002 0.026 5761 Dihedral : 7.723 156.330 4669 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 52.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.51 % Favored : 92.33 % Rotamer: Outliers : 0.51 % Allowed : 6.13 % Favored : 93.36 % 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: -0.13 (0.13), residues: 4368 helix: 2.13 (0.12), residues: 2058 sheet: -1.98 (0.20), residues: 581 loop : -2.26 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 44 HIS 0.001 0.000 HIS B 243 PHE 0.007 0.001 PHE D 195 TYR 0.016 0.001 TYR P 88 ARG 0.004 0.000 ARG P 20 *********************** 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 181 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 4.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.8951 (mmm) cc_final: 0.8529 (tmm) REVERT: A 332 MET cc_start: 0.8315 (mtp) cc_final: 0.7995 (tmm) REVERT: A 453 MET cc_start: 0.8932 (ttm) cc_final: 0.8059 (tpp) REVERT: U 84 ASP cc_start: 0.7852 (m-30) cc_final: 0.7625 (t0) REVERT: T 84 ASP cc_start: 0.7770 (m-30) cc_final: 0.7347 (t0) REVERT: T 85 ASP cc_start: 0.9112 (m-30) cc_final: 0.8738 (m-30) REVERT: Q 27 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8281 (p) REVERT: Q 85 ASP cc_start: 0.9010 (m-30) cc_final: 0.8769 (m-30) REVERT: G 166 MET cc_start: 0.7891 (tmm) cc_final: 0.7510 (tmm) REVERT: G 219 TYR cc_start: 0.8353 (m-80) cc_final: 0.8144 (m-80) REVERT: G 453 MET cc_start: 0.8928 (ttm) cc_final: 0.8078 (tpp) REVERT: F 166 MET cc_start: 0.8007 (tmm) cc_final: 0.7765 (tmm) REVERT: F 292 MET cc_start: 0.9316 (mtm) cc_final: 0.8601 (mtm) REVERT: F 332 MET cc_start: 0.8279 (mtm) cc_final: 0.8074 (mmm) REVERT: E 292 MET cc_start: 0.9536 (mtp) cc_final: 0.9126 (mtt) REVERT: E 332 MET cc_start: 0.8425 (mtp) cc_final: 0.8161 (mmm) REVERT: E 453 MET cc_start: 0.8984 (ttm) cc_final: 0.8453 (tmm) REVERT: D 292 MET cc_start: 0.9413 (mtm) cc_final: 0.8694 (mtt) REVERT: C 453 MET cc_start: 0.8980 (ttm) cc_final: 0.8123 (tmm) REVERT: B 221 LEU cc_start: 0.9542 (tp) cc_final: 0.9258 (tt) REVERT: B 453 MET cc_start: 0.8930 (ttm) cc_final: 0.8139 (tpp) outliers start: 18 outliers final: 12 residues processed: 175 average time/residue: 0.4356 time to fit residues: 130.9088 Evaluate side-chains 169 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 332 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 312 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 357 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 376 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 O 4 GLN ** U 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 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** E 243 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.147 33348 Z= 0.546 Angle : 0.907 20.193 44989 Z= 0.449 Chirality : 0.074 1.602 5425 Planarity : 0.004 0.040 5761 Dihedral : 8.260 155.730 4669 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 72.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.49 % Favored : 88.32 % Rotamer: Outliers : 1.10 % Allowed : 7.23 % Favored : 91.68 % 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: -1.58 (0.12), residues: 4368 helix: 0.50 (0.11), residues: 2058 sheet: -2.28 (0.18), residues: 567 loop : -2.53 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 44 HIS 0.003 0.001 HIS C 243 PHE 0.022 0.003 PHE D 195 TYR 0.012 0.002 TYR Q 88 ARG 0.006 0.001 ARG G 396 *********************** 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 186 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 3.873 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: A 166 MET cc_start: 0.8990 (mmm) cc_final: 0.8608 (tmm) REVERT: A 292 MET cc_start: 0.9331 (mtm) cc_final: 0.8896 (mtm) REVERT: A 332 MET cc_start: 0.8294 (mtp) cc_final: 0.8002 (tmm) REVERT: A 453 MET cc_start: 0.9134 (ttm) cc_final: 0.8847 (tmm) REVERT: T 85 ASP cc_start: 0.9127 (m-30) cc_final: 0.8909 (m-30) REVERT: Q 32 MET cc_start: 0.8205 (ppp) cc_final: 0.7942 (ppp) REVERT: G 121 MET cc_start: 0.9243 (mmt) cc_final: 0.8949 (mmp) REVERT: G 166 MET cc_start: 0.8075 (tmm) cc_final: 0.7716 (tmm) REVERT: G 453 MET cc_start: 0.9128 (ttm) cc_final: 0.8496 (tmm) REVERT: F 166 MET cc_start: 0.8212 (tmm) cc_final: 0.7977 (tmm) REVERT: E 31 MET cc_start: 0.8415 (ttm) cc_final: 0.8202 (ttm) REVERT: E 332 MET cc_start: 0.8370 (mtp) cc_final: 0.8128 (mmm) REVERT: E 453 MET cc_start: 0.9110 (ttm) cc_final: 0.8651 (tmm) REVERT: C 292 MET cc_start: 0.9473 (mtp) cc_final: 0.9191 (mtm) REVERT: C 453 MET cc_start: 0.9116 (ttm) cc_final: 0.8489 (tmm) REVERT: B 453 MET cc_start: 0.9058 (ttm) cc_final: 0.8577 (tmm) outliers start: 39 outliers final: 29 residues processed: 173 average time/residue: 0.4311 time to fit residues: 128.8413 Evaluate side-chains 170 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 53 SER 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 17 LEU Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 516 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 246 optimal weight: 0.2980 chunk 103 optimal weight: 8.9990 chunk 419 optimal weight: 7.9990 chunk 348 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 ** 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** F 211 GLN F 243 HIS ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2455 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= 0.156 Angle : 0.571 20.482 44989 Z= 0.283 Chirality : 0.073 1.632 5425 Planarity : 0.002 0.025 5761 Dihedral : 7.660 166.975 4669 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 57.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.63 % Favored : 91.21 % Rotamer: Outliers : 0.67 % Allowed : 7.56 % Favored : 91.76 % 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: -0.48 (0.13), residues: 4368 helix: 1.60 (0.12), residues: 2065 sheet: -1.87 (0.21), residues: 567 loop : -2.22 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 44 HIS 0.000 0.000 HIS G 243 PHE 0.011 0.001 PHE D 195 TYR 0.014 0.001 TYR R 88 ARG 0.004 0.000 ARG S 7 *********************** 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 172 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 4.726 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: A 166 MET cc_start: 0.8865 (mmm) cc_final: 0.8464 (tmm) REVERT: A 292 MET cc_start: 0.9326 (mtm) cc_final: 0.8591 (mtt) REVERT: A 332 MET cc_start: 0.8337 (mtp) cc_final: 0.8055 (tmm) REVERT: A 453 MET cc_start: 0.9026 (ttm) cc_final: 0.8769 (tmm) REVERT: T 84 ASP cc_start: 0.7702 (m-30) cc_final: 0.7216 (t0) REVERT: T 85 ASP cc_start: 0.9122 (m-30) cc_final: 0.8771 (m-30) REVERT: Q 32 MET cc_start: 0.8262 (ppp) cc_final: 0.7882 (ppp) REVERT: G 166 MET cc_start: 0.7930 (tmm) cc_final: 0.7576 (tmm) REVERT: G 453 MET cc_start: 0.9030 (ttm) cc_final: 0.8282 (tmm) REVERT: F 166 MET cc_start: 0.8015 (tmm) cc_final: 0.7780 (tmm) REVERT: F 292 MET cc_start: 0.9351 (mtm) cc_final: 0.8637 (mtt) REVERT: E 332 MET cc_start: 0.8446 (mtp) cc_final: 0.8179 (mmm) REVERT: E 453 MET cc_start: 0.9036 (ttm) cc_final: 0.8524 (tmm) REVERT: C 453 MET cc_start: 0.9028 (ttm) cc_final: 0.8332 (tmm) REVERT: B 453 MET cc_start: 0.9014 (ttm) cc_final: 0.8375 (tmm) outliers start: 24 outliers final: 20 residues processed: 161 average time/residue: 0.4359 time to fit residues: 122.5002 Evaluate side-chains 166 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 4.132 ------------------------------------------------------------------------------- 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 U residue 53 SER Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain R residue 53 SER 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 500 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 133 LYS Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 332 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 404 optimal weight: 0.0030 chunk 47 optimal weight: 1.9990 chunk 239 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 353 optimal weight: 1.9990 chunk 234 optimal weight: 7.9990 chunk 418 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- 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** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2675 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= 0.142 Angle : 0.544 20.342 44989 Z= 0.266 Chirality : 0.071 1.618 5425 Planarity : 0.002 0.024 5761 Dihedral : 7.124 177.089 4669 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 55.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.95 % Favored : 91.03 % Rotamer: Outliers : 0.65 % Allowed : 7.71 % Favored : 91.65 % 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: 0.10 (0.14), residues: 4368 helix: 2.11 (0.12), residues: 2100 sheet: -1.57 (0.22), residues: 567 loop : -2.06 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 44 HIS 0.001 0.000 HIS D 243 PHE 0.009 0.001 PHE D 195 TYR 0.019 0.001 TYR O 76 ARG 0.002 0.000 ARG R 20 *********************** 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 175 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 3.916 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: A 166 MET cc_start: 0.8847 (mmm) cc_final: 0.8435 (tmm) REVERT: A 292 MET cc_start: 0.9356 (mtm) cc_final: 0.8958 (mtm) REVERT: A 332 MET cc_start: 0.8338 (mtp) cc_final: 0.8025 (tmm) REVERT: A 453 MET cc_start: 0.8979 (ttm) cc_final: 0.8510 (tmm) REVERT: U 84 ASP cc_start: 0.8007 (m-30) cc_final: 0.7467 (t0) REVERT: T 85 ASP cc_start: 0.9150 (m-30) cc_final: 0.8898 (m-30) REVERT: Q 32 MET cc_start: 0.8175 (ppp) cc_final: 0.7762 (ppp) REVERT: Q 85 ASP cc_start: 0.9005 (m-30) cc_final: 0.8804 (m-30) REVERT: G 166 MET cc_start: 0.7922 (tmm) cc_final: 0.7562 (tmm) REVERT: G 453 MET cc_start: 0.9007 (ttm) cc_final: 0.8383 (tpp) REVERT: F 166 MET cc_start: 0.7990 (tmm) cc_final: 0.7719 (tmm) REVERT: F 225 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8512 (mmtp) REVERT: F 292 MET cc_start: 0.9363 (mtm) cc_final: 0.8641 (mtt) REVERT: E 292 MET cc_start: 0.9488 (mtp) cc_final: 0.9110 (mtt) REVERT: E 332 MET cc_start: 0.8365 (mtp) cc_final: 0.8164 (mmm) REVERT: E 453 MET cc_start: 0.9026 (ttm) cc_final: 0.8579 (tmm) REVERT: C 453 MET cc_start: 0.9015 (ttm) cc_final: 0.8317 (tmm) REVERT: C 489 MET cc_start: 0.9181 (mmt) cc_final: 0.8926 (mmt) REVERT: B 453 MET cc_start: 0.8990 (ttm) cc_final: 0.8483 (tmm) outliers start: 23 outliers final: 21 residues processed: 166 average time/residue: 0.4250 time to fit residues: 122.6646 Evaluate side-chains 168 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 4.244 ------------------------------------------------------------------------------- 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 U residue 53 SER Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain R 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 269 VAL Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 332 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 258 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 249 optimal weight: 0.9990 chunk 126 optimal weight: 0.0370 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 284 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 328 optimal weight: 8.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- 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** ** 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 ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2816 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= 0.106 Angle : 0.522 20.393 44989 Z= 0.253 Chirality : 0.072 1.625 5425 Planarity : 0.002 0.024 5761 Dihedral : 6.812 162.007 4669 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 54.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.48 % Allowed : 8.04 % Favored : 91.48 % 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: 0.47 (0.14), residues: 4368 helix: 2.50 (0.12), residues: 2093 sheet: -1.33 (0.22), residues: 567 loop : -2.02 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 44 HIS 0.000 0.000 HIS A 243 PHE 0.016 0.001 PHE A 281 TYR 0.007 0.001 TYR B 66 ARG 0.003 0.000 ARG S 7 *********************** 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 166 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 4.051 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: 0.8846 (mmm) cc_final: 0.8442 (tmm) REVERT: A 332 MET cc_start: 0.8226 (mtp) cc_final: 0.7934 (tmm) REVERT: A 453 MET cc_start: 0.8956 (ttm) cc_final: 0.8483 (tmm) REVERT: U 84 ASP cc_start: 0.7965 (m-30) cc_final: 0.7473 (t0) REVERT: T 85 ASP cc_start: 0.9103 (m-30) cc_final: 0.8881 (m-30) REVERT: Q 32 MET cc_start: 0.8125 (ppp) cc_final: 0.7752 (ppp) REVERT: G 166 MET cc_start: 0.7912 (tmm) cc_final: 0.7549 (tmm) REVERT: G 453 MET cc_start: 0.8990 (ttm) cc_final: 0.8286 (tpp) REVERT: F 166 MET cc_start: 0.7972 (tmm) cc_final: 0.7702 (tmm) REVERT: F 225 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8551 (mmtp) REVERT: F 292 MET cc_start: 0.9391 (mtm) cc_final: 0.8690 (mtt) REVERT: E 332 MET cc_start: 0.8448 (mtp) cc_final: 0.8223 (mtm) REVERT: E 453 MET cc_start: 0.8981 (ttm) cc_final: 0.8538 (tmm) REVERT: D 292 MET cc_start: 0.9220 (mtm) cc_final: 0.8622 (mtt) REVERT: C 453 MET cc_start: 0.9019 (ttm) cc_final: 0.8298 (tmm) REVERT: C 489 MET cc_start: 0.9176 (mmt) cc_final: 0.8930 (mmt) REVERT: B 453 MET cc_start: 0.8949 (ttm) cc_final: 0.8508 (tmm) outliers start: 17 outliers final: 14 residues processed: 158 average time/residue: 0.4468 time to fit residues: 121.6921 Evaluate side-chains 161 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 3.755 ------------------------------------------------------------------------------- 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 T residue 31 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain F residue 225 LYS 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 133 LYS Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 332 MET 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: 9.9990 chunk 365 optimal weight: 10.0000 chunk 389 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 306 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 352 optimal weight: 0.2980 chunk 368 optimal weight: 7.9990 chunk 388 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33348 Z= 0.180 Angle : 0.552 20.316 44989 Z= 0.269 Chirality : 0.071 1.608 5425 Planarity : 0.002 0.023 5761 Dihedral : 6.678 147.268 4669 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 56.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.62 % Allowed : 7.79 % Favored : 91.59 % 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: 2.40 (0.12), residues: 2100 sheet: -1.24 (0.22), residues: 567 loop : -1.99 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 44 HIS 0.001 0.000 HIS D 243 PHE 0.014 0.001 PHE B 281 TYR 0.008 0.001 TYR P 76 ARG 0.004 0.000 ARG S 7 *********************** 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 fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 4.173 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: A 166 MET cc_start: 0.8850 (mmm) cc_final: 0.8441 (tmm) REVERT: A 292 MET cc_start: 0.9371 (mtm) cc_final: 0.8983 (mtm) REVERT: A 332 MET cc_start: 0.8227 (mtp) cc_final: 0.7975 (tmm) REVERT: A 453 MET cc_start: 0.8993 (ttm) cc_final: 0.8533 (tmm) REVERT: O 32 MET cc_start: 0.9018 (ptt) cc_final: 0.8354 (ppp) REVERT: T 85 ASP cc_start: 0.9108 (m-30) cc_final: 0.8891 (m-30) REVERT: Q 32 MET cc_start: 0.8063 (ppp) cc_final: 0.7835 (ppp) REVERT: G 166 MET cc_start: 0.7924 (tmm) cc_final: 0.7567 (tmm) REVERT: G 453 MET cc_start: 0.8993 (ttm) cc_final: 0.8365 (tpp) REVERT: F 166 MET cc_start: 0.7998 (tmm) cc_final: 0.7743 (tmm) REVERT: F 225 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8525 (mmtp) REVERT: F 292 MET cc_start: 0.9372 (mtm) cc_final: 0.8677 (mtt) REVERT: E 453 MET cc_start: 0.9019 (ttm) cc_final: 0.8572 (tmm) REVERT: D 292 MET cc_start: 0.9239 (mtm) cc_final: 0.8616 (mtt) REVERT: C 453 MET cc_start: 0.9020 (ttm) cc_final: 0.8304 (tmm) REVERT: B 453 MET cc_start: 0.8980 (ttm) cc_final: 0.8533 (tmm) outliers start: 22 outliers final: 17 residues processed: 158 average time/residue: 0.4387 time to fit residues: 120.0199 Evaluate side-chains 162 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 3.859 ------------------------------------------------------------------------------- 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 T residue 31 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 255 optimal weight: 10.0000 chunk 412 optimal weight: 0.0670 chunk 251 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 286 optimal weight: 5.9990 chunk 432 optimal weight: 7.9990 chunk 397 optimal weight: 6.9990 chunk 344 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- 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 ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 367 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 HIS ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2951 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= 0.254 Angle : 0.613 20.029 44989 Z= 0.302 Chirality : 0.072 1.615 5425 Planarity : 0.003 0.023 5761 Dihedral : 6.732 129.784 4669 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 61.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.10 % Favored : 89.84 % Rotamer: Outliers : 0.56 % Allowed : 7.85 % Favored : 91.59 % 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: 0.11 (0.13), residues: 4368 helix: 2.06 (0.12), residues: 2093 sheet: -1.24 (0.22), residues: 567 loop : -2.09 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 44 HIS 0.002 0.000 HIS C 243 PHE 0.011 0.001 PHE D 195 TYR 0.008 0.001 TYR P 76 ARG 0.005 0.000 ARG S 7 ********************** 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 164 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 4.106 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: 0.8897 (mmm) cc_final: 0.8462 (tmm) REVERT: A 292 MET cc_start: 0.9375 (mtm) cc_final: 0.8965 (mtm) REVERT: A 332 MET cc_start: 0.8305 (mtp) cc_final: 0.7958 (mmm) REVERT: A 453 MET cc_start: 0.9029 (ttm) cc_final: 0.8589 (tmm) REVERT: O 32 MET cc_start: 0.9014 (ptt) cc_final: 0.8394 (ppp) REVERT: G 166 MET cc_start: 0.7932 (tmm) cc_final: 0.7527 (tmm) REVERT: G 453 MET cc_start: 0.9053 (ttm) cc_final: 0.8301 (tmm) REVERT: F 166 MET cc_start: 0.8033 (tmm) cc_final: 0.7790 (tmm) REVERT: F 225 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8633 (mmtm) REVERT: F 292 MET cc_start: 0.9382 (mtm) cc_final: 0.8695 (mtt) REVERT: E 453 MET cc_start: 0.9037 (ttm) cc_final: 0.8539 (tmm) REVERT: D 292 MET cc_start: 0.9294 (mtm) cc_final: 0.8688 (mtt) REVERT: C 292 MET cc_start: 0.9464 (mtp) cc_final: 0.9259 (mtm) REVERT: C 453 MET cc_start: 0.9046 (ttm) cc_final: 0.8372 (tmm) REVERT: B 453 MET cc_start: 0.9018 (ttm) cc_final: 0.8530 (tmm) outliers start: 20 outliers final: 18 residues processed: 156 average time/residue: 0.4348 time to fit residues: 117.8273 Evaluate side-chains 161 residues out of total 3556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 53 SER Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain F residue 225 LYS Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain B residue 332 MET 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: 10.0000 chunk 105 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 344 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 354 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- 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** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 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 ** 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 = 0.3024 r_free = 0.3024 target = 0.037957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.030154 restraints weight = 279770.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.031256 restraints weight = 150273.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.032017 restraints weight = 94322.588| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33348 Z= 0.212 Angle : 0.578 20.162 44989 Z= 0.284 Chirality : 0.072 1.621 5425 Planarity : 0.002 0.023 5761 Dihedral : 6.558 120.426 4669 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 60.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.56 % Allowed : 8.04 % Favored : 91.39 % 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: 0.17 (0.13), residues: 4368 helix: 2.16 (0.12), residues: 2072 sheet: -1.17 (0.22), residues: 567 loop : -2.10 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 44 HIS 0.001 0.000 HIS D 243 PHE 0.011 0.001 PHE D 195 TYR 0.007 0.001 TYR P 76 ARG 0.004 0.000 ARG S 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4823.81 seconds wall clock time: 92 minutes 9.90 seconds (5529.90 seconds total)