Starting phenix.real_space_refine on Sat Feb 17 04:13:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2024/7miu_23865_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2024/7miu_23865.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2024/7miu_23865_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2024/7miu_23865_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2024/7miu_23865_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2024/7miu_23865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2024/7miu_23865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2024/7miu_23865_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2024/7miu_23865_updated.pdb" } resolution = 2.6 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= 0.000 sd= 0.263 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 100 5.16 5 C 11116 2.51 5 N 2960 2.21 5 O 3220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 528": "OE1" <-> "OE2" Residue "D PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 343": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "H PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 322": "OE1" <-> "OE2" Residue "H TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 343": "OE1" <-> "OE2" Residue "H PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 423": "OE1" <-> "OE2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 460": "OE1" <-> "OE2" Residue "H GLU 476": "OE1" <-> "OE2" Residue "H PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 493": "OE1" <-> "OE2" Residue "H PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 528": "OE1" <-> "OE2" Residue "H PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 191": "OE1" <-> "OE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "G PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 322": "OE1" <-> "OE2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 343": "OE1" <-> "OE2" Residue "G GLU 423": "OE1" <-> "OE2" Residue "G GLU 438": "OE1" <-> "OE2" Residue "G PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 460": "OE1" <-> "OE2" Residue "G GLU 476": "OE1" <-> "OE2" Residue "G PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 493": "OE1" <-> "OE2" Residue "G PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 528": "OE1" <-> "OE2" Residue "G PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17412 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4280 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "C" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4280 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "H" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4280 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "G" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4280 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "D" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 8.93, per 1000 atoms: 0.51 Number of scatterers: 17412 At special positions: 0 Unit cell: (122.85, 133.35, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 12 15.00 Mg 4 11.99 O 3220 8.00 N 2960 7.00 C 11116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.12 Conformation dependent library (CDL) restraints added in 3.2 seconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 16 sheets defined 42.2% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'D' and resid 16 through 29 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 52 through 55 No H-bonds generated for 'chain 'D' and resid 52 through 55' Processing helix chain 'D' and resid 69 through 77 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 113 through 129 removed outlier: 7.159A pdb=" N THR D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 168 removed outlier: 4.217A pdb=" N ALA D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 161 " --> pdb=" O ALA D 158 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN D 167 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 224 through 234 Processing helix chain 'D' and resid 250 through 259 Proline residue: D 254 - end of helix Processing helix chain 'D' and resid 262 through 270 Processing helix chain 'D' and resid 283 through 294 removed outlier: 3.837A pdb=" N ARG D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 327 removed outlier: 6.328A pdb=" N SER D 316 " --> pdb=" O CYS D 313 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 319 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS D 323 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 325 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 326 " --> pdb=" O HIS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 342 Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 378 through 390 Processing helix chain 'D' and resid 399 through 412 removed outlier: 4.063A pdb=" N LEU D 404 " --> pdb=" O GLY D 401 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 408 " --> pdb=" O ALA D 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 409 " --> pdb=" O VAL D 406 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN D 412 " --> pdb=" O PHE D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 467 Processing helix chain 'D' and resid 488 through 491 Processing helix chain 'D' and resid 527 through 530 Processing helix chain 'D' and resid 538 through 548 Processing helix chain 'D' and resid 550 through 556 Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 52 through 55 No H-bonds generated for 'chain 'C' and resid 52 through 55' Processing helix chain 'C' and resid 69 through 77 Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 113 through 129 removed outlier: 7.159A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 168 removed outlier: 4.215A pdb=" N ALA C 158 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 161 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 167 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 224 through 234 Processing helix chain 'C' and resid 250 through 259 Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 262 through 270 Processing helix chain 'C' and resid 283 through 294 removed outlier: 3.834A pdb=" N ARG C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 327 removed outlier: 6.312A pdb=" N SER C 316 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS C 323 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 325 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 326 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'C' and resid 344 through 349 Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 399 through 413 removed outlier: 4.041A pdb=" N LEU C 404 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 409 " --> pdb=" O VAL C 406 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 412 " --> pdb=" O PHE C 409 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS C 413 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 467 Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 527 through 530 Processing helix chain 'C' and resid 538 through 548 Processing helix chain 'C' and resid 551 through 556 Processing helix chain 'H' and resid 16 through 29 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 52 through 55 No H-bonds generated for 'chain 'H' and resid 52 through 55' Processing helix chain 'H' and resid 69 through 77 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 113 through 129 removed outlier: 7.159A pdb=" N THR H 118 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 168 removed outlier: 4.217A pdb=" N ALA H 158 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU H 161 " --> pdb=" O ALA H 158 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN H 167 " --> pdb=" O ARG H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 Processing helix chain 'H' and resid 224 through 234 Processing helix chain 'H' and resid 250 through 259 Proline residue: H 254 - end of helix Processing helix chain 'H' and resid 262 through 270 Processing helix chain 'H' and resid 283 through 294 removed outlier: 3.837A pdb=" N ARG H 294 " --> pdb=" O ASP H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 327 removed outlier: 6.328A pdb=" N SER H 316 " --> pdb=" O CYS H 313 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS H 319 " --> pdb=" O SER H 316 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS H 323 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA H 325 " --> pdb=" O GLU H 322 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU H 326 " --> pdb=" O HIS H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 342 Processing helix chain 'H' and resid 344 through 349 Processing helix chain 'H' and resid 351 through 362 Processing helix chain 'H' and resid 378 through 390 Processing helix chain 'H' and resid 399 through 412 removed outlier: 4.063A pdb=" N LEU H 404 " --> pdb=" O GLY H 401 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU H 408 " --> pdb=" O ALA H 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE H 409 " --> pdb=" O VAL H 406 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN H 412 " --> pdb=" O PHE H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 467 Processing helix chain 'H' and resid 488 through 491 Processing helix chain 'H' and resid 527 through 530 Processing helix chain 'H' and resid 538 through 548 Processing helix chain 'H' and resid 550 through 556 Processing helix chain 'G' and resid 16 through 29 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 52 through 55 No H-bonds generated for 'chain 'G' and resid 52 through 55' Processing helix chain 'G' and resid 69 through 77 Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 90 through 102 Processing helix chain 'G' and resid 113 through 129 removed outlier: 7.159A pdb=" N THR G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 168 removed outlier: 4.215A pdb=" N ALA G 158 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU G 161 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN G 167 " --> pdb=" O ARG G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 224 through 234 Processing helix chain 'G' and resid 250 through 259 Proline residue: G 254 - end of helix Processing helix chain 'G' and resid 262 through 270 Processing helix chain 'G' and resid 283 through 294 removed outlier: 3.834A pdb=" N ARG G 294 " --> pdb=" O ASP G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 327 removed outlier: 6.312A pdb=" N SER G 316 " --> pdb=" O CYS G 313 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS G 323 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA G 325 " --> pdb=" O GLU G 322 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU G 326 " --> pdb=" O HIS G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 342 Processing helix chain 'G' and resid 344 through 349 Processing helix chain 'G' and resid 351 through 362 Processing helix chain 'G' and resid 378 through 390 Processing helix chain 'G' and resid 399 through 413 removed outlier: 4.041A pdb=" N LEU G 404 " --> pdb=" O GLY G 401 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE G 409 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN G 412 " --> pdb=" O PHE G 409 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS G 413 " --> pdb=" O ALA G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 467 Processing helix chain 'G' and resid 488 through 491 Processing helix chain 'G' and resid 527 through 530 Processing helix chain 'G' and resid 538 through 548 Processing helix chain 'G' and resid 551 through 556 Processing sheet with id= A, first strand: chain 'D' and resid 241 through 244 removed outlier: 6.358A pdb=" N ILE D 214 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE D 244 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N CYS D 216 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR D 3 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE D 178 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU D 5 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL D 180 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR D 7 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N LEU D 182 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY D 8 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 330 through 337 removed outlier: 6.817A pdb=" N LYS D 297 " --> pdb=" O LYS D 331 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN D 333 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS D 299 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET D 335 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE D 301 " --> pdb=" O MET D 335 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE D 337 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU D 303 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY D 366 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL D 304 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU D 368 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL D 369 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU D 396 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 482 through 484 removed outlier: 3.983A pdb=" N ASN D 420 " --> pdb=" O VAL D 430 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 473 through 480 Processing sheet with id= E, first strand: chain 'C' and resid 241 through 244 removed outlier: 6.358A pdb=" N ILE C 214 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE C 244 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS C 216 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR C 3 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY C 8 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 330 through 338 removed outlier: 6.819A pdb=" N LYS C 297 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASN C 333 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS C 299 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET C 335 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE C 301 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE C 337 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU C 303 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY C 366 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL C 304 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU C 368 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL C 369 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C 396 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 482 through 484 removed outlier: 3.944A pdb=" N ASN C 420 " --> pdb=" O VAL C 430 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 473 through 480 Processing sheet with id= I, first strand: chain 'H' and resid 241 through 244 removed outlier: 6.358A pdb=" N ILE H 214 " --> pdb=" O ILE H 242 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE H 244 " --> pdb=" O ILE H 214 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N CYS H 216 " --> pdb=" O ILE H 244 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR H 3 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE H 178 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU H 5 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL H 180 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR H 7 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N LEU H 182 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY H 8 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 330 through 337 removed outlier: 6.816A pdb=" N LYS H 297 " --> pdb=" O LYS H 331 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN H 333 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS H 299 " --> pdb=" O ASN H 333 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET H 335 " --> pdb=" O CYS H 299 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE H 301 " --> pdb=" O MET H 335 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE H 337 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU H 303 " --> pdb=" O ILE H 337 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY H 366 " --> pdb=" O ALA H 302 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL H 304 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU H 368 " --> pdb=" O VAL H 304 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL H 369 " --> pdb=" O PRO H 394 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU H 396 " --> pdb=" O VAL H 369 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 482 through 484 removed outlier: 3.983A pdb=" N ASN H 420 " --> pdb=" O VAL H 430 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 473 through 480 Processing sheet with id= M, first strand: chain 'G' and resid 241 through 244 removed outlier: 6.358A pdb=" N ILE G 214 " --> pdb=" O ILE G 242 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE G 244 " --> pdb=" O ILE G 214 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS G 216 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR G 3 " --> pdb=" O TYR G 176 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE G 178 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU G 5 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL G 180 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR G 7 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N LEU G 182 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY G 8 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 330 through 338 removed outlier: 6.818A pdb=" N LYS G 297 " --> pdb=" O LYS G 331 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASN G 333 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS G 299 " --> pdb=" O ASN G 333 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET G 335 " --> pdb=" O CYS G 299 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE G 301 " --> pdb=" O MET G 335 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE G 337 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU G 303 " --> pdb=" O ILE G 337 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY G 366 " --> pdb=" O ALA G 302 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL G 304 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU G 368 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL G 369 " --> pdb=" O PRO G 394 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU G 396 " --> pdb=" O VAL G 369 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 482 through 484 removed outlier: 3.943A pdb=" N ASN G 420 " --> pdb=" O VAL G 430 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 473 through 480 642 hydrogen bonds defined for protein. 1506 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: 5.84 Time building geometry restraints manager: 7.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5644 1.36 - 1.49: 4257 1.49 - 1.63: 7707 1.63 - 1.77: 28 1.77 - 1.90: 144 Bond restraints: 17780 Sorted by residual: bond pdb=" C2' UTP H 604 " pdb=" C3' UTP H 604 " ideal model delta sigma weight residual 1.301 1.530 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C2' UTP D 604 " pdb=" C3' UTP D 604 " ideal model delta sigma weight residual 1.301 1.530 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C2' UTP C 602 " pdb=" C3' UTP C 602 " ideal model delta sigma weight residual 1.301 1.529 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C2' UTP G 602 " pdb=" C3' UTP G 602 " ideal model delta sigma weight residual 1.301 1.529 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' UTP D 604 " pdb=" O4' UTP D 604 " ideal model delta sigma weight residual 1.553 1.398 0.155 2.00e-02 2.50e+03 6.03e+01 ... (remaining 17775 not shown) Histogram of bond angle deviations from ideal: 59.71 - 75.09: 24 75.09 - 90.47: 4 90.47 - 105.85: 682 105.85 - 121.23: 17961 121.23 - 136.61: 5425 Bond angle restraints: 24096 Sorted by residual: angle pdb=" N PRO G 538 " pdb=" CA PRO G 538 " pdb=" C PRO G 538 " ideal model delta sigma weight residual 110.70 120.23 -9.53 1.22e+00 6.72e-01 6.10e+01 angle pdb=" N PRO C 538 " pdb=" CA PRO C 538 " pdb=" C PRO C 538 " ideal model delta sigma weight residual 110.70 120.22 -9.52 1.22e+00 6.72e-01 6.09e+01 angle pdb=" N PRO D 538 " pdb=" CA PRO D 538 " pdb=" C PRO D 538 " ideal model delta sigma weight residual 110.70 120.18 -9.48 1.22e+00 6.72e-01 6.04e+01 angle pdb=" N PRO H 538 " pdb=" CA PRO H 538 " pdb=" C PRO H 538 " ideal model delta sigma weight residual 110.70 120.18 -9.48 1.22e+00 6.72e-01 6.04e+01 angle pdb=" C GLY H 9 " pdb=" N VAL H 10 " pdb=" CA VAL H 10 " ideal model delta sigma weight residual 121.97 133.55 -11.58 1.80e+00 3.09e-01 4.14e+01 ... (remaining 24091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9920 17.95 - 35.90: 652 35.90 - 53.85: 86 53.85 - 71.80: 66 71.80 - 89.75: 44 Dihedral angle restraints: 10768 sinusoidal: 4520 harmonic: 6248 Sorted by residual: dihedral pdb=" CA PRO C 115 " pdb=" C PRO C 115 " pdb=" N HIS C 116 " pdb=" CA HIS C 116 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA PRO H 115 " pdb=" C PRO H 115 " pdb=" N HIS H 116 " pdb=" CA HIS H 116 " ideal model delta harmonic sigma weight residual 180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA PRO G 115 " pdb=" C PRO G 115 " pdb=" N HIS G 116 " pdb=" CA HIS G 116 " ideal model delta harmonic sigma weight residual 180.00 -150.35 -29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 10765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1606 0.100 - 0.199: 788 0.199 - 0.298: 242 0.298 - 0.398: 44 0.398 - 0.497: 12 Chirality restraints: 2692 Sorted by residual: chirality pdb=" C1' UTP H 604 " pdb=" C2' UTP H 604 " pdb=" N1 UTP H 604 " pdb=" O4' UTP H 604 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C1' UTP D 604 " pdb=" C2' UTP D 604 " pdb=" N1 UTP D 604 " pdb=" O4' UTP D 604 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" C1' UTP C 602 " pdb=" C2' UTP C 602 " pdb=" N1 UTP C 602 " pdb=" O4' UTP C 602 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.04e+00 ... (remaining 2689 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' UTP G 602 " 0.123 2.00e-02 2.50e+03 8.06e-02 1.46e+02 pdb=" C2 UTP G 602 " -0.058 2.00e-02 2.50e+03 pdb=" C4 UTP G 602 " -0.032 2.00e-02 2.50e+03 pdb=" C5 UTP G 602 " -0.036 2.00e-02 2.50e+03 pdb=" C6 UTP G 602 " -0.037 2.00e-02 2.50e+03 pdb=" N1 UTP G 602 " -0.039 2.00e-02 2.50e+03 pdb=" N3 UTP G 602 " -0.103 2.00e-02 2.50e+03 pdb=" O2 UTP G 602 " 0.032 2.00e-02 2.50e+03 pdb=" O4 UTP G 602 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' UTP C 602 " 0.123 2.00e-02 2.50e+03 8.05e-02 1.46e+02 pdb=" C2 UTP C 602 " -0.058 2.00e-02 2.50e+03 pdb=" C4 UTP C 602 " -0.032 2.00e-02 2.50e+03 pdb=" C5 UTP C 602 " -0.036 2.00e-02 2.50e+03 pdb=" C6 UTP C 602 " -0.037 2.00e-02 2.50e+03 pdb=" N1 UTP C 602 " -0.039 2.00e-02 2.50e+03 pdb=" N3 UTP C 602 " -0.103 2.00e-02 2.50e+03 pdb=" O2 UTP C 602 " 0.032 2.00e-02 2.50e+03 pdb=" O4 UTP C 602 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' UTP D 604 " -0.119 2.00e-02 2.50e+03 7.86e-02 1.39e+02 pdb=" C2 UTP D 604 " 0.057 2.00e-02 2.50e+03 pdb=" C4 UTP D 604 " 0.032 2.00e-02 2.50e+03 pdb=" C5 UTP D 604 " 0.033 2.00e-02 2.50e+03 pdb=" C6 UTP D 604 " 0.036 2.00e-02 2.50e+03 pdb=" N1 UTP D 604 " 0.039 2.00e-02 2.50e+03 pdb=" N3 UTP D 604 " 0.102 2.00e-02 2.50e+03 pdb=" O2 UTP D 604 " -0.033 2.00e-02 2.50e+03 pdb=" O4 UTP D 604 " -0.148 2.00e-02 2.50e+03 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 50 2.55 - 3.14: 12897 3.14 - 3.73: 29405 3.73 - 4.31: 44186 4.31 - 4.90: 70375 Nonbonded interactions: 156913 Sorted by model distance: nonbonded pdb="MG MG D 603 " pdb=" O1G UTP D 604 " model vdw 1.966 2.170 nonbonded pdb="MG MG H 603 " pdb=" O2G UTP H 604 " model vdw 1.966 2.170 nonbonded pdb=" O2G UTP C 602 " pdb="MG MG C 603 " model vdw 1.967 2.170 nonbonded pdb=" O1G UTP G 602 " pdb="MG MG G 603 " model vdw 1.967 2.170 nonbonded pdb=" CG2 THR C 49 " pdb=" OE2 GLU G 101 " model vdw 2.052 3.460 ... (remaining 156908 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 'C' and (resid 1 through 557 or resid 601 or resid 603)) selection = (chain 'D' and (resid 1 through 557 or resid 601 or resid 603)) selection = (chain 'G' and (resid 1 through 557 or resid 601 or resid 603)) selection = (chain 'H' and (resid 1 through 557 or resid 601 or resid 603)) } 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 individual isotropic 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: 1.230 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: 0.010 Extract box with map and model: 6.170 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 47.860 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.015 0.229 17780 Z= 1.025 Angle : 2.024 15.503 24096 Z= 1.332 Chirality : 0.124 0.497 2692 Planarity : 0.013 0.081 3068 Dihedral : 14.674 89.748 6752 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.29 % Favored : 95.06 % Rotamer: Outliers : 2.22 % Allowed : 3.28 % Favored : 94.50 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.57 % 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: -1.19 (0.17), residues: 2144 helix: -0.54 (0.15), residues: 908 sheet: -0.61 (0.27), residues: 316 loop : -0.95 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.015 TRP D 387 HIS 0.024 0.005 HIS H 480 PHE 0.071 0.018 PHE C 318 TYR 0.107 0.023 TYR H 336 ARG 0.006 0.001 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 536 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 TYR cc_start: 0.7577 (m-80) cc_final: 0.7290 (m-80) REVERT: D 268 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6371 (mt-10) REVERT: D 338 ASP cc_start: 0.7325 (t0) cc_final: 0.7100 (t0) REVERT: D 341 ASP cc_start: 0.7990 (m-30) cc_final: 0.7775 (m-30) REVERT: D 390 THR cc_start: 0.8429 (p) cc_final: 0.8205 (p) REVERT: C 176 TYR cc_start: 0.7535 (m-80) cc_final: 0.7277 (m-80) REVERT: C 268 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6241 (mt-10) REVERT: C 390 THR cc_start: 0.8411 (p) cc_final: 0.8139 (p) REVERT: H 54 GLU cc_start: 0.7984 (tp30) cc_final: 0.7741 (tp30) REVERT: H 176 TYR cc_start: 0.7568 (m-80) cc_final: 0.7297 (m-80) REVERT: H 268 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6381 (mt-10) REVERT: H 338 ASP cc_start: 0.7366 (t0) cc_final: 0.7128 (t0) REVERT: H 341 ASP cc_start: 0.8013 (m-30) cc_final: 0.7741 (m-30) REVERT: H 390 THR cc_start: 0.8357 (p) cc_final: 0.8129 (p) REVERT: G 126 MET cc_start: 0.7187 (mmm) cc_final: 0.6930 (tpt) REVERT: G 176 TYR cc_start: 0.7556 (m-80) cc_final: 0.7276 (m-80) REVERT: G 284 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7612 (mmtm) REVERT: G 390 THR cc_start: 0.8389 (p) cc_final: 0.8109 (p) outliers start: 42 outliers final: 2 residues processed: 556 average time/residue: 1.2792 time to fit residues: 794.9470 Evaluate side-chains 392 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 390 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain H residue 378 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 0.0070 chunk 196 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 HIS D 198 GLN D 235 HIS D 415 ASN ** D 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 ASN D 556 GLN C 55 HIS C 198 GLN C 235 HIS C 412 ASN C 415 ASN C 556 GLN H 198 GLN H 235 HIS H 415 ASN ** H 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 ASN H 556 GLN G 55 HIS G 198 GLN G 235 HIS G 415 ASN G 556 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17780 Z= 0.234 Angle : 0.599 8.300 24096 Z= 0.308 Chirality : 0.047 0.161 2692 Planarity : 0.004 0.036 3068 Dihedral : 7.097 48.370 2502 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.49 % Favored : 98.32 % Rotamer: Outliers : 1.96 % Allowed : 12.05 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.19 (0.18), residues: 2144 helix: 0.43 (0.16), residues: 924 sheet: -0.42 (0.26), residues: 340 loop : -0.44 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 358 HIS 0.005 0.001 HIS G 355 PHE 0.016 0.002 PHE G 318 TYR 0.017 0.002 TYR D 336 ARG 0.004 0.001 ARG C 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 392 time to evaluate : 1.982 Fit side-chains revert: symmetry clash REVERT: D 28 LYS cc_start: 0.8100 (tttp) cc_final: 0.7775 (tttt) REVERT: D 409 PHE cc_start: 0.7824 (t80) cc_final: 0.7598 (t80) REVERT: D 481 ARG cc_start: 0.7641 (mtt90) cc_final: 0.7233 (mtp85) REVERT: C 126 MET cc_start: 0.7287 (mmm) cc_final: 0.7081 (tpt) REVERT: C 390 THR cc_start: 0.8417 (p) cc_final: 0.8211 (p) REVERT: H 390 THR cc_start: 0.8377 (p) cc_final: 0.8172 (p) REVERT: H 409 PHE cc_start: 0.7799 (t80) cc_final: 0.7570 (t80) REVERT: G 268 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6640 (mt-10) REVERT: G 288 MET cc_start: 0.7855 (mtm) cc_final: 0.7473 (mtp) REVERT: G 456 VAL cc_start: 0.8250 (t) cc_final: 0.7960 (m) outliers start: 37 outliers final: 8 residues processed: 417 average time/residue: 1.2254 time to fit residues: 572.9287 Evaluate side-chains 364 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 356 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 378 THR Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain G residue 316 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 212 optimal weight: 0.0770 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 HIS H 177 ASN ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 ASN G 177 ASN G 198 GLN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17780 Z= 0.305 Angle : 0.628 8.507 24096 Z= 0.318 Chirality : 0.049 0.155 2692 Planarity : 0.005 0.046 3068 Dihedral : 7.329 50.672 2502 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.07 % Allowed : 15.06 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.03 (0.18), residues: 2144 helix: 0.49 (0.17), residues: 920 sheet: -0.69 (0.26), residues: 352 loop : -0.08 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 387 HIS 0.007 0.002 HIS G 355 PHE 0.016 0.002 PHE G 163 TYR 0.028 0.002 TYR G 176 ARG 0.004 0.001 ARG H 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 384 time to evaluate : 1.963 Fit side-chains REVERT: D 28 LYS cc_start: 0.8157 (tttp) cc_final: 0.7940 (tttt) REVERT: D 53 TYR cc_start: 0.7819 (m-80) cc_final: 0.7596 (m-80) REVERT: D 123 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: D 132 SER cc_start: 0.8150 (p) cc_final: 0.7809 (t) REVERT: D 157 MET cc_start: 0.7317 (mmp) cc_final: 0.7087 (mmt) REVERT: D 375 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7384 (pp) REVERT: D 409 PHE cc_start: 0.8030 (t80) cc_final: 0.7703 (t80) REVERT: D 466 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7832 (mtmm) REVERT: D 481 ARG cc_start: 0.7665 (mtt90) cc_final: 0.7207 (mtt-85) REVERT: D 510 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7092 (mm-30) REVERT: C 28 LYS cc_start: 0.8196 (tttp) cc_final: 0.7932 (tttt) REVERT: C 57 GLU cc_start: 0.7860 (pp20) cc_final: 0.7652 (pp20) REVERT: C 123 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7333 (tp30) REVERT: C 132 SER cc_start: 0.8194 (p) cc_final: 0.7836 (t) REVERT: C 157 MET cc_start: 0.7236 (mmp) cc_final: 0.7014 (mmt) REVERT: C 292 TYR cc_start: 0.8497 (t80) cc_final: 0.8220 (t80) REVERT: C 329 ASN cc_start: 0.8007 (m-40) cc_final: 0.7660 (t0) REVERT: C 389 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7570 (ttp80) REVERT: C 413 CYS cc_start: 0.7949 (m) cc_final: 0.7461 (m) REVERT: H 53 TYR cc_start: 0.8011 (m-80) cc_final: 0.7782 (m-80) REVERT: H 57 GLU cc_start: 0.7792 (pp20) cc_final: 0.7580 (pp20) REVERT: H 123 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: H 132 SER cc_start: 0.8155 (p) cc_final: 0.7830 (t) REVERT: H 157 MET cc_start: 0.7291 (mmp) cc_final: 0.7046 (mmt) REVERT: H 375 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7581 (pp) REVERT: H 409 PHE cc_start: 0.8047 (t80) cc_final: 0.7699 (t80) REVERT: H 510 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7087 (mm-30) REVERT: G 28 LYS cc_start: 0.8203 (tttp) cc_final: 0.7935 (tttt) REVERT: G 123 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: G 157 MET cc_start: 0.7335 (mmp) cc_final: 0.7081 (mmt) REVERT: G 212 ASP cc_start: 0.8292 (m-30) cc_final: 0.8085 (m-30) REVERT: G 268 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6688 (mt-10) REVERT: G 288 MET cc_start: 0.7917 (mtm) cc_final: 0.7573 (mtp) outliers start: 58 outliers final: 18 residues processed: 406 average time/residue: 1.2127 time to fit residues: 553.2714 Evaluate side-chains 393 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 366 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 248 SER Chi-restraints excluded: chain H residue 365 ASP Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 365 ASP Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN D 552 ASN C 177 ASN H 177 ASN H 552 ASN G 177 ASN G 198 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17780 Z= 0.214 Angle : 0.534 7.308 24096 Z= 0.270 Chirality : 0.046 0.136 2692 Planarity : 0.005 0.049 3068 Dihedral : 6.807 54.488 2500 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.91 % Allowed : 16.33 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.14 (0.18), residues: 2144 helix: 0.68 (0.17), residues: 896 sheet: -0.56 (0.25), residues: 372 loop : -0.03 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 387 HIS 0.005 0.001 HIS C 116 PHE 0.016 0.002 PHE C 354 TYR 0.014 0.001 TYR C 42 ARG 0.004 0.000 ARG D 508 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 400 time to evaluate : 2.139 Fit side-chains REVERT: D 123 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7312 (tp30) REVERT: D 132 SER cc_start: 0.8288 (p) cc_final: 0.7888 (t) REVERT: D 157 MET cc_start: 0.7430 (mmp) cc_final: 0.7082 (mmt) REVERT: D 288 MET cc_start: 0.8147 (mtp) cc_final: 0.7938 (mtm) REVERT: D 341 ASP cc_start: 0.7864 (m-30) cc_final: 0.7640 (m-30) REVERT: D 375 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7701 (pp) REVERT: D 409 PHE cc_start: 0.8037 (t80) cc_final: 0.7711 (t80) REVERT: D 466 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7824 (mtmm) REVERT: D 481 ARG cc_start: 0.7643 (mtt90) cc_final: 0.7210 (mtt-85) REVERT: C 28 LYS cc_start: 0.8173 (tttp) cc_final: 0.7924 (tttt) REVERT: C 57 GLU cc_start: 0.7865 (pp20) cc_final: 0.7612 (pp20) REVERT: C 123 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7338 (tp30) REVERT: C 132 SER cc_start: 0.8251 (p) cc_final: 0.7883 (t) REVERT: C 157 MET cc_start: 0.7314 (mmp) cc_final: 0.6988 (mmt) REVERT: C 268 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6819 (mt-10) REVERT: C 329 ASN cc_start: 0.8025 (m-40) cc_final: 0.7686 (t0) REVERT: C 413 CYS cc_start: 0.7858 (m) cc_final: 0.7390 (m) REVERT: H 53 TYR cc_start: 0.8006 (m-80) cc_final: 0.7742 (m-80) REVERT: H 57 GLU cc_start: 0.7836 (pp20) cc_final: 0.7609 (pp20) REVERT: H 123 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7339 (tp30) REVERT: H 132 SER cc_start: 0.8310 (p) cc_final: 0.7934 (t) REVERT: H 157 MET cc_start: 0.7405 (mmp) cc_final: 0.7035 (mmt) REVERT: H 268 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6745 (mt-10) REVERT: H 341 ASP cc_start: 0.8105 (m-30) cc_final: 0.7845 (m-30) REVERT: H 375 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7761 (pp) REVERT: H 409 PHE cc_start: 0.8049 (t80) cc_final: 0.7690 (t80) REVERT: G 28 LYS cc_start: 0.8184 (tttp) cc_final: 0.7913 (tttt) REVERT: G 123 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7216 (tp30) REVERT: G 132 SER cc_start: 0.8198 (p) cc_final: 0.7845 (t) REVERT: G 157 MET cc_start: 0.7446 (mmp) cc_final: 0.7095 (mmt) REVERT: G 212 ASP cc_start: 0.8352 (m-30) cc_final: 0.8080 (m-30) REVERT: G 268 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6688 (mt-10) REVERT: G 379 LEU cc_start: 0.7931 (mt) cc_final: 0.7707 (mm) outliers start: 55 outliers final: 15 residues processed: 419 average time/residue: 1.1981 time to fit residues: 565.9689 Evaluate side-chains 413 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 391 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 248 SER Chi-restraints excluded: chain H residue 365 ASP Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 248 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 178 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 187 optimal weight: 0.5980 chunk 52 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 ASN C 177 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 ASN ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 ASN G 177 ASN G 412 ASN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17780 Z= 0.182 Angle : 0.517 7.026 24096 Z= 0.258 Chirality : 0.045 0.135 2692 Planarity : 0.005 0.049 3068 Dihedral : 6.541 59.969 2500 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.75 % Allowed : 16.97 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.30 (0.18), residues: 2144 helix: 0.82 (0.17), residues: 896 sheet: -0.49 (0.24), residues: 372 loop : 0.05 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 387 HIS 0.004 0.001 HIS H 116 PHE 0.016 0.001 PHE C 354 TYR 0.014 0.001 TYR H 42 ARG 0.002 0.000 ARG C 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 405 time to evaluate : 2.013 Fit side-chains REVERT: D 123 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7293 (tp30) REVERT: D 132 SER cc_start: 0.8271 (p) cc_final: 0.7881 (t) REVERT: D 157 MET cc_start: 0.7462 (mmp) cc_final: 0.7050 (mmt) REVERT: D 268 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6696 (mt-10) REVERT: D 288 MET cc_start: 0.8193 (mtp) cc_final: 0.7979 (mtm) REVERT: D 341 ASP cc_start: 0.7880 (m-30) cc_final: 0.7653 (m-30) REVERT: D 375 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7620 (pp) REVERT: D 409 PHE cc_start: 0.8009 (t80) cc_final: 0.7642 (t80) REVERT: D 466 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7862 (mtmm) REVERT: D 481 ARG cc_start: 0.7588 (mtt90) cc_final: 0.7174 (mtt-85) REVERT: D 510 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7174 (mm-30) REVERT: C 28 LYS cc_start: 0.8146 (tttp) cc_final: 0.7913 (tttt) REVERT: C 123 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7293 (tp30) REVERT: C 132 SER cc_start: 0.8283 (p) cc_final: 0.7906 (t) REVERT: C 157 MET cc_start: 0.7408 (mmp) cc_final: 0.6993 (mmt) REVERT: C 268 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6624 (mt-10) REVERT: C 329 ASN cc_start: 0.8056 (m-40) cc_final: 0.7706 (t0) REVERT: C 331 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7335 (mttp) REVERT: C 387 TRP cc_start: 0.7871 (t-100) cc_final: 0.7644 (t-100) REVERT: C 413 CYS cc_start: 0.7741 (m) cc_final: 0.7287 (m) REVERT: H 53 TYR cc_start: 0.7992 (m-80) cc_final: 0.7734 (m-80) REVERT: H 123 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: H 132 SER cc_start: 0.8293 (p) cc_final: 0.7921 (t) REVERT: H 157 MET cc_start: 0.7442 (mmp) cc_final: 0.7086 (mmt) REVERT: H 268 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6720 (mt-10) REVERT: H 341 ASP cc_start: 0.8087 (m-30) cc_final: 0.7834 (m-30) REVERT: H 375 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7647 (pp) REVERT: H 409 PHE cc_start: 0.7981 (t80) cc_final: 0.7627 (t80) REVERT: G 28 LYS cc_start: 0.8173 (tttp) cc_final: 0.7952 (tttt) REVERT: G 123 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7261 (tp30) REVERT: G 132 SER cc_start: 0.8230 (p) cc_final: 0.7868 (t) REVERT: G 157 MET cc_start: 0.7473 (mmp) cc_final: 0.7056 (mmt) REVERT: G 212 ASP cc_start: 0.8299 (m-30) cc_final: 0.8041 (m-30) REVERT: G 268 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6700 (mt-10) REVERT: G 510 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7051 (mm-30) outliers start: 52 outliers final: 20 residues processed: 414 average time/residue: 1.2223 time to fit residues: 567.9199 Evaluate side-chains 416 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 387 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 248 SER Chi-restraints excluded: chain H residue 365 ASP Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 365 ASP Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.0870 chunk 109 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN D 552 ASN C 177 ASN H 177 ASN H 552 ASN G 177 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17780 Z= 0.200 Angle : 0.526 8.457 24096 Z= 0.263 Chirality : 0.045 0.132 2692 Planarity : 0.005 0.049 3068 Dihedral : 6.522 57.988 2500 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.75 % Allowed : 17.39 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.32 (0.18), residues: 2144 helix: 0.84 (0.17), residues: 904 sheet: -0.49 (0.24), residues: 372 loop : 0.06 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 387 HIS 0.004 0.001 HIS C 355 PHE 0.016 0.001 PHE H 354 TYR 0.015 0.001 TYR D 42 ARG 0.008 0.000 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 397 time to evaluate : 2.138 Fit side-chains revert: symmetry clash REVERT: D 123 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: D 132 SER cc_start: 0.8355 (p) cc_final: 0.7951 (t) REVERT: D 157 MET cc_start: 0.7568 (mmp) cc_final: 0.7167 (mmt) REVERT: D 231 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8571 (t) REVERT: D 232 MET cc_start: 0.7401 (mtm) cc_final: 0.7148 (mtp) REVERT: D 268 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6799 (mt-10) REVERT: D 341 ASP cc_start: 0.7872 (m-30) cc_final: 0.7661 (m-30) REVERT: D 375 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7657 (pp) REVERT: D 466 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7835 (mtmm) REVERT: D 481 ARG cc_start: 0.7536 (mtt90) cc_final: 0.7133 (mtt-85) REVERT: D 510 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: C 28 LYS cc_start: 0.8201 (tttp) cc_final: 0.7967 (tttt) REVERT: C 123 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: C 132 SER cc_start: 0.8372 (p) cc_final: 0.7968 (t) REVERT: C 157 MET cc_start: 0.7485 (mmp) cc_final: 0.7050 (mmt) REVERT: C 268 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6877 (mt-10) REVERT: C 293 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6900 (mm-30) REVERT: C 329 ASN cc_start: 0.7999 (m-40) cc_final: 0.7668 (t0) REVERT: C 375 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7515 (pp) REVERT: C 387 TRP cc_start: 0.7985 (t-100) cc_final: 0.7681 (t-100) REVERT: C 413 CYS cc_start: 0.7777 (m) cc_final: 0.7323 (m) REVERT: H 53 TYR cc_start: 0.7981 (m-80) cc_final: 0.7745 (m-80) REVERT: H 123 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7331 (tp30) REVERT: H 132 SER cc_start: 0.8379 (p) cc_final: 0.7986 (t) REVERT: H 157 MET cc_start: 0.7542 (mmp) cc_final: 0.7118 (mmt) REVERT: H 264 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6975 (tttp) REVERT: H 268 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6795 (mt-10) REVERT: H 341 ASP cc_start: 0.8036 (m-30) cc_final: 0.7819 (m-30) REVERT: H 375 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7653 (pp) REVERT: H 409 PHE cc_start: 0.7993 (t80) cc_final: 0.7652 (t80) REVERT: H 456 VAL cc_start: 0.8259 (t) cc_final: 0.7971 (m) REVERT: H 510 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7164 (mm-30) REVERT: G 28 LYS cc_start: 0.8171 (tttp) cc_final: 0.7970 (tttt) REVERT: G 123 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: G 132 SER cc_start: 0.8325 (p) cc_final: 0.7945 (t) REVERT: G 157 MET cc_start: 0.7564 (mmp) cc_final: 0.7058 (mmt) REVERT: G 212 ASP cc_start: 0.8290 (m-30) cc_final: 0.8046 (m-30) REVERT: G 268 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6733 (mt-10) REVERT: G 293 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6890 (mm-30) REVERT: G 375 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7535 (pp) REVERT: G 510 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7058 (mm-30) outliers start: 52 outliers final: 19 residues processed: 406 average time/residue: 1.2130 time to fit residues: 553.8804 Evaluate side-chains 425 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 392 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 248 SER Chi-restraints excluded: chain H residue 264 LYS Chi-restraints excluded: chain H residue 365 ASP Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 365 ASP Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 152 optimal weight: 0.0980 chunk 118 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 126 optimal weight: 0.0030 chunk 96 optimal weight: 7.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN D 552 ASN C 177 ASN H 177 ASN H 552 ASN G 177 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17780 Z= 0.271 Angle : 0.571 8.628 24096 Z= 0.283 Chirality : 0.047 0.143 2692 Planarity : 0.005 0.048 3068 Dihedral : 6.971 57.294 2500 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.70 % Allowed : 17.65 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2144 helix: 0.81 (0.17), residues: 900 sheet: -0.45 (0.24), residues: 380 loop : 0.10 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 387 HIS 0.006 0.002 HIS H 355 PHE 0.016 0.002 PHE D 354 TYR 0.015 0.002 TYR C 42 ARG 0.006 0.001 ARG D 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 412 time to evaluate : 2.031 Fit side-chains REVERT: D 123 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: D 132 SER cc_start: 0.8359 (p) cc_final: 0.7960 (t) REVERT: D 157 MET cc_start: 0.7604 (mmp) cc_final: 0.7129 (mmt) REVERT: D 268 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6743 (mt-10) REVERT: D 341 ASP cc_start: 0.7920 (m-30) cc_final: 0.7683 (m-30) REVERT: D 375 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7660 (pp) REVERT: D 466 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7876 (mtmm) REVERT: D 481 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7206 (mtt-85) REVERT: D 483 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6301 (mt-10) REVERT: D 508 ARG cc_start: 0.7848 (mtt-85) cc_final: 0.7283 (mtt90) REVERT: D 510 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7133 (mm-30) REVERT: C 28 LYS cc_start: 0.8213 (tttp) cc_final: 0.7972 (tttt) REVERT: C 123 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7307 (tp30) REVERT: C 157 MET cc_start: 0.7540 (mmp) cc_final: 0.7080 (mmt) REVERT: C 268 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6693 (mt-10) REVERT: C 293 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6911 (mm-30) REVERT: C 341 ASP cc_start: 0.7959 (m-30) cc_final: 0.7705 (m-30) REVERT: C 375 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7537 (pp) REVERT: C 413 CYS cc_start: 0.7791 (m) cc_final: 0.7298 (m) REVERT: C 483 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6679 (mt-10) REVERT: H 53 TYR cc_start: 0.7999 (m-80) cc_final: 0.7623 (m-80) REVERT: H 123 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7415 (tp30) REVERT: H 132 SER cc_start: 0.8386 (p) cc_final: 0.8003 (t) REVERT: H 157 MET cc_start: 0.7561 (mmp) cc_final: 0.7064 (mmt) REVERT: H 264 LYS cc_start: 0.7228 (tttp) cc_final: 0.6960 (tttp) REVERT: H 268 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6689 (mt-10) REVERT: H 375 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7673 (pp) REVERT: H 409 PHE cc_start: 0.8038 (t80) cc_final: 0.7652 (t80) REVERT: H 483 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6773 (mt-10) REVERT: H 510 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: G 28 LYS cc_start: 0.8227 (tttp) cc_final: 0.7965 (tttt) REVERT: G 123 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: G 132 SER cc_start: 0.8353 (p) cc_final: 0.7979 (t) REVERT: G 157 MET cc_start: 0.7596 (mmp) cc_final: 0.7132 (mmt) REVERT: G 212 ASP cc_start: 0.8326 (m-30) cc_final: 0.8066 (m-30) REVERT: G 268 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6800 (mt-10) REVERT: G 293 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6945 (mm-30) REVERT: G 375 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7557 (pp) REVERT: G 389 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7443 (ttp80) REVERT: G 483 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6408 (mt-10) outliers start: 51 outliers final: 22 residues processed: 425 average time/residue: 1.1475 time to fit residues: 549.0517 Evaluate side-chains 438 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 405 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 248 SER Chi-restraints excluded: chain H residue 365 ASP Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 365 ASP Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 0.0870 chunk 19 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 189 optimal weight: 0.0040 overall best weight: 0.4770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN D 552 ASN C 177 ASN C 296 GLN H 177 ASN G 177 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17780 Z= 0.182 Angle : 0.537 9.607 24096 Z= 0.265 Chirality : 0.045 0.145 2692 Planarity : 0.005 0.048 3068 Dihedral : 6.376 52.323 2500 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.27 % Allowed : 17.92 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.43 (0.18), residues: 2144 helix: 0.87 (0.17), residues: 924 sheet: -0.44 (0.24), residues: 380 loop : 0.20 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 387 HIS 0.003 0.001 HIS H 355 PHE 0.016 0.001 PHE C 409 TYR 0.013 0.001 TYR G 42 ARG 0.005 0.000 ARG D 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 406 time to evaluate : 1.932 Fit side-chains REVERT: D 123 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7320 (tp30) REVERT: D 132 SER cc_start: 0.8347 (p) cc_final: 0.7957 (t) REVERT: D 157 MET cc_start: 0.7587 (mmp) cc_final: 0.7184 (mmt) REVERT: D 268 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6741 (mt-10) REVERT: D 341 ASP cc_start: 0.7925 (m-30) cc_final: 0.7688 (m-30) REVERT: D 375 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7520 (pp) REVERT: D 466 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7874 (mtmm) REVERT: D 481 ARG cc_start: 0.7616 (mtt90) cc_final: 0.7211 (mtt-85) REVERT: D 510 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7121 (mm-30) REVERT: C 28 LYS cc_start: 0.8212 (tttp) cc_final: 0.7979 (tttt) REVERT: C 123 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7294 (tp30) REVERT: C 132 SER cc_start: 0.8388 (p) cc_final: 0.8004 (t) REVERT: C 157 MET cc_start: 0.7539 (mmp) cc_final: 0.7094 (mmt) REVERT: C 268 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6790 (mt-10) REVERT: C 293 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6914 (mm-30) REVERT: C 329 ASN cc_start: 0.7998 (m-40) cc_final: 0.7635 (t0) REVERT: C 375 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7357 (pp) REVERT: C 413 CYS cc_start: 0.7727 (m) cc_final: 0.7247 (m) REVERT: H 123 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7368 (tp30) REVERT: H 132 SER cc_start: 0.8364 (p) cc_final: 0.7984 (t) REVERT: H 157 MET cc_start: 0.7565 (mmp) cc_final: 0.7134 (mmt) REVERT: H 264 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6992 (tttp) REVERT: H 268 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6735 (mt-10) REVERT: H 375 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7478 (pp) REVERT: H 409 PHE cc_start: 0.7968 (t80) cc_final: 0.7612 (t80) REVERT: H 510 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: G 28 LYS cc_start: 0.8228 (tttp) cc_final: 0.7979 (tttt) REVERT: G 123 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: G 132 SER cc_start: 0.8344 (p) cc_final: 0.7977 (t) REVERT: G 157 MET cc_start: 0.7599 (mmp) cc_final: 0.7200 (mmt) REVERT: G 212 ASP cc_start: 0.8299 (m-30) cc_final: 0.8032 (m-30) REVERT: G 268 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6797 (mt-10) REVERT: G 375 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7422 (pp) REVERT: G 483 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6550 (mt-10) REVERT: G 510 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7088 (mm-30) outliers start: 43 outliers final: 18 residues processed: 417 average time/residue: 1.1866 time to fit residues: 556.1231 Evaluate side-chains 423 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 392 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 264 LYS Chi-restraints excluded: chain H residue 365 ASP Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 365 ASP Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN C 177 ASN H 177 ASN H 552 ASN G 177 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17780 Z= 0.233 Angle : 0.562 10.284 24096 Z= 0.277 Chirality : 0.046 0.137 2692 Planarity : 0.005 0.048 3068 Dihedral : 6.646 53.239 2500 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.70 % Allowed : 17.71 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2144 helix: 0.81 (0.17), residues: 928 sheet: -0.38 (0.24), residues: 384 loop : 0.14 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 387 HIS 0.005 0.001 HIS H 355 PHE 0.019 0.002 PHE G 409 TYR 0.014 0.001 TYR G 42 ARG 0.004 0.000 ARG H 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 418 time to evaluate : 1.817 Fit side-chains REVERT: D 123 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: D 132 SER cc_start: 0.8347 (p) cc_final: 0.7958 (t) REVERT: D 157 MET cc_start: 0.7595 (mmp) cc_final: 0.7171 (mmt) REVERT: D 268 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6637 (mt-10) REVERT: D 341 ASP cc_start: 0.7922 (m-30) cc_final: 0.7681 (m-30) REVERT: D 375 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7615 (pp) REVERT: D 466 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7903 (mtmm) REVERT: D 481 ARG cc_start: 0.7641 (mtt90) cc_final: 0.7205 (mtt-85) REVERT: D 510 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7131 (mm-30) REVERT: C 28 LYS cc_start: 0.8219 (tttp) cc_final: 0.7986 (tttt) REVERT: C 123 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7308 (tp30) REVERT: C 132 SER cc_start: 0.8388 (p) cc_final: 0.8006 (t) REVERT: C 157 MET cc_start: 0.7546 (mmp) cc_final: 0.7142 (mmt) REVERT: C 268 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6769 (mt-10) REVERT: C 293 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6938 (mm-30) REVERT: C 329 ASN cc_start: 0.7999 (m-40) cc_final: 0.7647 (t0) REVERT: C 375 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7385 (pp) REVERT: C 413 CYS cc_start: 0.7695 (m) cc_final: 0.7207 (m) REVERT: H 123 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7384 (tp30) REVERT: H 132 SER cc_start: 0.8378 (p) cc_final: 0.7990 (t) REVERT: H 157 MET cc_start: 0.7575 (mmp) cc_final: 0.7182 (mmt) REVERT: H 264 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6984 (tttp) REVERT: H 268 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6689 (mt-10) REVERT: H 331 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7482 (mmmm) REVERT: H 375 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7579 (pp) REVERT: H 409 PHE cc_start: 0.8009 (t80) cc_final: 0.7650 (t80) REVERT: H 485 ASN cc_start: 0.8487 (t0) cc_final: 0.8272 (t0) REVERT: H 510 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: G 28 LYS cc_start: 0.8228 (tttp) cc_final: 0.7974 (tttt) REVERT: G 123 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7244 (tp30) REVERT: G 157 MET cc_start: 0.7586 (mmp) cc_final: 0.7216 (mmt) REVERT: G 212 ASP cc_start: 0.8301 (m-30) cc_final: 0.8040 (m-30) REVERT: G 268 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6781 (mt-10) REVERT: G 341 ASP cc_start: 0.8077 (m-30) cc_final: 0.7826 (m-30) REVERT: G 375 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7444 (pp) REVERT: G 483 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6530 (mt-10) REVERT: G 510 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7115 (mm-30) outliers start: 51 outliers final: 21 residues processed: 434 average time/residue: 1.1823 time to fit residues: 577.8174 Evaluate side-chains 437 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 402 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 264 LYS Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain H residue 365 ASP Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 378 THR Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 365 ASP Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 198 optimal weight: 4.9990 chunk 171 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 136 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN ** D 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN C 296 GLN C 333 ASN H 177 ASN G 177 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17780 Z= 0.283 Angle : 0.593 10.697 24096 Z= 0.293 Chirality : 0.047 0.145 2692 Planarity : 0.005 0.048 3068 Dihedral : 6.940 57.003 2500 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.33 % Allowed : 18.55 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.32 (0.18), residues: 2144 helix: 0.78 (0.17), residues: 924 sheet: -0.46 (0.23), residues: 380 loop : 0.10 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 387 HIS 0.005 0.002 HIS G 355 PHE 0.022 0.002 PHE G 409 TYR 0.016 0.002 TYR C 176 ARG 0.004 0.000 ARG D 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 418 time to evaluate : 2.074 Fit side-chains REVERT: D 123 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: D 132 SER cc_start: 0.8362 (p) cc_final: 0.7974 (t) REVERT: D 157 MET cc_start: 0.7605 (mmp) cc_final: 0.7192 (mmt) REVERT: D 341 ASP cc_start: 0.8047 (m-30) cc_final: 0.7805 (m-30) REVERT: D 375 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7716 (pp) REVERT: D 481 ARG cc_start: 0.7720 (mtt90) cc_final: 0.7245 (mtt-85) REVERT: D 510 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7130 (mm-30) REVERT: C 28 LYS cc_start: 0.8238 (tttp) cc_final: 0.7989 (tttt) REVERT: C 123 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7318 (tp30) REVERT: C 132 SER cc_start: 0.8392 (p) cc_final: 0.8012 (t) REVERT: C 157 MET cc_start: 0.7550 (mmp) cc_final: 0.7127 (mmt) REVERT: C 268 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6744 (mt-10) REVERT: C 341 ASP cc_start: 0.7965 (m-30) cc_final: 0.7699 (m-30) REVERT: C 375 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7497 (pp) REVERT: C 413 CYS cc_start: 0.7687 (m) cc_final: 0.7186 (m) REVERT: C 510 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7007 (mm-30) REVERT: H 123 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: H 132 SER cc_start: 0.8395 (p) cc_final: 0.8006 (t) REVERT: H 157 MET cc_start: 0.7596 (mmp) cc_final: 0.7220 (mmt) REVERT: H 264 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.7028 (tttp) REVERT: H 268 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6687 (mt-10) REVERT: H 375 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7692 (pp) REVERT: H 409 PHE cc_start: 0.8032 (t80) cc_final: 0.7665 (t80) REVERT: H 510 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7158 (mm-30) REVERT: G 28 LYS cc_start: 0.8241 (tttp) cc_final: 0.7977 (tttt) REVERT: G 123 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: G 157 MET cc_start: 0.7602 (mmp) cc_final: 0.7242 (mmt) REVERT: G 212 ASP cc_start: 0.8320 (m-30) cc_final: 0.8078 (m-30) REVERT: G 268 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6711 (mt-10) REVERT: G 341 ASP cc_start: 0.8107 (m-30) cc_final: 0.7800 (m-30) REVERT: G 375 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7475 (pp) REVERT: G 389 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7329 (ttp80) REVERT: G 483 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6575 (mt-10) REVERT: G 510 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7115 (mm-30) outliers start: 44 outliers final: 21 residues processed: 431 average time/residue: 1.1699 time to fit residues: 568.7503 Evaluate side-chains 443 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 409 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 264 LYS Chi-restraints excluded: chain H residue 365 ASP Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 378 THR Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 365 ASP Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 25 optimal weight: 0.0770 chunk 47 optimal weight: 0.8980 chunk 171 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN C 177 ASN C 296 GLN H 177 ASN G 177 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.149889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.121946 restraints weight = 18292.082| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.54 r_work: 0.3150 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17780 Z= 0.211 Angle : 0.553 10.314 24096 Z= 0.273 Chirality : 0.045 0.168 2692 Planarity : 0.005 0.047 3068 Dihedral : 6.493 52.741 2500 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.17 % Allowed : 19.03 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.40 (0.18), residues: 2144 helix: 0.91 (0.17), residues: 924 sheet: -0.42 (0.23), residues: 384 loop : 0.07 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 387 HIS 0.004 0.001 HIS C 554 PHE 0.021 0.002 PHE G 409 TYR 0.013 0.001 TYR G 42 ARG 0.004 0.000 ARG H 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8437.57 seconds wall clock time: 149 minutes 59.44 seconds (8999.44 seconds total)