Starting phenix.real_space_refine on Fri Mar 22 23:07:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miv_23866/03_2024/7miv_23866_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miv_23866/03_2024/7miv_23866.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miv_23866/03_2024/7miv_23866_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miv_23866/03_2024/7miv_23866_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miv_23866/03_2024/7miv_23866_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miv_23866/03_2024/7miv_23866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miv_23866/03_2024/7miv_23866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miv_23866/03_2024/7miv_23866_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7miv_23866/03_2024/7miv_23866_trim_updated.pdb" } resolution = 2.8 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 100 5.16 5 C 11108 2.51 5 N 2960 2.21 5 O 3224 1.98 5 H 17412 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 528": "OE1" <-> "OE2" Residue "D PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 343": "OE1" <-> "OE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "H PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 322": "OE1" <-> "OE2" Residue "H TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 343": "OE1" <-> "OE2" Residue "H PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 423": "OE1" <-> "OE2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 460": "OE1" <-> "OE2" Residue "H GLU 476": "OE1" <-> "OE2" Residue "H PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 493": "OE1" <-> "OE2" Residue "H PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 528": "OE1" <-> "OE2" Residue "H PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 191": "OE1" <-> "OE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "G PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 322": "OE1" <-> "OE2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 343": "OE1" <-> "OE2" Residue "G PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 423": "OE1" <-> "OE2" Residue "G GLU 438": "OE1" <-> "OE2" Residue "G PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 460": "OE1" <-> "OE2" Residue "G GLU 476": "OE1" <-> "OE2" Residue "G PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 493": "OE1" <-> "OE2" Residue "G PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 528": "OE1" <-> "OE2" Residue "G PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34820 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8622 Classifications: {'peptide': 542} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "C" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8622 Classifications: {'peptide': 542} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "H" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8622 Classifications: {'peptide': 542} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "G" Number of atoms: 8622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 8622 Classifications: {'peptide': 542} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Time building chain proxies: 15.58, per 1000 atoms: 0.45 Number of scatterers: 34820 At special positions: 0 Unit cell: (124.95, 133.35, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 12 15.00 Mg 4 11.99 O 3224 8.00 N 2960 7.00 C 11108 6.00 H 17412 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.85 Conformation dependent library (CDL) restraints added in 3.5 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: 100 helices and 16 sheets defined 43.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.49 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 103 Processing helix chain 'D' and resid 113 through 129 removed outlier: 7.115A pdb=" N THR D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 168 removed outlier: 4.307A pdb=" N ALA D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 161 " --> pdb=" O ALA D 158 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN D 167 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 207 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 250 through 260 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 Processing helix chain 'D' and resid 311 through 328 removed outlier: 6.379A pdb=" N SER D 316 " --> pdb=" O CYS D 313 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 319 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS D 323 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 3.760A 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: 4.054A pdb=" N LEU D 404 " --> pdb=" O GLY D 401 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 407 " --> pdb=" O LEU D 404 " (cutoff:3.500A) removed outlier: 3.600A 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 551 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 103 Processing helix chain 'C' and resid 113 through 129 removed outlier: 7.116A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 168 removed outlier: 4.307A pdb=" N ALA C 158 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 161 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN C 167 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 207 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 250 through 260 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 Processing helix chain 'C' and resid 311 through 328 removed outlier: 6.378A pdb=" N SER C 316 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 319 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS C 323 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 3.760A 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 412 removed outlier: 4.055A pdb=" N LEU C 404 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 407 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 412 " --> pdb=" O PHE C 409 " (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 103 Processing helix chain 'H' and resid 113 through 129 removed outlier: 7.115A pdb=" N THR H 118 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 168 removed outlier: 4.307A pdb=" N ALA H 158 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU H 161 " --> pdb=" O ALA H 158 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN H 167 " --> pdb=" O ARG H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 207 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 238 through 240 No H-bonds generated for 'chain 'H' and resid 238 through 240' Processing helix chain 'H' and resid 250 through 260 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 Processing helix chain 'H' and resid 311 through 328 removed outlier: 6.378A pdb=" N SER H 316 " --> pdb=" O CYS H 313 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS H 319 " --> pdb=" O SER H 316 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS H 323 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 3.760A 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: 4.054A pdb=" N LEU H 404 " --> pdb=" O GLY H 401 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE H 407 " --> pdb=" O LEU H 404 " (cutoff:3.500A) removed outlier: 3.600A 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 551 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 103 Processing helix chain 'G' and resid 113 through 129 removed outlier: 7.115A pdb=" N THR G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 168 removed outlier: 4.307A pdb=" N ALA G 158 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU G 161 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN G 167 " --> pdb=" O ARG G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 207 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 238 through 240 No H-bonds generated for 'chain 'G' and resid 238 through 240' Processing helix chain 'G' and resid 250 through 260 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 Processing helix chain 'G' and resid 311 through 328 removed outlier: 6.378A pdb=" N SER G 316 " --> pdb=" O CYS G 313 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS G 319 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS G 323 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 3.760A 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 412 removed outlier: 4.055A pdb=" N LEU G 404 " --> pdb=" O GLY G 401 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE G 407 " --> pdb=" O LEU G 404 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN G 412 " --> pdb=" O PHE G 409 " (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: 6.306A pdb=" N ILE D 214 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE D 244 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N CYS D 216 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR D 3 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE D 178 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU D 5 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL D 180 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR D 7 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N LEU D 182 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY D 8 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 331 through 337 removed outlier: 6.735A pdb=" N GLY D 366 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL D 304 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU D 368 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL D 369 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU D 396 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 433 through 435 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: 6.306A pdb=" N ILE C 214 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE C 244 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS C 216 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 3 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY C 8 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 331 through 337 removed outlier: 6.735A pdb=" N GLY C 366 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL C 304 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU C 368 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL C 369 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU C 396 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 433 through 435 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: 6.306A pdb=" N ILE H 214 " --> pdb=" O ILE H 242 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE H 244 " --> pdb=" O ILE H 214 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS H 216 " --> pdb=" O ILE H 244 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR H 3 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE H 178 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU H 5 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL H 180 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR H 7 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU H 182 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY H 8 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 331 through 337 removed outlier: 6.735A pdb=" N GLY H 366 " --> pdb=" O ALA H 302 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL H 304 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU H 368 " --> pdb=" O VAL H 304 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL H 369 " --> pdb=" O PRO H 394 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU H 396 " --> pdb=" O VAL H 369 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 433 through 435 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: 6.306A pdb=" N ILE G 214 " --> pdb=" O ILE G 242 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE G 244 " --> pdb=" O ILE G 214 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS G 216 " --> pdb=" O ILE G 244 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR G 3 " --> pdb=" O TYR G 176 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE G 178 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU G 5 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL G 180 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR G 7 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU G 182 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY G 8 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 331 through 337 removed outlier: 6.735A pdb=" N GLY G 366 " --> pdb=" O ALA G 302 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL G 304 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU G 368 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL G 369 " --> pdb=" O PRO G 394 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU G 396 " --> pdb=" O VAL G 369 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 433 through 435 Processing sheet with id= P, first strand: chain 'G' and resid 473 through 480 680 hydrogen bonds defined for protein. 1584 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: 14.23 Time building geometry restraints manager: 31.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.14: 17368 1.14 - 1.32: 2876 1.32 - 1.50: 7120 1.50 - 1.67: 7664 1.67 - 1.85: 160 Bond restraints: 35188 Sorted by residual: bond pdb=" C2' UTP G 603 " pdb=" C3' UTP G 603 " ideal model delta sigma weight residual 1.301 1.524 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C2' UTP C 603 " pdb=" C3' UTP C 603 " ideal model delta sigma weight residual 1.301 1.524 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C2' UTP D 603 " pdb=" C3' UTP D 603 " ideal model delta sigma weight residual 1.301 1.524 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C2' UTP H 603 " pdb=" C3' UTP H 603 " ideal model delta sigma weight residual 1.301 1.524 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C1' UTP C 603 " pdb=" O4' UTP C 603 " ideal model delta sigma weight residual 1.553 1.394 0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 35183 not shown) Histogram of bond angle deviations from ideal: 58.80 - 77.64: 24 77.64 - 96.47: 12 96.47 - 115.30: 43014 115.30 - 134.13: 20722 134.13 - 152.97: 20 Bond angle restraints: 63792 Sorted by residual: angle pdb=" CA LEU D 281 " pdb=" N LEU D 281 " pdb=" H LEU D 281 " ideal model delta sigma weight residual 114.00 152.97 -38.97 3.00e+00 1.11e-01 1.69e+02 angle pdb=" CA LEU C 281 " pdb=" N LEU C 281 " pdb=" H LEU C 281 " ideal model delta sigma weight residual 114.00 152.97 -38.97 3.00e+00 1.11e-01 1.69e+02 angle pdb=" CA LEU H 281 " pdb=" N LEU H 281 " pdb=" H LEU H 281 " ideal model delta sigma weight residual 114.00 152.97 -38.97 3.00e+00 1.11e-01 1.69e+02 angle pdb=" CA LEU G 281 " pdb=" N LEU G 281 " pdb=" H LEU G 281 " ideal model delta sigma weight residual 114.00 152.94 -38.94 3.00e+00 1.11e-01 1.68e+02 angle pdb=" N PRO D 538 " pdb=" CA PRO D 538 " pdb=" C PRO D 538 " ideal model delta sigma weight residual 110.70 119.88 -9.18 1.22e+00 6.72e-01 5.66e+01 ... (remaining 63787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14592 17.94 - 35.89: 1094 35.89 - 53.83: 447 53.83 - 71.78: 320 71.78 - 89.72: 43 Dihedral angle restraints: 16496 sinusoidal: 9212 harmonic: 7284 Sorted by residual: dihedral pdb=" CA LYS D 169 " pdb=" C LYS D 169 " pdb=" N ALA D 170 " pdb=" CA ALA D 170 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA LYS H 169 " pdb=" C LYS H 169 " pdb=" N ALA H 170 " pdb=" CA ALA H 170 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS G 169 " pdb=" C LYS G 169 " pdb=" N ALA G 170 " pdb=" CA ALA G 170 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 16493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1543 0.098 - 0.196: 829 0.196 - 0.294: 244 0.294 - 0.392: 60 0.392 - 0.490: 16 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CB THR D 150 " pdb=" CA THR D 150 " pdb=" OG1 THR D 150 " pdb=" CG2 THR D 150 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CB THR H 150 " pdb=" CA THR H 150 " pdb=" OG1 THR H 150 " pdb=" CG2 THR H 150 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CB THR G 150 " pdb=" CA THR G 150 " pdb=" OG1 THR G 150 " pdb=" CG2 THR G 150 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.00e+00 ... (remaining 2689 not shown) Planarity restraints: 5112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 285 " 0.211 2.00e-02 2.50e+03 8.36e-02 2.80e+02 pdb=" CG TRP H 285 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 285 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP H 285 " -0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP H 285 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP H 285 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP H 285 " -0.050 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 285 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 285 " -0.043 2.00e-02 2.50e+03 pdb=" CH2 TRP H 285 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 TRP H 285 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 TRP H 285 " -0.118 2.00e-02 2.50e+03 pdb=" HE3 TRP H 285 " -0.082 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 285 " 0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 285 " -0.108 2.00e-02 2.50e+03 pdb=" HH2 TRP H 285 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 285 " 0.210 2.00e-02 2.50e+03 8.36e-02 2.80e+02 pdb=" CG TRP G 285 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP G 285 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP G 285 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP G 285 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP G 285 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP G 285 " -0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 285 " 0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 285 " -0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP G 285 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 TRP G 285 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP G 285 " -0.119 2.00e-02 2.50e+03 pdb=" HE3 TRP G 285 " -0.080 2.00e-02 2.50e+03 pdb=" HZ2 TRP G 285 " 0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP G 285 " -0.110 2.00e-02 2.50e+03 pdb=" HH2 TRP G 285 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 285 " -0.210 2.00e-02 2.50e+03 8.36e-02 2.80e+02 pdb=" CG TRP C 285 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP C 285 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 285 " 0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP C 285 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP C 285 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 285 " 0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 285 " -0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 285 " 0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP C 285 " -0.048 2.00e-02 2.50e+03 pdb=" HD1 TRP C 285 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP C 285 " 0.119 2.00e-02 2.50e+03 pdb=" HE3 TRP C 285 " 0.080 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 285 " -0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 285 " 0.110 2.00e-02 2.50e+03 pdb=" HH2 TRP C 285 " -0.122 2.00e-02 2.50e+03 ... (remaining 5109 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.86: 373 1.86 - 2.55: 29655 2.55 - 3.23: 113306 3.23 - 3.92: 153267 3.92 - 4.60: 233649 Nonbonded interactions: 530250 Sorted by model distance: nonbonded pdb=" OD2 ASP C 46 " pdb="HH12 ARG G 102 " model vdw 1.176 1.850 nonbonded pdb="HH12 ARG C 102 " pdb=" OD2 ASP G 46 " model vdw 1.185 1.850 nonbonded pdb="HH11 ARG D 102 " pdb=" OD2 ASP H 46 " model vdw 1.191 1.850 nonbonded pdb=" OD2 ASP D 46 " pdb="HH12 ARG H 102 " model vdw 1.200 1.850 nonbonded pdb="HH22 ARG C 102 " pdb=" OD1 ASP G 46 " model vdw 1.674 1.850 ... (remaining 530245 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: 0.010 Normalize map: mean=0, sd=1: 1.680 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: 0.540 Extract box with map and model: 7.440 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 113.180 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.130 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:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.014 0.223 17776 Z= 0.910 Angle : 2.060 15.064 24092 Z= 1.355 Chirality : 0.129 0.490 2692 Planarity : 0.013 0.106 3068 Dihedral : 14.658 89.721 6748 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.54 % Favored : 96.27 % Rotamer: Outliers : 1.69 % Allowed : 4.76 % Favored : 93.55 % 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: -1.26 (0.17), residues: 2144 helix: -0.75 (0.15), residues: 916 sheet: -0.32 (0.25), residues: 368 loop : -0.97 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.125 0.028 TRP D 285 HIS 0.023 0.005 HIS H 480 PHE 0.080 0.018 PHE H 50 TYR 0.135 0.021 TYR D 176 ARG 0.007 0.001 ARG D 449 *********************** 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 618 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 586 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 SER cc_start: 0.8470 (t) cc_final: 0.8146 (p) REVERT: D 119 ASP cc_start: 0.7844 (m-30) cc_final: 0.7632 (m-30) REVERT: D 132 SER cc_start: 0.7850 (p) cc_final: 0.7613 (t) REVERT: D 286 LYS cc_start: 0.7673 (ttpt) cc_final: 0.7007 (ttpp) REVERT: D 300 SER cc_start: 0.8448 (m) cc_final: 0.8241 (t) REVERT: D 363 LEU cc_start: 0.8393 (mp) cc_final: 0.8069 (mt) REVERT: D 475 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7741 (mt-10) REVERT: D 502 GLU cc_start: 0.6948 (pt0) cc_final: 0.6686 (pt0) REVERT: C 51 SER cc_start: 0.8472 (t) cc_final: 0.8143 (p) REVERT: C 132 SER cc_start: 0.7863 (p) cc_final: 0.7641 (t) REVERT: C 251 TYR cc_start: 0.8420 (m-80) cc_final: 0.8177 (m-80) REVERT: C 286 LYS cc_start: 0.7687 (ttpt) cc_final: 0.7048 (ttpp) REVERT: C 300 SER cc_start: 0.8435 (m) cc_final: 0.8218 (t) REVERT: C 363 LEU cc_start: 0.8384 (mp) cc_final: 0.8078 (mt) REVERT: C 475 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7738 (mt-10) REVERT: C 502 GLU cc_start: 0.6990 (pt0) cc_final: 0.6728 (pt0) REVERT: H 51 SER cc_start: 0.8394 (t) cc_final: 0.8127 (p) REVERT: H 66 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8202 (mt-10) REVERT: H 119 ASP cc_start: 0.7873 (m-30) cc_final: 0.7668 (m-30) REVERT: H 132 SER cc_start: 0.7852 (p) cc_final: 0.7607 (t) REVERT: H 251 TYR cc_start: 0.8415 (m-80) cc_final: 0.8158 (m-80) REVERT: H 286 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7059 (ttpp) REVERT: H 363 LEU cc_start: 0.8300 (mp) cc_final: 0.8042 (mt) REVERT: H 475 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7760 (mt-10) REVERT: H 502 GLU cc_start: 0.7011 (pt0) cc_final: 0.6716 (pt0) REVERT: G 51 SER cc_start: 0.8441 (t) cc_final: 0.8146 (p) REVERT: G 132 SER cc_start: 0.7862 (p) cc_final: 0.7610 (t) REVERT: G 286 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7450 (ttpp) REVERT: G 363 LEU cc_start: 0.8302 (mp) cc_final: 0.8039 (mt) REVERT: G 466 LYS cc_start: 0.8291 (mttm) cc_final: 0.7946 (mtmp) REVERT: G 475 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7742 (mt-10) outliers start: 32 outliers final: 8 residues processed: 598 average time/residue: 1.9970 time to fit residues: 1389.6881 Evaluate side-chains 492 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 484 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain H residue 134 ASP Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain G residue 308 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 GLN D 174 ASN D 177 ASN D 185 GLN C 122 GLN C 174 ASN C 177 ASN C 185 GLN H 122 GLN H 174 ASN H 177 ASN H 185 GLN G 122 GLN G 174 ASN G 177 ASN G 185 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17776 Z= 0.224 Angle : 0.591 5.292 24092 Z= 0.302 Chirality : 0.047 0.164 2692 Planarity : 0.005 0.054 3068 Dihedral : 7.267 61.229 2512 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.38 % Allowed : 12.79 % Favored : 84.83 % 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: -0.67 (0.17), residues: 2144 helix: -0.06 (0.16), residues: 928 sheet: -0.25 (0.25), residues: 376 loop : -0.80 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 387 HIS 0.004 0.001 HIS G 96 PHE 0.022 0.002 PHE G 318 TYR 0.016 0.002 TYR C 42 ARG 0.007 0.001 ARG D 269 *********************** 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 537 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 492 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 ASP cc_start: 0.8027 (p0) cc_final: 0.7760 (p0) REVERT: D 51 SER cc_start: 0.8423 (t) cc_final: 0.8200 (p) REVERT: D 157 MET cc_start: 0.7090 (mmp) cc_final: 0.6636 (mmp) REVERT: D 167 GLN cc_start: 0.7472 (tt0) cc_final: 0.7230 (tt0) REVERT: D 286 LYS cc_start: 0.7688 (ttpt) cc_final: 0.7328 (ttpp) REVERT: D 298 ILE cc_start: 0.8764 (mt) cc_final: 0.8527 (mm) REVERT: D 322 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7479 (mm-30) REVERT: D 363 LEU cc_start: 0.8495 (mp) cc_final: 0.8264 (mt) REVERT: D 498 CYS cc_start: 0.7256 (t) cc_final: 0.6753 (t) REVERT: D 502 GLU cc_start: 0.7175 (pt0) cc_final: 0.6785 (pt0) REVERT: C 51 SER cc_start: 0.8425 (t) cc_final: 0.8205 (p) REVERT: C 157 MET cc_start: 0.7072 (mmp) cc_final: 0.6606 (mmp) REVERT: C 167 GLN cc_start: 0.7485 (tt0) cc_final: 0.7241 (tt0) REVERT: C 286 LYS cc_start: 0.7695 (ttpt) cc_final: 0.7315 (ttpp) REVERT: C 290 ASP cc_start: 0.7369 (m-30) cc_final: 0.7167 (m-30) REVERT: C 298 ILE cc_start: 0.8762 (mt) cc_final: 0.8534 (mm) REVERT: C 322 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7533 (mt-10) REVERT: C 363 LEU cc_start: 0.8487 (mp) cc_final: 0.8269 (mt) REVERT: C 502 GLU cc_start: 0.7195 (pt0) cc_final: 0.6854 (pt0) REVERT: H 46 ASP cc_start: 0.8024 (p0) cc_final: 0.7774 (p0) REVERT: H 51 SER cc_start: 0.8416 (t) cc_final: 0.8190 (p) REVERT: H 66 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8013 (mt-10) REVERT: H 157 MET cc_start: 0.7097 (mmp) cc_final: 0.6620 (mmp) REVERT: H 167 GLN cc_start: 0.7460 (tt0) cc_final: 0.7207 (tt0) REVERT: H 286 LYS cc_start: 0.7646 (ttpt) cc_final: 0.7294 (ttpp) REVERT: H 298 ILE cc_start: 0.8764 (mt) cc_final: 0.8529 (mm) REVERT: H 322 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7487 (mm-30) REVERT: H 363 LEU cc_start: 0.8487 (mp) cc_final: 0.8257 (mt) REVERT: G 46 ASP cc_start: 0.8032 (p0) cc_final: 0.7763 (p0) REVERT: G 157 MET cc_start: 0.7099 (mmp) cc_final: 0.6638 (mmp) REVERT: G 167 GLN cc_start: 0.7431 (tt0) cc_final: 0.7195 (tt0) REVERT: G 286 LYS cc_start: 0.7722 (ttpt) cc_final: 0.7282 (ttpp) REVERT: G 290 ASP cc_start: 0.7373 (m-30) cc_final: 0.7073 (m-30) REVERT: G 298 ILE cc_start: 0.8754 (mt) cc_final: 0.8517 (mm) REVERT: G 322 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7476 (mt-10) REVERT: G 363 LEU cc_start: 0.8501 (mp) cc_final: 0.8278 (mt) REVERT: G 534 MET cc_start: 0.8089 (mmm) cc_final: 0.7858 (mpp) outliers start: 45 outliers final: 10 residues processed: 511 average time/residue: 2.1260 time to fit residues: 1255.0292 Evaluate side-chains 447 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 437 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 311 ARG Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 311 ARG Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 537 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: 0.9990 chunk 163 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17776 Z= 0.316 Angle : 0.570 5.235 24092 Z= 0.290 Chirality : 0.047 0.188 2692 Planarity : 0.004 0.041 3068 Dihedral : 7.500 59.886 2501 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.70 % Allowed : 15.64 % Favored : 81.66 % 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: -0.45 (0.17), residues: 2144 helix: 0.12 (0.17), residues: 928 sheet: -0.15 (0.24), residues: 372 loop : -0.67 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 387 HIS 0.006 0.002 HIS H 116 PHE 0.014 0.002 PHE H 163 TYR 0.014 0.002 TYR D 42 ARG 0.003 0.000 ARG H 269 *********************** 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 514 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 463 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 161 GLU cc_start: 0.7606 (tp30) cc_final: 0.7344 (tp30) REVERT: D 167 GLN cc_start: 0.7787 (tt0) cc_final: 0.7473 (tt0) REVERT: D 286 LYS cc_start: 0.7839 (ttpt) cc_final: 0.7559 (ttpp) REVERT: D 322 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7710 (mm-30) REVERT: D 353 LYS cc_start: 0.7203 (mtmt) cc_final: 0.6953 (mttm) REVERT: D 392 LYS cc_start: 0.7952 (mmmm) cc_final: 0.7731 (mmmm) REVERT: D 473 TYR cc_start: 0.8269 (p90) cc_final: 0.8049 (p90) REVERT: D 498 CYS cc_start: 0.7643 (t) cc_final: 0.7297 (t) REVERT: C 161 GLU cc_start: 0.7603 (tp30) cc_final: 0.7374 (tp30) REVERT: C 167 GLN cc_start: 0.7788 (tt0) cc_final: 0.7461 (tt0) REVERT: C 286 LYS cc_start: 0.7880 (ttpt) cc_final: 0.7557 (ttpp) REVERT: C 322 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7715 (mm-30) REVERT: C 353 LYS cc_start: 0.7274 (mtmt) cc_final: 0.7037 (mttp) REVERT: H 161 GLU cc_start: 0.7601 (tp30) cc_final: 0.7346 (tp30) REVERT: H 167 GLN cc_start: 0.7772 (tt0) cc_final: 0.7437 (tt0) REVERT: H 286 LYS cc_start: 0.7813 (ttpt) cc_final: 0.7515 (ttpp) REVERT: H 322 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7716 (mm-30) REVERT: H 392 LYS cc_start: 0.7971 (mmmm) cc_final: 0.7770 (mmmm) REVERT: G 161 GLU cc_start: 0.7563 (tp30) cc_final: 0.7336 (tp30) REVERT: G 167 GLN cc_start: 0.7758 (tt0) cc_final: 0.7423 (tt0) REVERT: G 286 LYS cc_start: 0.7932 (ttpt) cc_final: 0.7576 (ttpp) REVERT: G 322 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7702 (mm-30) REVERT: G 392 LYS cc_start: 0.7920 (mmmm) cc_final: 0.7716 (mmmm) REVERT: G 454 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7730 (ttm-80) REVERT: G 534 MET cc_start: 0.8156 (mmm) cc_final: 0.7935 (mpp) outliers start: 51 outliers final: 21 residues processed: 482 average time/residue: 2.2049 time to fit residues: 1223.7337 Evaluate side-chains 448 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 427 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 311 ARG Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 311 ARG Chi-restraints excluded: chain H residue 500 VAL Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 412 ASN ** H 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 412 ASN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 412 ASN G 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17776 Z= 0.396 Angle : 0.572 5.326 24092 Z= 0.291 Chirality : 0.047 0.147 2692 Planarity : 0.006 0.095 3068 Dihedral : 7.435 60.811 2500 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.06 % Allowed : 17.44 % Favored : 80.50 % 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: -0.50 (0.17), residues: 2144 helix: 0.05 (0.16), residues: 936 sheet: -0.25 (0.24), residues: 372 loop : -0.61 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 387 HIS 0.007 0.002 HIS D 116 PHE 0.013 0.002 PHE C 163 TYR 0.013 0.002 TYR H 42 ARG 0.013 0.001 ARG G 389 *********************** 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 471 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 432 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 157 MET cc_start: 0.7693 (mmp) cc_final: 0.7056 (mmp) REVERT: D 161 GLU cc_start: 0.7615 (tp30) cc_final: 0.7385 (tp30) REVERT: D 167 GLN cc_start: 0.7972 (tt0) cc_final: 0.7669 (tt0) REVERT: D 284 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7530 (mmmm) REVERT: D 286 LYS cc_start: 0.7865 (ttpt) cc_final: 0.7519 (ttpp) REVERT: D 322 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7683 (mm-30) REVERT: D 353 LYS cc_start: 0.7286 (mtmt) cc_final: 0.7018 (mttm) REVERT: D 392 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7749 (mmmm) REVERT: D 473 TYR cc_start: 0.8208 (p90) cc_final: 0.7973 (p90) REVERT: D 498 CYS cc_start: 0.7660 (t) cc_final: 0.7280 (t) REVERT: D 502 GLU cc_start: 0.7236 (pt0) cc_final: 0.6798 (pp20) REVERT: C 157 MET cc_start: 0.7683 (mmp) cc_final: 0.7035 (mmp) REVERT: C 161 GLU cc_start: 0.7595 (tp30) cc_final: 0.7383 (tp30) REVERT: C 167 GLN cc_start: 0.7984 (tt0) cc_final: 0.7680 (tt0) REVERT: C 286 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7538 (ttpp) REVERT: C 322 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7714 (mm-30) REVERT: C 353 LYS cc_start: 0.7294 (mtmt) cc_final: 0.7037 (mttp) REVERT: C 498 CYS cc_start: 0.7650 (t) cc_final: 0.7325 (t) REVERT: H 157 MET cc_start: 0.7712 (mmp) cc_final: 0.7060 (mmp) REVERT: H 161 GLU cc_start: 0.7611 (tp30) cc_final: 0.7375 (tp30) REVERT: H 167 GLN cc_start: 0.7976 (tt0) cc_final: 0.7654 (tt0) REVERT: H 284 LYS cc_start: 0.7937 (mmtm) cc_final: 0.7553 (mmmm) REVERT: H 286 LYS cc_start: 0.7850 (ttpt) cc_final: 0.7504 (ttpp) REVERT: H 322 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7689 (mm-30) REVERT: H 353 LYS cc_start: 0.7296 (mtmt) cc_final: 0.7040 (mttm) REVERT: H 392 LYS cc_start: 0.7967 (mmmm) cc_final: 0.7700 (mmmm) REVERT: H 473 TYR cc_start: 0.8248 (p90) cc_final: 0.8044 (p90) REVERT: H 498 CYS cc_start: 0.7676 (t) cc_final: 0.7354 (t) REVERT: G 1 MET cc_start: 0.8029 (ttt) cc_final: 0.7828 (ttt) REVERT: G 157 MET cc_start: 0.7703 (mmp) cc_final: 0.7060 (mmp) REVERT: G 161 GLU cc_start: 0.7517 (tp30) cc_final: 0.7275 (tp30) REVERT: G 167 GLN cc_start: 0.7977 (tt0) cc_final: 0.7663 (tt0) REVERT: G 286 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7734 (tttm) REVERT: G 322 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7683 (mm-30) REVERT: G 353 LYS cc_start: 0.7319 (mtmt) cc_final: 0.7055 (mttp) REVERT: G 392 LYS cc_start: 0.7966 (mmmm) cc_final: 0.7688 (mmmm) REVERT: G 534 MET cc_start: 0.8207 (mmm) cc_final: 0.7965 (mpp) outliers start: 39 outliers final: 18 residues processed: 451 average time/residue: 2.1255 time to fit residues: 1113.8389 Evaluate side-chains 441 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 423 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 500 VAL Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 500 VAL Chi-restraints excluded: chain G residue 537 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: 0.7980 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17776 Z= 0.214 Angle : 0.508 5.517 24092 Z= 0.253 Chirality : 0.044 0.132 2692 Planarity : 0.005 0.078 3068 Dihedral : 6.908 57.662 2500 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.96 % Allowed : 18.39 % 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: -0.06 (0.18), residues: 2144 helix: 0.48 (0.17), residues: 928 sheet: -0.23 (0.24), residues: 372 loop : -0.36 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 387 HIS 0.005 0.001 HIS C 116 PHE 0.010 0.001 PHE H 409 TYR 0.015 0.001 TYR H 42 ARG 0.010 0.000 ARG H 389 *********************** 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 470 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 433 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 161 GLU cc_start: 0.7529 (tp30) cc_final: 0.7293 (tp30) REVERT: D 167 GLN cc_start: 0.7774 (tt0) cc_final: 0.7165 (pt0) REVERT: D 284 LYS cc_start: 0.7914 (mmtm) cc_final: 0.7526 (mmmm) REVERT: D 286 LYS cc_start: 0.7820 (ttpt) cc_final: 0.7519 (ttpp) REVERT: D 322 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7679 (mm-30) REVERT: D 353 LYS cc_start: 0.7305 (mtmt) cc_final: 0.7024 (mttm) REVERT: D 473 TYR cc_start: 0.8253 (p90) cc_final: 0.8025 (p90) REVERT: D 498 CYS cc_start: 0.7612 (t) cc_final: 0.7264 (t) REVERT: D 502 GLU cc_start: 0.7208 (pt0) cc_final: 0.6761 (pp20) REVERT: C 161 GLU cc_start: 0.7508 (tp30) cc_final: 0.7274 (tp30) REVERT: C 167 GLN cc_start: 0.7769 (tt0) cc_final: 0.7180 (pt0) REVERT: C 286 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7546 (ttpp) REVERT: C 322 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7684 (mm-30) REVERT: C 353 LYS cc_start: 0.7319 (mtmt) cc_final: 0.7046 (mttm) REVERT: C 420 ASN cc_start: 0.8887 (t0) cc_final: 0.8664 (t0) REVERT: C 498 CYS cc_start: 0.7599 (t) cc_final: 0.7323 (t) REVERT: H 136 ASN cc_start: 0.6856 (t0) cc_final: 0.6560 (m110) REVERT: H 161 GLU cc_start: 0.7522 (tp30) cc_final: 0.7289 (tp30) REVERT: H 167 GLN cc_start: 0.7769 (tt0) cc_final: 0.7137 (pt0) REVERT: H 284 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7504 (mmmm) REVERT: H 286 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7511 (ttpp) REVERT: H 322 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7664 (mm-30) REVERT: H 353 LYS cc_start: 0.7332 (mtmt) cc_final: 0.7071 (mttm) REVERT: H 392 LYS cc_start: 0.7980 (mmmm) cc_final: 0.7708 (mmmm) REVERT: H 473 TYR cc_start: 0.8235 (p90) cc_final: 0.8032 (p90) REVERT: H 498 CYS cc_start: 0.7635 (t) cc_final: 0.7339 (t) REVERT: G 136 ASN cc_start: 0.6836 (t0) cc_final: 0.6510 (m110) REVERT: G 167 GLN cc_start: 0.7769 (tt0) cc_final: 0.7474 (tt0) REVERT: G 286 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7739 (tttm) REVERT: G 322 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7657 (mm-30) REVERT: G 353 LYS cc_start: 0.7360 (mtmt) cc_final: 0.7089 (mttm) REVERT: G 392 LYS cc_start: 0.7969 (mmmm) cc_final: 0.7701 (mmmm) REVERT: G 413 CYS cc_start: 0.6860 (m) cc_final: 0.6452 (m) REVERT: G 498 CYS cc_start: 0.7586 (t) cc_final: 0.7257 (t) REVERT: G 534 MET cc_start: 0.8196 (mmm) cc_final: 0.7958 (mpp) outliers start: 37 outliers final: 15 residues processed: 456 average time/residue: 2.1619 time to fit residues: 1142.8821 Evaluate side-chains 439 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 424 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17776 Z= 0.318 Angle : 0.542 5.940 24092 Z= 0.272 Chirality : 0.046 0.158 2692 Planarity : 0.005 0.092 3068 Dihedral : 7.145 59.216 2500 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.01 % Allowed : 19.13 % Favored : 78.86 % 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: -0.08 (0.18), residues: 2144 helix: 0.48 (0.17), residues: 928 sheet: -0.27 (0.24), residues: 372 loop : -0.38 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 387 HIS 0.006 0.001 HIS G 116 PHE 0.011 0.002 PHE C 409 TYR 0.014 0.001 TYR H 292 ARG 0.012 0.000 ARG G 389 *********************** 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 469 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 431 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 161 GLU cc_start: 0.7506 (tp30) cc_final: 0.7283 (tp30) REVERT: D 167 GLN cc_start: 0.7931 (tt0) cc_final: 0.7591 (tt0) REVERT: D 173 GLU cc_start: 0.7286 (pm20) cc_final: 0.6727 (pm20) REVERT: D 286 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7613 (ttpp) REVERT: D 296 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7666 (mm110) REVERT: D 322 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7679 (mm-30) REVERT: D 353 LYS cc_start: 0.7348 (mtmt) cc_final: 0.7049 (mttm) REVERT: D 498 CYS cc_start: 0.7611 (t) cc_final: 0.7234 (t) REVERT: D 502 GLU cc_start: 0.7243 (pt0) cc_final: 0.6776 (pp20) REVERT: C 161 GLU cc_start: 0.7492 (tp30) cc_final: 0.7264 (tp30) REVERT: C 167 GLN cc_start: 0.7909 (tt0) cc_final: 0.7624 (tt0) REVERT: C 286 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7655 (tttm) REVERT: C 322 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7706 (mm-30) REVERT: C 353 LYS cc_start: 0.7361 (mtmt) cc_final: 0.7080 (mttm) REVERT: C 498 CYS cc_start: 0.7595 (t) cc_final: 0.7354 (t) REVERT: H 161 GLU cc_start: 0.7502 (tp30) cc_final: 0.7237 (tp30) REVERT: H 167 GLN cc_start: 0.7914 (tt0) cc_final: 0.7603 (tt0) REVERT: H 284 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7529 (mmmm) REVERT: H 286 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7557 (ttpp) REVERT: H 322 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7670 (mm-30) REVERT: H 353 LYS cc_start: 0.7377 (mtmt) cc_final: 0.7092 (mttm) REVERT: H 392 LYS cc_start: 0.8059 (mmmm) cc_final: 0.7788 (mmmm) REVERT: H 473 TYR cc_start: 0.8257 (p90) cc_final: 0.8053 (p90) REVERT: H 498 CYS cc_start: 0.7655 (t) cc_final: 0.7405 (t) REVERT: G 136 ASN cc_start: 0.6846 (t0) cc_final: 0.6626 (m-40) REVERT: G 167 GLN cc_start: 0.7919 (tt0) cc_final: 0.7601 (tt0) REVERT: G 286 LYS cc_start: 0.7922 (ttpt) cc_final: 0.7688 (tttm) REVERT: G 322 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7668 (mm-30) REVERT: G 353 LYS cc_start: 0.7380 (mtmt) cc_final: 0.7098 (mttm) REVERT: G 392 LYS cc_start: 0.8025 (mmmm) cc_final: 0.7759 (mmmm) REVERT: G 473 TYR cc_start: 0.8291 (p90) cc_final: 0.8050 (p90) REVERT: G 498 CYS cc_start: 0.7606 (t) cc_final: 0.7352 (t) REVERT: G 534 MET cc_start: 0.8215 (mmm) cc_final: 0.7990 (mpp) outliers start: 38 outliers final: 17 residues processed: 451 average time/residue: 2.1861 time to fit residues: 1143.0211 Evaluate side-chains 440 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 423 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 119 optimal weight: 0.0870 chunk 152 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN H 296 GLN G 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17776 Z= 0.217 Angle : 0.508 6.129 24092 Z= 0.251 Chirality : 0.044 0.130 2692 Planarity : 0.004 0.068 3068 Dihedral : 6.751 58.164 2500 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.27 % Allowed : 20.61 % Favored : 78.12 % 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: 0.21 (0.18), residues: 2144 helix: 0.75 (0.17), residues: 928 sheet: -0.17 (0.25), residues: 368 loop : -0.24 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 387 HIS 0.005 0.001 HIS G 116 PHE 0.015 0.001 PHE H 409 TYR 0.014 0.001 TYR H 42 ARG 0.008 0.000 ARG D 389 *********************** 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 451 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 427 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 161 GLU cc_start: 0.7481 (tp30) cc_final: 0.7220 (tp30) REVERT: D 167 GLN cc_start: 0.7844 (tt0) cc_final: 0.7270 (pt0) REVERT: D 286 LYS cc_start: 0.7842 (ttpt) cc_final: 0.7576 (ttpp) REVERT: D 322 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7666 (mm-30) REVERT: D 353 LYS cc_start: 0.7334 (mtmt) cc_final: 0.7062 (mttp) REVERT: D 498 CYS cc_start: 0.7558 (t) cc_final: 0.7182 (t) REVERT: D 534 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7382 (mpt) REVERT: C 161 GLU cc_start: 0.7451 (tp30) cc_final: 0.7218 (tp30) REVERT: C 167 GLN cc_start: 0.7863 (tt0) cc_final: 0.7284 (pt0) REVERT: C 173 GLU cc_start: 0.7465 (pm20) cc_final: 0.6917 (pm20) REVERT: C 286 LYS cc_start: 0.7880 (ttpt) cc_final: 0.7673 (tttm) REVERT: C 322 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7684 (mm-30) REVERT: C 353 LYS cc_start: 0.7348 (mtmt) cc_final: 0.7075 (mttp) REVERT: C 498 CYS cc_start: 0.7517 (t) cc_final: 0.7236 (t) REVERT: H 157 MET cc_start: 0.7689 (mmp) cc_final: 0.7137 (mmp) REVERT: H 167 GLN cc_start: 0.7808 (tt0) cc_final: 0.7197 (pt0) REVERT: H 286 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7610 (tttm) REVERT: H 322 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7649 (mm-30) REVERT: H 353 LYS cc_start: 0.7351 (mtmt) cc_final: 0.7084 (mttp) REVERT: H 498 CYS cc_start: 0.7611 (t) cc_final: 0.7352 (t) REVERT: G 136 ASN cc_start: 0.6847 (t0) cc_final: 0.6605 (m-40) REVERT: G 157 MET cc_start: 0.7692 (mmp) cc_final: 0.7167 (mmp) REVERT: G 167 GLN cc_start: 0.7812 (tt0) cc_final: 0.7193 (pt0) REVERT: G 286 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7670 (tttm) REVERT: G 322 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7642 (mm-30) REVERT: G 534 MET cc_start: 0.8200 (mmm) cc_final: 0.7982 (mpp) outliers start: 24 outliers final: 18 residues processed: 439 average time/residue: 2.1999 time to fit residues: 1113.6785 Evaluate side-chains 436 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 417 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 534 MET Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 163 optimal weight: 0.2980 chunk 189 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 ASN D 296 GLN C 296 GLN ** H 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17776 Z= 0.281 Angle : 0.528 6.757 24092 Z= 0.262 Chirality : 0.045 0.134 2692 Planarity : 0.004 0.064 3068 Dihedral : 6.882 58.254 2500 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.80 % Allowed : 20.61 % Favored : 77.59 % 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: 0.23 (0.18), residues: 2144 helix: 0.78 (0.17), residues: 928 sheet: -0.14 (0.25), residues: 368 loop : -0.24 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 387 HIS 0.006 0.001 HIS H 116 PHE 0.018 0.002 PHE D 409 TYR 0.014 0.001 TYR C 292 ARG 0.007 0.000 ARG G 389 *********************** 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: 34 poor density : 427 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 157 MET cc_start: 0.7662 (mmp) cc_final: 0.7134 (mmp) REVERT: D 161 GLU cc_start: 0.7508 (tp30) cc_final: 0.7265 (tp30) REVERT: D 167 GLN cc_start: 0.7886 (tt0) cc_final: 0.7610 (tt0) REVERT: D 286 LYS cc_start: 0.7888 (ttpt) cc_final: 0.7634 (ttpp) REVERT: D 322 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7660 (mm-30) REVERT: D 353 LYS cc_start: 0.7323 (mtmt) cc_final: 0.7043 (mttm) REVERT: D 498 CYS cc_start: 0.7608 (t) cc_final: 0.7229 (t) REVERT: D 534 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7308 (mpt) REVERT: C 157 MET cc_start: 0.7614 (mmp) cc_final: 0.7068 (mmp) REVERT: C 161 GLU cc_start: 0.7481 (tp30) cc_final: 0.7250 (tp30) REVERT: C 167 GLN cc_start: 0.7893 (tt0) cc_final: 0.7639 (tt0) REVERT: C 286 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7664 (tttm) REVERT: C 322 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7691 (mm-30) REVERT: C 353 LYS cc_start: 0.7329 (mtmt) cc_final: 0.7046 (mttp) REVERT: C 392 LYS cc_start: 0.8190 (mmmm) cc_final: 0.7928 (mmmm) REVERT: H 1 MET cc_start: 0.8053 (ttt) cc_final: 0.7598 (ttt) REVERT: H 161 GLU cc_start: 0.7479 (tp30) cc_final: 0.7235 (tp30) REVERT: H 167 GLN cc_start: 0.7870 (tt0) cc_final: 0.7577 (tt0) REVERT: H 286 LYS cc_start: 0.7843 (ttpt) cc_final: 0.7529 (tttm) REVERT: H 322 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7646 (mm-30) REVERT: H 353 LYS cc_start: 0.7317 (mtmt) cc_final: 0.7044 (mttm) REVERT: H 498 CYS cc_start: 0.7628 (t) cc_final: 0.7410 (t) REVERT: H 534 MET cc_start: 0.7629 (mpp) cc_final: 0.7310 (mpp) REVERT: G 1 MET cc_start: 0.8083 (ttt) cc_final: 0.7734 (ttt) REVERT: G 136 ASN cc_start: 0.7020 (t0) cc_final: 0.6762 (m-40) REVERT: G 167 GLN cc_start: 0.7873 (tt0) cc_final: 0.7579 (tt0) REVERT: G 173 GLU cc_start: 0.7485 (pm20) cc_final: 0.6962 (pm20) REVERT: G 286 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7790 (tttm) REVERT: G 322 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7653 (mm-30) REVERT: G 534 MET cc_start: 0.8213 (mmm) cc_final: 0.7971 (mpp) outliers start: 34 outliers final: 17 residues processed: 448 average time/residue: 2.2006 time to fit residues: 1135.8743 Evaluate side-chains 439 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 421 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 534 MET Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 425 GLU Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 GLN C 296 GLN H 296 GLN ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17776 Z= 0.223 Angle : 0.509 7.055 24092 Z= 0.250 Chirality : 0.044 0.151 2692 Planarity : 0.004 0.059 3068 Dihedral : 6.688 58.160 2500 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.43 % Allowed : 21.35 % Favored : 77.22 % 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: 0.90 (0.17), residues: 928 sheet: -0.10 (0.25), residues: 368 loop : -0.16 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 358 HIS 0.005 0.001 HIS H 116 PHE 0.015 0.001 PHE D 409 TYR 0.013 0.001 TYR H 42 ARG 0.007 0.000 ARG D 389 *********************** 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 457 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 430 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8054 (ttt) cc_final: 0.7597 (ttt) REVERT: D 161 GLU cc_start: 0.7483 (tp30) cc_final: 0.7226 (tp30) REVERT: D 167 GLN cc_start: 0.7842 (tt0) cc_final: 0.7244 (pt0) REVERT: D 173 GLU cc_start: 0.7319 (pm20) cc_final: 0.6891 (pm20) REVERT: D 286 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7633 (ttpp) REVERT: D 322 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 498 CYS cc_start: 0.7534 (t) cc_final: 0.7228 (t) REVERT: D 534 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7507 (mpt) REVERT: C 161 GLU cc_start: 0.7463 (tp30) cc_final: 0.7209 (tp30) REVERT: C 167 GLN cc_start: 0.7865 (tt0) cc_final: 0.7291 (pt0) REVERT: C 286 LYS cc_start: 0.7876 (ttpt) cc_final: 0.7670 (tttm) REVERT: C 322 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7668 (mm-30) REVERT: C 353 LYS cc_start: 0.7301 (mtmt) cc_final: 0.7012 (mttp) REVERT: C 392 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7933 (mmmm) REVERT: H 1 MET cc_start: 0.8038 (ttt) cc_final: 0.7579 (ttt) REVERT: H 157 MET cc_start: 0.7687 (mmp) cc_final: 0.7102 (mmp) REVERT: H 161 GLU cc_start: 0.7454 (tp30) cc_final: 0.7213 (tp30) REVERT: H 167 GLN cc_start: 0.7841 (tt0) cc_final: 0.7252 (pt0) REVERT: H 286 LYS cc_start: 0.7831 (ttpt) cc_final: 0.7524 (tttm) REVERT: H 322 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7647 (mm-30) REVERT: H 353 LYS cc_start: 0.7304 (mtmt) cc_final: 0.7024 (mttm) REVERT: H 534 MET cc_start: 0.7592 (mpp) cc_final: 0.7292 (mpp) REVERT: G 1 MET cc_start: 0.8075 (ttt) cc_final: 0.7716 (ttt) REVERT: G 136 ASN cc_start: 0.7019 (t0) cc_final: 0.6768 (m-40) REVERT: G 157 MET cc_start: 0.7711 (mmp) cc_final: 0.7137 (mmp) REVERT: G 167 GLN cc_start: 0.7843 (tt0) cc_final: 0.7266 (pt0) REVERT: G 286 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7780 (tttm) REVERT: G 322 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7655 (mm-30) REVERT: G 534 MET cc_start: 0.8198 (mmm) cc_final: 0.7934 (mpp) outliers start: 27 outliers final: 13 residues processed: 446 average time/residue: 2.2562 time to fit residues: 1158.9121 Evaluate side-chains 441 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 427 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 534 MET Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 243 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17776 Z= 0.261 Angle : 0.527 8.357 24092 Z= 0.259 Chirality : 0.044 0.132 2692 Planarity : 0.004 0.066 3068 Dihedral : 6.764 57.742 2500 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.32 % Allowed : 21.72 % Favored : 76.96 % 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: 0.32 (0.18), residues: 2144 helix: 0.87 (0.17), residues: 928 sheet: -0.11 (0.25), residues: 368 loop : -0.21 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 124 HIS 0.005 0.001 HIS H 116 PHE 0.018 0.001 PHE D 409 TYR 0.013 0.001 TYR H 42 ARG 0.009 0.000 ARG H 389 ********************** 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 449 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 424 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8081 (ttt) cc_final: 0.7624 (ttt) REVERT: D 157 MET cc_start: 0.7669 (mmp) cc_final: 0.7088 (mmp) REVERT: D 161 GLU cc_start: 0.7495 (tp30) cc_final: 0.7254 (tp30) REVERT: D 167 GLN cc_start: 0.7885 (tt0) cc_final: 0.7621 (tt0) REVERT: D 173 GLU cc_start: 0.7333 (pm20) cc_final: 0.6758 (pm20) REVERT: D 322 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7650 (mm-30) REVERT: D 363 LEU cc_start: 0.8674 (mp) cc_final: 0.8212 (tt) REVERT: D 402 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7733 (ttt) REVERT: D 534 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7317 (mpt) REVERT: C 1 MET cc_start: 0.8055 (ttt) cc_final: 0.7589 (ttt) REVERT: C 157 MET cc_start: 0.7638 (mmp) cc_final: 0.7066 (mmp) REVERT: C 161 GLU cc_start: 0.7471 (tp30) cc_final: 0.7255 (tp30) REVERT: C 167 GLN cc_start: 0.7902 (tt0) cc_final: 0.7610 (tt0) REVERT: C 322 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7659 (mm-30) REVERT: C 353 LYS cc_start: 0.7308 (mtmt) cc_final: 0.7012 (mttp) REVERT: C 392 LYS cc_start: 0.8180 (mmmm) cc_final: 0.7960 (mmmm) REVERT: H 1 MET cc_start: 0.8063 (ttt) cc_final: 0.7602 (ttt) REVERT: H 161 GLU cc_start: 0.7474 (tp30) cc_final: 0.7233 (tp30) REVERT: H 167 GLN cc_start: 0.7863 (tt0) cc_final: 0.7595 (tt0) REVERT: H 286 LYS cc_start: 0.7832 (ttpt) cc_final: 0.7514 (tttm) REVERT: H 322 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7635 (mm-30) REVERT: H 353 LYS cc_start: 0.7329 (mtmt) cc_final: 0.7040 (mttm) REVERT: H 420 ASN cc_start: 0.9010 (t0) cc_final: 0.8803 (t0) REVERT: H 534 MET cc_start: 0.7568 (mpp) cc_final: 0.7260 (mpp) REVERT: G 1 MET cc_start: 0.8105 (ttt) cc_final: 0.7753 (ttt) REVERT: G 136 ASN cc_start: 0.7019 (t0) cc_final: 0.6760 (m-40) REVERT: G 167 GLN cc_start: 0.7865 (tt0) cc_final: 0.7552 (tt0) REVERT: G 173 GLU cc_start: 0.7460 (pm20) cc_final: 0.6847 (pm20) REVERT: G 286 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7792 (tttm) REVERT: G 322 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7659 (mm-30) REVERT: G 534 MET cc_start: 0.8212 (mmm) cc_final: 0.7932 (mpp) outliers start: 25 outliers final: 11 residues processed: 436 average time/residue: 2.2363 time to fit residues: 1118.9059 Evaluate side-chains 429 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 416 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 534 MET Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 537 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110783 restraints weight = 58641.070| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.83 r_work: 0.3040 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17776 Z= 0.186 Angle : 0.502 7.043 24092 Z= 0.244 Chirality : 0.043 0.130 2692 Planarity : 0.004 0.060 3068 Dihedral : 6.457 59.503 2500 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.90 % Allowed : 22.25 % Favored : 76.85 % 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: 0.55 (0.18), residues: 2144 helix: 1.05 (0.18), residues: 928 sheet: -0.01 (0.25), residues: 368 loop : -0.08 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 358 HIS 0.004 0.001 HIS H 116 PHE 0.016 0.001 PHE D 409 TYR 0.013 0.001 TYR C 42 ARG 0.009 0.000 ARG H 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16552.94 seconds wall clock time: 288 minutes 23.84 seconds (17303.84 seconds total)