Starting phenix.real_space_refine (version: dev) on Wed Feb 22 14:03:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2023/7miu_23865_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2023/7miu_23865.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2023/7miu_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_2023/7miu_23865_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2023/7miu_23865_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2023/7miu_23865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2023/7miu_23865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2023/7miu_23865_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miu_23865/02_2023/7miu_23865_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 9.89, per 1000 atoms: 0.57 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: 7.11 Conformation dependent library (CDL) restraints added in 2.5 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: 2.00 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: 5.38 Time building geometry restraints manager: 7.75 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: 9896 17.95 - 35.90: 648 35.90 - 53.85: 82 53.85 - 71.80: 54 71.80 - 89.75: 44 Dihedral angle restraints: 10724 sinusoidal: 4476 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 10721 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 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. 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: 0.010 Normalize map: mean=0, sd=1: 1.080 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: 7.030 Check model and map are aligned: 0.270 Process input model: 46.160 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 14.403 89.748 6708 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 % 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 *********************** 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 : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 2 residues processed: 556 average time/residue: 1.2417 time to fit residues: 771.2787 Evaluate side-chains 394 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 392 time to evaluate : 2.066 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.8458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 55 HIS 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 17780 Z= 0.235 Angle : 0.603 8.341 24096 Z= 0.309 Chirality : 0.048 0.160 2692 Planarity : 0.004 0.036 3068 Dihedral : 5.982 42.944 2456 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.68 % Favored : 98.13 % Rotamer Outliers : 1.96 % 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: -0.22 (0.18), residues: 2144 helix: 0.37 (0.16), residues: 924 sheet: -0.63 (0.25), residues: 368 loop : -0.31 (0.22), residues: 852 *********************** 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 439 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 402 time to evaluate : 2.318 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 7 residues processed: 429 average time/residue: 1.1876 time to fit residues: 572.0103 Evaluate side-chains 375 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 368 time to evaluate : 2.094 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 2.3598 time to fit residues: 5.4187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 0.3980 chunk 212 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN D 198 GLN ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 ASN C 177 ASN C 198 GLN ** 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 198 GLN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 17780 Z= 0.330 Angle : 0.640 9.182 24096 Z= 0.324 Chirality : 0.050 0.149 2692 Planarity : 0.005 0.044 3068 Dihedral : 6.310 47.119 2456 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 3.81 % 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: -0.08 (0.18), residues: 2144 helix: 0.41 (0.17), residues: 920 sheet: -0.65 (0.26), residues: 352 loop : -0.08 (0.21), residues: 872 *********************** 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 461 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 389 time to evaluate : 2.163 Fit side-chains outliers start: 72 outliers final: 22 residues processed: 415 average time/residue: 1.2061 time to fit residues: 562.5686 Evaluate side-chains 384 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 362 time to evaluate : 2.060 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 12 residues processed: 10 average time/residue: 0.4287 time to fit residues: 8.6282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 131 optimal weight: 0.0050 chunk 197 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN D 198 GLN ** D 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 ASN C 177 ASN C 198 GLN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 ASN ** H 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 ASN G 177 ASN G 198 GLN G 412 ASN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 17780 Z= 0.199 Angle : 0.527 7.442 24096 Z= 0.266 Chirality : 0.045 0.134 2692 Planarity : 0.005 0.048 3068 Dihedral : 5.619 54.623 2456 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 3.01 % 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: -0.01 (0.18), residues: 2144 helix: 0.63 (0.17), residues: 920 sheet: -0.70 (0.24), residues: 392 loop : -0.17 (0.21), residues: 832 *********************** 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 450 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 393 time to evaluate : 2.143 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 25 residues processed: 416 average time/residue: 1.2152 time to fit residues: 568.9559 Evaluate side-chains 403 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 378 time to evaluate : 2.179 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 14 residues processed: 11 average time/residue: 0.3418 time to fit residues: 8.0834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 155 optimal weight: 0.1980 chunk 86 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 0.0040 chunk 187 optimal weight: 0.8980 chunk 52 optimal weight: 0.0770 overall best weight: 0.3150 ------------------------------------------------------------------------------- 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 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 ASN G 177 ASN G 480 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 17780 Z= 0.153 Angle : 0.498 7.071 24096 Z= 0.250 Chirality : 0.044 0.132 2692 Planarity : 0.004 0.048 3068 Dihedral : 5.356 59.359 2456 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 2.59 % 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: 0.18 (0.18), residues: 2144 helix: 0.74 (0.17), residues: 932 sheet: -0.54 (0.23), residues: 420 loop : -0.04 (0.22), residues: 792 *********************** 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 437 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 388 time to evaluate : 2.280 Fit side-chains outliers start: 49 outliers final: 18 residues processed: 405 average time/residue: 1.1909 time to fit residues: 544.0171 Evaluate side-chains 390 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 372 time to evaluate : 2.031 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.1740 time to fit residues: 4.9141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 41 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 ASN H 552 ASN G 177 ASN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4068 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= 0.219 Angle : 0.530 8.221 24096 Z= 0.265 Chirality : 0.045 0.146 2692 Planarity : 0.005 0.047 3068 Dihedral : 5.641 59.741 2456 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 2.43 % 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: 0.15 (0.18), residues: 2144 helix: 0.77 (0.17), residues: 928 sheet: -0.63 (0.23), residues: 412 loop : -0.08 (0.22), residues: 804 *********************** 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 440 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 394 time to evaluate : 2.094 Fit side-chains outliers start: 46 outliers final: 21 residues processed: 407 average time/residue: 1.1711 time to fit residues: 537.7917 Evaluate side-chains 407 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 386 time to evaluate : 2.283 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 11 residues processed: 10 average time/residue: 0.1960 time to fit residues: 6.4851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 119 optimal weight: 2.9990 chunk 152 optimal weight: 0.0970 chunk 118 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 116 optimal weight: 0.4980 chunk 208 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** D 552 ASN C 177 ASN H 177 ASN H 478 HIS G 177 ASN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4207 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= 0.251 Angle : 0.552 8.732 24096 Z= 0.275 Chirality : 0.046 0.138 2692 Planarity : 0.005 0.048 3068 Dihedral : 5.701 56.704 2456 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 2.33 % 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: 0.77 (0.17), residues: 928 sheet: -0.59 (0.23), residues: 420 loop : -0.01 (0.22), residues: 796 *********************** 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 452 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 408 time to evaluate : 2.168 Fit side-chains outliers start: 44 outliers final: 24 residues processed: 427 average time/residue: 1.1822 time to fit residues: 570.4986 Evaluate side-chains 426 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 402 time to evaluate : 2.086 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 12 residues processed: 12 average time/residue: 0.5641 time to fit residues: 11.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 62 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN H 177 ASN H 329 ASN G 177 ASN G 198 GLN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4330 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= 0.322 Angle : 0.601 10.524 24096 Z= 0.298 Chirality : 0.048 0.141 2692 Planarity : 0.005 0.047 3068 Dihedral : 6.108 59.150 2456 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 2.38 % 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: 0.20 (0.18), residues: 2144 helix: 0.67 (0.17), residues: 924 sheet: -0.52 (0.24), residues: 380 loop : 0.07 (0.22), residues: 840 *********************** 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 461 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 416 time to evaluate : 2.036 Fit side-chains outliers start: 45 outliers final: 23 residues processed: 434 average time/residue: 1.1643 time to fit residues: 572.0438 Evaluate side-chains 434 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 411 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 12 residues processed: 11 average time/residue: 0.2051 time to fit residues: 6.6334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 152 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 ASN D 333 ASN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN H 177 ASN H 333 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: 0.8138 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 17780 Z= 0.215 Angle : 0.552 11.008 24096 Z= 0.272 Chirality : 0.045 0.167 2692 Planarity : 0.005 0.048 3068 Dihedral : 5.541 53.346 2456 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.59 % 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: 0.24 (0.18), residues: 2144 helix: 0.84 (0.17), residues: 920 sheet: -0.64 (0.23), residues: 420 loop : 0.02 (0.23), residues: 804 *********************** 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 443 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 413 time to evaluate : 1.841 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 431 average time/residue: 1.1406 time to fit residues: 556.8731 Evaluate side-chains 412 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 395 time to evaluate : 2.268 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.7173 time to fit residues: 6.2397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 0.0970 chunk 136 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN H 177 ASN H 333 ASN G 177 ASN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 17780 Z= 0.303 Angle : 0.605 10.579 24096 Z= 0.299 Chirality : 0.048 0.151 2692 Planarity : 0.005 0.047 3068 Dihedral : 5.974 56.717 2456 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 1.53 % 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: 0.21 (0.18), residues: 2144 helix: 0.73 (0.17), residues: 924 sheet: -0.53 (0.23), residues: 380 loop : -0.00 (0.22), residues: 840 ********************** 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 440 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 411 time to evaluate : 1.993 Fit side-chains outliers start: 29 outliers final: 23 residues processed: 426 average time/residue: 1.2002 time to fit residues: 578.4587 Evaluate side-chains 427 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 404 time to evaluate : 1.892 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 9 average time/residue: 0.6957 time to fit residues: 10.4044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 158 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.0270 chunk 171 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 176 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN C 296 GLN H 177 ASN G 177 ASN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.150078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.121975 restraints weight = 18426.153| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.57 r_work: 0.3164 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4475 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= 0.193 Angle : 0.544 10.709 24096 Z= 0.269 Chirality : 0.045 0.147 2692 Planarity : 0.005 0.048 3068 Dihedral : 5.390 51.120 2456 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.16 % 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: 0.31 (0.18), residues: 2144 helix: 0.91 (0.17), residues: 924 sheet: -0.62 (0.23), residues: 420 loop : 0.06 (0.23), residues: 800 =============================================================================== Job complete usr+sys time: 8172.66 seconds wall clock time: 144 minutes 40.53 seconds (8680.53 seconds total)