Starting phenix.real_space_refine on Mon Apr 15 08:53:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mif_23848/04_2024/7mif_23848_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mif_23848/04_2024/7mif_23848.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mif_23848/04_2024/7mif_23848_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mif_23848/04_2024/7mif_23848_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mif_23848/04_2024/7mif_23848_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mif_23848/04_2024/7mif_23848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mif_23848/04_2024/7mif_23848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mif_23848/04_2024/7mif_23848_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mif_23848/04_2024/7mif_23848_trim_updated.pdb" } resolution = 3.1 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= 0.208 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 96 5.16 5 C 10968 2.51 5 N 2944 2.21 5 O 3224 1.98 5 H 17036 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 203": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 287": "OE1" <-> "OE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C GLU 507": "OE1" <-> "OE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 40": "OD1" <-> "OD2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G GLU 191": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 258": "OE1" <-> "OE2" Residue "G TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "G GLU 333": "OE1" <-> "OE2" Residue "G TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 356": "OE1" <-> "OE2" Residue "G PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 476": "OE1" <-> "OE2" Residue "G PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 483": "OE1" <-> "OE2" Residue "G GLU 507": "OE1" <-> "OE2" Residue "G GLU 510": "OE1" <-> "OE2" Residue "G TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 40": "OD1" <-> "OD2" Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "H GLU 237": "OE1" <-> "OE2" Residue "H TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 258": "OE1" <-> "OE2" Residue "H TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 287": "OE1" <-> "OE2" Residue "H TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 297": "OE1" <-> "OE2" Residue "H GLU 333": "OE1" <-> "OE2" Residue "H TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 356": "OE1" <-> "OE2" Residue "H PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 476": "OE1" <-> "OE2" Residue "H PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 483": "OE1" <-> "OE2" Residue "H GLU 507": "OE1" <-> "OE2" Residue "H GLU 510": "OE1" <-> "OE2" Residue "H TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 40": "OD1" <-> "OD2" Residue "I TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I GLU 191": "OE1" <-> "OE2" Residue "I GLU 203": "OE1" <-> "OE2" Residue "I GLU 228": "OE1" <-> "OE2" Residue "I GLU 237": "OE1" <-> "OE2" Residue "I TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 258": "OE1" <-> "OE2" Residue "I TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 287": "OE1" <-> "OE2" Residue "I TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 297": "OE1" <-> "OE2" Residue "I GLU 333": "OE1" <-> "OE2" Residue "I TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 356": "OE1" <-> "OE2" Residue "I PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 476": "OE1" <-> "OE2" Residue "I PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 483": "OE1" <-> "OE2" Residue "I GLU 507": "OE1" <-> "OE2" Residue "I GLU 510": "OE1" <-> "OE2" Residue "I TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 34284 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 8488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8488 Classifications: {'peptide': 533} Modifications used: {'ACID-GLU': 4, 'NH2NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "G" Number of atoms: 8488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8488 Classifications: {'peptide': 533} Modifications used: {'ACID-GLU': 4, 'NH2NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "H" Number of atoms: 8488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8488 Classifications: {'peptide': 533} Modifications used: {'ACID-GLU': 4, 'NH2NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "I" Number of atoms: 8488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8488 Classifications: {'peptide': 533} Modifications used: {'ACID-GLU': 4, 'NH2NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 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: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Inner-chain residues flagged as termini: ['pdbres="GLN G 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 84 Unusual residues: {' MG': 2, 'UTP': 1, 'ZG4': 1} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 4} Chain: "I" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {'UTP': 1, 'ZG4': 1} Inner-chain residues flagged as termini: ['pdbres="GLN I 602 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Time building chain proxies: 15.00, per 1000 atoms: 0.44 Number of scatterers: 34284 At special positions: 0 Unit cell: (124.95, 133.35, 87.15, 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 96 16.00 P 12 15.00 Mg 4 11.99 O 3224 8.00 N 2944 7.00 C 10968 6.00 H 17036 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 243 " distance=2.05 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 243 " distance=2.05 Simple disulfide: pdb=" SG CYS H 218 " - pdb=" SG CYS H 243 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 243 " distance=2.05 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: 31.24 Conformation dependent library (CDL) restraints added in 3.4 seconds 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 16 sheets defined 39.9% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.95 Creating SS restraints... Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 69 through 77 Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 113 through 130 removed outlier: 7.220A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 169 removed outlier: 4.684A pdb=" N PHE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 195 through 206 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 259 Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 262 through 269 Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 315 through 328 Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 351 through 363 Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 400 through 412 Processing helix chain 'C' and resid 463 through 467 Processing helix chain 'C' and resid 488 through 490 No H-bonds generated for 'chain 'C' and resid 488 through 490' Processing helix chain 'C' and resid 527 through 530 Processing helix chain 'C' and resid 538 through 547 Processing helix chain 'C' and resid 550 through 554 Processing helix chain 'G' and resid 16 through 30 Processing helix chain 'G' and resid 69 through 77 Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 90 through 102 Processing helix chain 'G' and resid 113 through 130 removed outlier: 7.220A pdb=" N THR G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 169 removed outlier: 4.684A pdb=" N PHE G 168 " --> pdb=" O ARG G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 195 through 206 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 259 Proline residue: G 254 - end of helix Processing helix chain 'G' and resid 262 through 269 Processing helix chain 'G' and resid 283 through 294 Processing helix chain 'G' and resid 315 through 328 Processing helix chain 'G' and resid 346 through 349 No H-bonds generated for 'chain 'G' and resid 346 through 349' Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 378 through 390 Processing helix chain 'G' and resid 400 through 412 Processing helix chain 'G' and resid 463 through 467 Processing helix chain 'G' and resid 488 through 490 No H-bonds generated for 'chain 'G' and resid 488 through 490' Processing helix chain 'G' and resid 527 through 530 Processing helix chain 'G' and resid 538 through 547 Processing helix chain 'G' and resid 550 through 554 Processing helix chain 'H' and resid 16 through 30 Processing helix chain 'H' and resid 69 through 77 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 113 through 130 removed outlier: 7.219A pdb=" N THR H 118 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 169 removed outlier: 4.684A pdb=" N PHE H 168 " --> pdb=" O ARG H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 195 through 206 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 259 Proline residue: H 254 - end of helix Processing helix chain 'H' and resid 262 through 269 Processing helix chain 'H' and resid 283 through 294 Processing helix chain 'H' and resid 315 through 328 Processing helix chain 'H' and resid 346 through 349 No H-bonds generated for 'chain 'H' and resid 346 through 349' Processing helix chain 'H' and resid 351 through 363 Processing helix chain 'H' and resid 378 through 390 Processing helix chain 'H' and resid 400 through 412 Processing helix chain 'H' and resid 463 through 467 Processing helix chain 'H' and resid 488 through 490 No H-bonds generated for 'chain 'H' and resid 488 through 490' Processing helix chain 'H' and resid 527 through 530 Processing helix chain 'H' and resid 538 through 547 Processing helix chain 'H' and resid 550 through 554 Processing helix chain 'I' and resid 16 through 30 Processing helix chain 'I' and resid 69 through 77 Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 90 through 102 Processing helix chain 'I' and resid 113 through 130 removed outlier: 7.219A pdb=" N THR I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 130 " --> pdb=" O MET I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 169 removed outlier: 4.684A pdb=" N PHE I 168 " --> pdb=" O ARG I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 195 through 206 Processing helix chain 'I' and resid 224 through 233 Processing helix chain 'I' and resid 238 through 240 No H-bonds generated for 'chain 'I' and resid 238 through 240' Processing helix chain 'I' and resid 250 through 259 Proline residue: I 254 - end of helix Processing helix chain 'I' and resid 262 through 269 Processing helix chain 'I' and resid 283 through 294 Processing helix chain 'I' and resid 315 through 328 Processing helix chain 'I' and resid 346 through 349 No H-bonds generated for 'chain 'I' and resid 346 through 349' Processing helix chain 'I' and resid 351 through 363 Processing helix chain 'I' and resid 378 through 390 Processing helix chain 'I' and resid 400 through 412 Processing helix chain 'I' and resid 463 through 467 Processing helix chain 'I' and resid 488 through 490 No H-bonds generated for 'chain 'I' and resid 488 through 490' Processing helix chain 'I' and resid 527 through 530 Processing helix chain 'I' and resid 538 through 547 Processing helix chain 'I' and resid 550 through 554 Processing sheet with id= A, first strand: chain 'C' and resid 241 through 244 removed outlier: 6.234A pdb=" N VAL C 214 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL C 244 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N CYS C 216 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS C 143 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL C 6 " --> pdb=" O CYS C 143 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 145 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLY C 8 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU C 147 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 331 through 338 removed outlier: 6.835A pdb=" N GLY C 366 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL C 304 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 368 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL C 369 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU C 396 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 433 through 435 Processing sheet with id= D, first strand: chain 'C' and resid 473 through 480 Processing sheet with id= E, first strand: chain 'G' and resid 241 through 244 removed outlier: 6.233A pdb=" N VAL G 214 " --> pdb=" O ILE G 242 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL G 244 " --> pdb=" O VAL G 214 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N CYS G 216 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR G 3 " --> pdb=" O CYS G 176 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE G 178 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU G 5 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL G 180 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR G 7 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU G 182 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS G 143 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL G 6 " --> pdb=" O CYS G 143 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE G 145 " --> pdb=" O VAL G 6 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLY G 8 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU G 147 " --> pdb=" O GLY G 8 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 331 through 338 removed outlier: 6.835A pdb=" N GLY G 366 " --> pdb=" O ALA G 302 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL G 304 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU G 368 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL G 369 " --> pdb=" O PRO G 394 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU G 396 " --> pdb=" O VAL G 369 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 433 through 435 Processing sheet with id= H, first strand: chain 'G' and resid 473 through 480 Processing sheet with id= I, first strand: chain 'H' and resid 241 through 244 removed outlier: 6.234A pdb=" N VAL H 214 " --> pdb=" O ILE H 242 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL H 244 " --> pdb=" O VAL H 214 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N CYS H 216 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR H 3 " --> pdb=" O CYS H 176 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE H 178 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU H 5 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL H 180 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR H 7 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU H 182 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS H 143 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL H 6 " --> pdb=" O CYS H 143 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE H 145 " --> pdb=" O VAL H 6 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLY H 8 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU H 147 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 331 through 338 removed outlier: 6.835A pdb=" N GLY H 366 " --> pdb=" O ALA H 302 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL H 304 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU H 368 " --> pdb=" O VAL H 304 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL H 369 " --> pdb=" O PRO H 394 " (cutoff:3.500A) removed outlier: 7.004A 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 'I' and resid 241 through 244 removed outlier: 6.234A pdb=" N VAL I 214 " --> pdb=" O ILE I 242 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL I 244 " --> pdb=" O VAL I 214 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N CYS I 216 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR I 3 " --> pdb=" O CYS I 176 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE I 178 " --> pdb=" O TYR I 3 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU I 5 " --> pdb=" O ILE I 178 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL I 180 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR I 7 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU I 182 " --> pdb=" O THR I 7 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS I 143 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL I 6 " --> pdb=" O CYS I 143 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE I 145 " --> pdb=" O VAL I 6 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLY I 8 " --> pdb=" O ILE I 145 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU I 147 " --> pdb=" O GLY I 8 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 331 through 338 removed outlier: 6.834A pdb=" N GLY I 366 " --> pdb=" O ALA I 302 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL I 304 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU I 368 " --> pdb=" O VAL I 304 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL I 369 " --> pdb=" O PRO I 394 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU I 396 " --> pdb=" O VAL I 369 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 433 through 435 Processing sheet with id= P, first strand: chain 'I' and resid 473 through 480 632 hydrogen bonds defined for protein. 1788 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: 16.23 Time building geometry restraints manager: 31.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.24: 19305 1.24 - 1.54: 10830 1.54 - 1.83: 4513 1.83 - 2.12: 4 2.12 - 2.42: 12 Bond restraints: 34664 Sorted by residual: bond pdb=" OE2 GLU G 203 " pdb=" HE2 GLU G 203 " ideal model delta sigma weight residual 0.948 2.419 -1.471 2.00e-02 2.50e+03 5.41e+03 bond pdb=" OE2 GLU I 203 " pdb=" HE2 GLU I 203 " ideal model delta sigma weight residual 0.948 2.418 -1.470 2.00e-02 2.50e+03 5.40e+03 bond pdb=" OE2 GLU C 203 " pdb=" HE2 GLU C 203 " ideal model delta sigma weight residual 0.948 2.418 -1.470 2.00e-02 2.50e+03 5.40e+03 bond pdb=" OE2 GLU H 203 " pdb=" HE2 GLU H 203 " ideal model delta sigma weight residual 0.948 2.417 -1.469 2.00e-02 2.50e+03 5.40e+03 bond pdb=" OE2 GLU H 476 " pdb=" HE2 GLU H 476 " ideal model delta sigma weight residual 0.948 2.401 -1.453 2.00e-02 2.50e+03 5.28e+03 ... (remaining 34659 not shown) Histogram of bond angle deviations from ideal: 52.83 - 70.27: 36 70.27 - 87.70: 0 87.70 - 105.13: 1233 105.13 - 122.57: 56712 122.57 - 140.00: 4735 Bond angle restraints: 62716 Sorted by residual: angle pdb=" CD GLU I 203 " pdb=" OE2 GLU I 203 " pdb=" HE2 GLU I 203 " ideal model delta sigma weight residual 108.32 52.83 55.49 3.00e+00 1.11e-01 3.42e+02 angle pdb=" CD GLU C 203 " pdb=" OE2 GLU C 203 " pdb=" HE2 GLU C 203 " ideal model delta sigma weight residual 108.32 52.84 55.48 3.00e+00 1.11e-01 3.42e+02 angle pdb=" CD GLU G 203 " pdb=" OE2 GLU G 203 " pdb=" HE2 GLU G 203 " ideal model delta sigma weight residual 108.32 52.84 55.48 3.00e+00 1.11e-01 3.42e+02 angle pdb=" CD GLU H 203 " pdb=" OE2 GLU H 203 " pdb=" HE2 GLU H 203 " ideal model delta sigma weight residual 108.32 52.85 55.47 3.00e+00 1.11e-01 3.42e+02 angle pdb=" CD GLU C 476 " pdb=" OE2 GLU C 476 " pdb=" HE2 GLU C 476 " ideal model delta sigma weight residual 108.32 53.52 54.80 3.00e+00 1.11e-01 3.34e+02 ... (remaining 62711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 14450 17.48 - 34.96: 1108 34.96 - 52.44: 505 52.44 - 69.92: 177 69.92 - 87.39: 44 Dihedral angle restraints: 16284 sinusoidal: 9044 harmonic: 7240 Sorted by residual: dihedral pdb=" CB CYS I 218 " pdb=" SG CYS I 218 " pdb=" SG CYS I 243 " pdb=" CB CYS I 243 " ideal model delta sinusoidal sigma weight residual -86.00 -173.39 87.39 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS C 218 " pdb=" SG CYS C 218 " pdb=" SG CYS C 243 " pdb=" CB CYS C 243 " ideal model delta sinusoidal sigma weight residual -86.00 -173.39 87.39 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS H 218 " pdb=" SG CYS H 218 " pdb=" SG CYS H 243 " pdb=" CB CYS H 243 " ideal model delta sinusoidal sigma weight residual -86.00 -173.39 87.39 1 1.00e+01 1.00e-02 9.16e+01 ... (remaining 16281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1484 0.091 - 0.181: 744 0.181 - 0.272: 323 0.272 - 0.363: 69 0.363 - 0.453: 20 Chirality restraints: 2640 Sorted by residual: chirality pdb=" C1' UTP I 601 " pdb=" C2' UTP I 601 " pdb=" N1 UTP I 601 " pdb=" O4' UTP I 601 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" C1' UTP G 602 " pdb=" C2' UTP G 602 " pdb=" N1 UTP G 602 " pdb=" O4' UTP G 602 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C1' UTP C 604 " pdb=" C2' UTP C 604 " pdb=" N1 UTP C 604 " pdb=" O4' UTP C 604 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 2637 not shown) Planarity restraints: 5060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 387 " 0.152 2.00e-02 2.50e+03 6.05e-02 1.47e+02 pdb=" CG TRP G 387 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP G 387 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP G 387 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 387 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP G 387 " 0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP G 387 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 387 " 0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 387 " -0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP G 387 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP G 387 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 TRP G 387 " -0.084 2.00e-02 2.50e+03 pdb=" HE3 TRP G 387 " -0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP G 387 " 0.112 2.00e-02 2.50e+03 pdb=" HZ3 TRP G 387 " -0.058 2.00e-02 2.50e+03 pdb=" HH2 TRP G 387 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 387 " 0.152 2.00e-02 2.50e+03 6.05e-02 1.47e+02 pdb=" CG TRP I 387 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP I 387 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP I 387 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP I 387 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP I 387 " 0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP I 387 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 387 " 0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 387 " -0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP I 387 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP I 387 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 TRP I 387 " -0.084 2.00e-02 2.50e+03 pdb=" HE3 TRP I 387 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP I 387 " 0.112 2.00e-02 2.50e+03 pdb=" HZ3 TRP I 387 " -0.058 2.00e-02 2.50e+03 pdb=" HH2 TRP I 387 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 387 " -0.152 2.00e-02 2.50e+03 6.05e-02 1.46e+02 pdb=" CG TRP H 387 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP H 387 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP H 387 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 387 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP H 387 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP H 387 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 387 " -0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 387 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP H 387 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP H 387 " 0.038 2.00e-02 2.50e+03 pdb=" HE1 TRP H 387 " 0.084 2.00e-02 2.50e+03 pdb=" HE3 TRP H 387 " 0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 387 " -0.111 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 387 " 0.059 2.00e-02 2.50e+03 pdb=" HH2 TRP H 387 " -0.014 2.00e-02 2.50e+03 ... (remaining 5057 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.69: 51 1.69 - 2.42: 12438 2.42 - 3.14: 114119 3.14 - 3.87: 159039 3.87 - 4.60: 245031 Warning: very small nonbonded interaction distances. Nonbonded interactions: 530678 Sorted by model distance: nonbonded pdb=" OE1 GLU I 483 " pdb=" HE2 GLU I 483 " model vdw 0.959 1.960 nonbonded pdb=" OE1 GLU C 476 " pdb=" HE2 GLU C 476 " model vdw 0.960 1.960 nonbonded pdb=" OE1 GLU G 483 " pdb=" HE2 GLU G 483 " model vdw 0.960 1.960 nonbonded pdb=" OE1 GLU I 476 " pdb=" HE2 GLU I 476 " model vdw 0.960 1.960 nonbonded pdb=" OE1 GLU H 476 " pdb=" HE2 GLU H 476 " model vdw 0.960 1.960 ... (remaining 530673 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 556) selection = (chain 'G' and resid 1 through 556) selection = (chain 'H' and resid 1 through 556) selection = (chain 'I' and resid 1 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.520 Extract box with map and model: 7.310 Check model and map are aligned: 0.540 Set scattering table: 0.360 Process input model: 116.120 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 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 : 0.016 0.233 17628 Z= 1.036 Angle : 2.040 16.412 23896 Z= 1.334 Chirality : 0.125 0.453 2640 Planarity : 0.014 0.096 3060 Dihedral : 14.523 85.910 6672 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.72 % Allowed : 3.68 % Favored : 95.60 % Rotamer: Outliers : 1.48 % Allowed : 5.92 % Favored : 92.60 % Cbeta Deviations : 0.66 % 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: -1.46 (0.18), residues: 2092 helix: -1.12 (0.16), residues: 864 sheet: -0.81 (0.27), residues: 344 loop : -0.62 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.017 TRP I 387 HIS 0.021 0.006 HIS H 439 PHE 0.101 0.020 PHE H 163 TYR 0.070 0.012 TYR I 74 ARG 0.008 0.001 ARG I 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 530 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 502 time to evaluate : 2.797 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: 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: C 176 CYS cc_start: 0.7143 (t) cc_final: 0.6910 (t) REVERT: C 240 GLN cc_start: 0.6664 (mt0) cc_final: 0.6105 (mt0) REVERT: C 330 HIS cc_start: 0.7772 (m-70) cc_final: 0.7561 (m170) REVERT: C 402 MET cc_start: 0.6892 (ttt) cc_final: 0.6601 (ttt) REVERT: G 103 LYS cc_start: 0.7013 (mmmm) cc_final: 0.6805 (mtpt) REVERT: G 240 GLN cc_start: 0.7515 (mt0) cc_final: 0.7234 (mt0) REVERT: G 393 LYS cc_start: 0.7148 (mmtt) cc_final: 0.6902 (mmtt) REVERT: G 452 LYS cc_start: 0.7806 (tttt) cc_final: 0.7270 (ttpt) REVERT: G 466 LYS cc_start: 0.7969 (mttt) cc_final: 0.7702 (mtpt) REVERT: H 84 LYS cc_start: 0.7638 (mtmt) cc_final: 0.7393 (mttt) REVERT: H 240 GLN cc_start: 0.7475 (mt0) cc_final: 0.7205 (mt0) REVERT: H 393 LYS cc_start: 0.7130 (mmtt) cc_final: 0.6871 (mmtt) REVERT: H 452 LYS cc_start: 0.7792 (tttt) cc_final: 0.7420 (ttpt) REVERT: H 466 LYS cc_start: 0.7981 (mttt) cc_final: 0.7730 (mtpt) REVERT: I 103 LYS cc_start: 0.7039 (mmmm) cc_final: 0.6836 (mtpt) REVERT: I 240 GLN cc_start: 0.7515 (mt0) cc_final: 0.7244 (mt0) REVERT: I 393 LYS cc_start: 0.7143 (mmtt) cc_final: 0.6881 (mmtt) REVERT: I 466 LYS cc_start: 0.7982 (mttt) cc_final: 0.7716 (mtpt) outliers start: 28 outliers final: 10 residues processed: 524 average time/residue: 0.8204 time to fit residues: 610.2439 Evaluate side-chains 407 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 397 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 264 ASP Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 264 ASP Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain I residue 89 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 166 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN G 87 ASN G 185 GLN ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 556 GLN H 87 ASN H 185 GLN H 220 ASN ** H 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 556 GLN I 87 ASN I 185 GLN I 220 ASN ** I 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 556 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17628 Z= 0.240 Angle : 0.606 5.860 23896 Z= 0.318 Chirality : 0.044 0.146 2640 Planarity : 0.005 0.045 3060 Dihedral : 6.968 59.858 2489 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 1.27 % Allowed : 7.98 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2092 helix: 0.34 (0.17), residues: 916 sheet: -0.62 (0.27), residues: 356 loop : -0.44 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 387 HIS 0.005 0.001 HIS C 116 PHE 0.020 0.002 PHE C 163 TYR 0.013 0.002 TYR I 265 ARG 0.006 0.001 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 468 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 444 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: 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: C 66 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6536 (mt-10) REVERT: C 84 LYS cc_start: 0.7718 (mtmt) cc_final: 0.7474 (mttt) REVERT: C 139 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6791 (tp30) REVERT: C 176 CYS cc_start: 0.7422 (t) cc_final: 0.7174 (t) REVERT: C 293 ASP cc_start: 0.5800 (m-30) cc_final: 0.5595 (m-30) REVERT: C 528 GLU cc_start: 0.7811 (pm20) cc_final: 0.7398 (pm20) REVERT: G 265 TYR cc_start: 0.7513 (t80) cc_final: 0.7102 (t80) REVERT: G 379 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6653 (mm-30) REVERT: G 383 GLN cc_start: 0.7408 (mt0) cc_final: 0.6990 (mt0) REVERT: G 393 LYS cc_start: 0.7378 (mmtt) cc_final: 0.7129 (mmtt) REVERT: G 412 ASN cc_start: 0.6692 (m-40) cc_final: 0.6092 (m110) REVERT: G 466 LYS cc_start: 0.7895 (mttt) cc_final: 0.7601 (mtpt) REVERT: G 541 PHE cc_start: 0.8340 (t80) cc_final: 0.8133 (t80) REVERT: H 66 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6971 (mt-10) REVERT: H 84 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7566 (mttt) REVERT: H 265 TYR cc_start: 0.7502 (t80) cc_final: 0.7013 (t80) REVERT: H 379 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6502 (mm-30) REVERT: H 383 GLN cc_start: 0.7346 (mt0) cc_final: 0.6836 (mt0) REVERT: H 393 LYS cc_start: 0.7376 (mmtt) cc_final: 0.7095 (mmtt) REVERT: H 412 ASN cc_start: 0.6715 (m-40) cc_final: 0.6112 (m110) REVERT: H 466 LYS cc_start: 0.7921 (mttt) cc_final: 0.7630 (mtpt) REVERT: I 265 TYR cc_start: 0.7499 (t80) cc_final: 0.7080 (t80) REVERT: I 338 ASP cc_start: 0.7711 (t0) cc_final: 0.7220 (m-30) REVERT: I 379 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6971 (mm-30) REVERT: I 393 LYS cc_start: 0.7394 (mmtt) cc_final: 0.7104 (mmtt) REVERT: I 412 ASN cc_start: 0.6759 (m-40) cc_final: 0.6160 (m110) REVERT: I 458 GLN cc_start: 0.7583 (mt0) cc_final: 0.7242 (mt0) REVERT: I 466 LYS cc_start: 0.7915 (mttt) cc_final: 0.7613 (mtpt) outliers start: 24 outliers final: 17 residues processed: 464 average time/residue: 0.8149 time to fit residues: 547.1493 Evaluate side-chains 418 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 400 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 264 ASP Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 191 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 235 HIS C 260 GLN C 329 ASN ** C 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 ASN ** G 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 ASN H 329 ASN ** H 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 ASN ** I 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17628 Z= 0.304 Angle : 0.616 6.922 23896 Z= 0.320 Chirality : 0.045 0.197 2640 Planarity : 0.005 0.072 3060 Dihedral : 6.475 55.641 2483 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.97 % Favored : 95.89 % Rotamer: Outliers : 1.90 % Allowed : 10.31 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2092 helix: 0.63 (0.17), residues: 892 sheet: -0.55 (0.26), residues: 360 loop : -0.25 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 387 HIS 0.007 0.001 HIS G 116 PHE 0.024 0.002 PHE H 163 TYR 0.014 0.002 TYR G 42 ARG 0.007 0.001 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 464 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 428 time to evaluate : 3.335 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: C 84 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7686 (mttt) REVERT: C 139 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: C 176 CYS cc_start: 0.7823 (t) cc_final: 0.7586 (t) REVERT: C 259 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7116 (tp30) REVERT: C 271 ASP cc_start: 0.6595 (t0) cc_final: 0.6357 (t0) REVERT: C 293 ASP cc_start: 0.6213 (m-30) cc_final: 0.5949 (m-30) REVERT: C 365 HIS cc_start: 0.8208 (m90) cc_final: 0.7967 (m170) REVERT: C 528 GLU cc_start: 0.7715 (pm20) cc_final: 0.7342 (pm20) REVERT: C 550 ARG cc_start: 0.7577 (tpp80) cc_final: 0.7278 (tpp80) REVERT: G 103 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7488 (tppp) REVERT: G 157 MET cc_start: 0.6975 (mtp) cc_final: 0.6687 (mmp) REVERT: G 169 LYS cc_start: 0.8092 (tttt) cc_final: 0.7891 (ttpp) REVERT: G 265 TYR cc_start: 0.7681 (t80) cc_final: 0.7274 (t80) REVERT: G 292 TYR cc_start: 0.8383 (t80) cc_final: 0.8169 (t80) REVERT: G 448 MET cc_start: 0.8270 (ttt) cc_final: 0.7923 (ttt) REVERT: G 452 LYS cc_start: 0.8085 (tttt) cc_final: 0.7398 (ttpt) REVERT: G 466 LYS cc_start: 0.8087 (mttt) cc_final: 0.7746 (mtpt) REVERT: G 475 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: H 84 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7544 (mttt) REVERT: H 103 LYS cc_start: 0.7790 (mmtp) cc_final: 0.7453 (tppp) REVERT: H 139 GLU cc_start: 0.7590 (tt0) cc_final: 0.7065 (tt0) REVERT: H 157 MET cc_start: 0.6919 (mtp) cc_final: 0.6661 (mmp) REVERT: H 265 TYR cc_start: 0.7668 (t80) cc_final: 0.7150 (t80) REVERT: H 292 TYR cc_start: 0.8361 (t80) cc_final: 0.8139 (t80) REVERT: H 383 GLN cc_start: 0.7466 (mt0) cc_final: 0.6925 (mt0) REVERT: H 393 LYS cc_start: 0.7369 (mmtt) cc_final: 0.7160 (mmtt) REVERT: H 412 ASN cc_start: 0.7173 (m-40) cc_final: 0.6698 (m-40) REVERT: H 448 MET cc_start: 0.8251 (ttt) cc_final: 0.7973 (ttt) REVERT: H 466 LYS cc_start: 0.8114 (mttt) cc_final: 0.7775 (mtpt) REVERT: H 543 LEU cc_start: 0.8316 (tp) cc_final: 0.8099 (tt) REVERT: H 550 ARG cc_start: 0.7513 (mmt90) cc_final: 0.7019 (mmt-90) REVERT: I 66 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7252 (mt-10) REVERT: I 103 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7706 (mtmm) REVERT: I 157 MET cc_start: 0.6939 (mtp) cc_final: 0.6687 (mmp) REVERT: I 265 TYR cc_start: 0.7645 (t80) cc_final: 0.7223 (t80) REVERT: I 292 TYR cc_start: 0.8359 (t80) cc_final: 0.8132 (t80) REVERT: I 448 MET cc_start: 0.8285 (ttt) cc_final: 0.8006 (ttt) REVERT: I 466 LYS cc_start: 0.8101 (mttt) cc_final: 0.7769 (mttp) REVERT: I 475 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: I 550 ARG cc_start: 0.7516 (mmt90) cc_final: 0.6999 (mmt-90) outliers start: 36 outliers final: 18 residues processed: 450 average time/residue: 0.8580 time to fit residues: 552.1224 Evaluate side-chains 422 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 399 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 475 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 GLN ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 524 GLN ** H 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN ** I 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17628 Z= 0.333 Angle : 0.584 5.745 23896 Z= 0.299 Chirality : 0.044 0.154 2640 Planarity : 0.005 0.047 3060 Dihedral : 6.258 55.357 2478 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.64 % Allowed : 12.47 % Favored : 85.89 % 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: -0.04 (0.18), residues: 2092 helix: 0.67 (0.17), residues: 892 sheet: -0.63 (0.26), residues: 360 loop : -0.33 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 358 HIS 0.008 0.001 HIS C 116 PHE 0.022 0.002 PHE G 163 TYR 0.021 0.002 TYR C 265 ARG 0.008 0.001 ARG I 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 431 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 400 time to evaluate : 2.828 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: C 84 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7567 (mttt) REVERT: C 139 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: C 259 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7107 (tp30) REVERT: C 271 ASP cc_start: 0.6977 (t0) cc_final: 0.6769 (t0) REVERT: C 292 TYR cc_start: 0.8308 (t80) cc_final: 0.8034 (t80) REVERT: C 293 ASP cc_start: 0.6332 (m-30) cc_final: 0.6022 (m-30) REVERT: C 528 GLU cc_start: 0.7658 (pm20) cc_final: 0.7355 (pm20) REVERT: C 550 ARG cc_start: 0.7603 (tpp80) cc_final: 0.7386 (tpp80) REVERT: G 46 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8122 (p0) REVERT: G 103 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7453 (tppp) REVERT: G 139 GLU cc_start: 0.7624 (tt0) cc_final: 0.7168 (tt0) REVERT: G 207 LEU cc_start: 0.8966 (mt) cc_final: 0.8628 (mt) REVERT: G 259 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6625 (mm-30) REVERT: G 265 TYR cc_start: 0.7681 (t80) cc_final: 0.7392 (t80) REVERT: G 292 TYR cc_start: 0.8472 (t80) cc_final: 0.8188 (t80) REVERT: G 365 HIS cc_start: 0.8515 (m170) cc_final: 0.8201 (m-70) REVERT: G 402 MET cc_start: 0.7646 (tmm) cc_final: 0.7093 (tmm) REVERT: G 406 VAL cc_start: 0.7875 (t) cc_final: 0.7598 (p) REVERT: G 452 LYS cc_start: 0.8180 (tttt) cc_final: 0.7443 (ttpt) REVERT: G 466 LYS cc_start: 0.8112 (mttt) cc_final: 0.7785 (mtpt) REVERT: G 481 ARG cc_start: 0.6146 (mtt180) cc_final: 0.5881 (mtm180) REVERT: H 46 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8026 (p0) REVERT: H 84 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7592 (mttt) REVERT: H 103 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7461 (tppp) REVERT: H 139 GLU cc_start: 0.7407 (tt0) cc_final: 0.7022 (tt0) REVERT: H 207 LEU cc_start: 0.8967 (mt) cc_final: 0.8606 (mt) REVERT: H 292 TYR cc_start: 0.8459 (t80) cc_final: 0.8166 (t80) REVERT: H 365 HIS cc_start: 0.8515 (m170) cc_final: 0.8182 (m-70) REVERT: H 383 GLN cc_start: 0.7552 (mt0) cc_final: 0.6912 (mt0) REVERT: H 393 LYS cc_start: 0.7320 (mmtt) cc_final: 0.7116 (mmtt) REVERT: H 466 LYS cc_start: 0.8145 (mttt) cc_final: 0.7816 (mtpt) REVERT: H 528 GLU cc_start: 0.7541 (pm20) cc_final: 0.7099 (pm20) REVERT: I 46 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7966 (p0) REVERT: I 169 LYS cc_start: 0.8105 (tttt) cc_final: 0.7721 (ttmm) REVERT: I 207 LEU cc_start: 0.8975 (mt) cc_final: 0.8616 (mt) REVERT: I 265 TYR cc_start: 0.7656 (t80) cc_final: 0.7300 (t80) REVERT: I 292 TYR cc_start: 0.8456 (t80) cc_final: 0.8159 (t80) REVERT: I 365 HIS cc_start: 0.8485 (m170) cc_final: 0.8057 (m90) REVERT: I 466 LYS cc_start: 0.8119 (mttt) cc_final: 0.7784 (mtpt) REVERT: I 528 GLU cc_start: 0.7556 (pm20) cc_final: 0.7120 (pm20) outliers start: 31 outliers final: 20 residues processed: 419 average time/residue: 0.8586 time to fit residues: 507.1317 Evaluate side-chains 417 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 391 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain G residue 537 SER Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 537 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.0770 chunk 116 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 GLN ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17628 Z= 0.242 Angle : 0.535 5.246 23896 Z= 0.272 Chirality : 0.042 0.173 2640 Planarity : 0.005 0.057 3060 Dihedral : 5.820 56.175 2478 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.11 % Allowed : 12.53 % Favored : 85.36 % 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: 0.29 (0.19), residues: 2092 helix: 0.99 (0.17), residues: 900 sheet: -0.51 (0.26), residues: 360 loop : -0.21 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 387 HIS 0.006 0.001 HIS H 116 PHE 0.016 0.002 PHE H 163 TYR 0.014 0.001 TYR C 265 ARG 0.009 0.001 ARG I 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 396 time to evaluate : 2.770 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: C 84 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7578 (mttt) REVERT: C 139 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: C 271 ASP cc_start: 0.7055 (t0) cc_final: 0.6786 (t0) REVERT: C 292 TYR cc_start: 0.8346 (t80) cc_final: 0.8076 (t80) REVERT: C 293 ASP cc_start: 0.6279 (m-30) cc_final: 0.5982 (m-30) REVERT: C 525 TYR cc_start: 0.8300 (p90) cc_final: 0.8081 (p90) REVERT: C 528 GLU cc_start: 0.7616 (pm20) cc_final: 0.7316 (pm20) REVERT: G 46 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8132 (p0) REVERT: G 103 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7472 (tppp) REVERT: G 139 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: G 265 TYR cc_start: 0.7770 (t80) cc_final: 0.7535 (t80) REVERT: G 292 TYR cc_start: 0.8449 (t80) cc_final: 0.8131 (t80) REVERT: G 365 HIS cc_start: 0.8454 (m170) cc_final: 0.8132 (m-70) REVERT: G 383 GLN cc_start: 0.7611 (mt0) cc_final: 0.7235 (mt0) REVERT: G 402 MET cc_start: 0.7669 (tmm) cc_final: 0.7148 (tmm) REVERT: G 406 VAL cc_start: 0.7871 (t) cc_final: 0.7606 (p) REVERT: G 452 LYS cc_start: 0.8206 (tttt) cc_final: 0.7477 (ttpt) REVERT: G 466 LYS cc_start: 0.8127 (mttt) cc_final: 0.7777 (mtpt) REVERT: G 481 ARG cc_start: 0.6116 (mtt180) cc_final: 0.5861 (mtm180) REVERT: G 528 GLU cc_start: 0.7541 (pm20) cc_final: 0.7166 (pm20) REVERT: H 84 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7733 (mttt) REVERT: H 103 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7493 (tppp) REVERT: H 139 GLU cc_start: 0.7393 (tt0) cc_final: 0.7034 (tt0) REVERT: H 265 TYR cc_start: 0.7682 (t80) cc_final: 0.7389 (t80) REVERT: H 292 TYR cc_start: 0.8432 (t80) cc_final: 0.8110 (t80) REVERT: H 365 HIS cc_start: 0.8460 (m170) cc_final: 0.8139 (m-70) REVERT: H 393 LYS cc_start: 0.7318 (mmtt) cc_final: 0.7100 (mmtt) REVERT: H 466 LYS cc_start: 0.8147 (mttt) cc_final: 0.7794 (mtpt) REVERT: H 528 GLU cc_start: 0.7529 (pm20) cc_final: 0.7139 (pm20) REVERT: I 46 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8034 (p0) REVERT: I 265 TYR cc_start: 0.7725 (t80) cc_final: 0.7491 (t80) REVERT: I 292 TYR cc_start: 0.8466 (t80) cc_final: 0.8139 (t80) REVERT: I 365 HIS cc_start: 0.8445 (m170) cc_final: 0.8136 (m-70) REVERT: I 466 LYS cc_start: 0.8130 (mttt) cc_final: 0.7771 (mtpt) REVERT: I 528 GLU cc_start: 0.7534 (pm20) cc_final: 0.7145 (pm20) outliers start: 40 outliers final: 32 residues processed: 418 average time/residue: 0.8332 time to fit residues: 501.4485 Evaluate side-chains 422 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 384 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain G residue 537 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain I residue 36 SER Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 537 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 205 optimal weight: 0.0170 chunk 170 optimal weight: 0.0670 chunk 94 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 ASN ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 524 GLN ** I 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17628 Z= 0.146 Angle : 0.488 5.730 23896 Z= 0.245 Chirality : 0.041 0.171 2640 Planarity : 0.004 0.055 3060 Dihedral : 5.286 57.460 2478 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.48 % Allowed : 13.16 % Favored : 85.36 % 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: 0.80 (0.19), residues: 2092 helix: 1.45 (0.18), residues: 892 sheet: -0.42 (0.27), residues: 360 loop : 0.11 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 387 HIS 0.004 0.001 HIS I 116 PHE 0.007 0.001 PHE G 520 TYR 0.024 0.001 TYR H 468 ARG 0.010 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 427 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 399 time to evaluate : 3.039 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: C 271 ASP cc_start: 0.7095 (t0) cc_final: 0.6825 (t0) REVERT: C 292 TYR cc_start: 0.8304 (t80) cc_final: 0.8048 (t80) REVERT: C 293 ASP cc_start: 0.6327 (m-30) cc_final: 0.6027 (m-30) REVERT: C 467 LEU cc_start: 0.7907 (mt) cc_final: 0.7692 (mt) REVERT: C 468 TYR cc_start: 0.7552 (m-80) cc_final: 0.7215 (m-80) REVERT: C 525 TYR cc_start: 0.8371 (p90) cc_final: 0.8013 (p90) REVERT: C 528 GLU cc_start: 0.7639 (pm20) cc_final: 0.7331 (pm20) REVERT: C 550 ARG cc_start: 0.7565 (tpp80) cc_final: 0.7293 (mmt90) REVERT: G 103 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7466 (tppp) REVERT: G 155 GLU cc_start: 0.7602 (mp0) cc_final: 0.7349 (mp0) REVERT: G 161 GLU cc_start: 0.7535 (tp30) cc_final: 0.7050 (tp30) REVERT: G 259 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6627 (mm-30) REVERT: G 292 TYR cc_start: 0.8459 (t80) cc_final: 0.8148 (t80) REVERT: G 365 HIS cc_start: 0.8383 (m170) cc_final: 0.8063 (m-70) REVERT: G 383 GLN cc_start: 0.7558 (mt0) cc_final: 0.7211 (mt0) REVERT: G 402 MET cc_start: 0.7629 (tmm) cc_final: 0.7127 (tmm) REVERT: G 406 VAL cc_start: 0.7863 (t) cc_final: 0.7642 (p) REVERT: G 452 LYS cc_start: 0.8082 (tttt) cc_final: 0.7340 (ttpt) REVERT: G 466 LYS cc_start: 0.8120 (mttt) cc_final: 0.7772 (mtpt) REVERT: G 481 ARG cc_start: 0.6111 (mtt180) cc_final: 0.5875 (mtm180) REVERT: G 528 GLU cc_start: 0.7581 (pm20) cc_final: 0.7182 (pm20) REVERT: H 84 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7712 (mttt) REVERT: H 103 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7467 (tppp) REVERT: H 139 GLU cc_start: 0.7438 (tt0) cc_final: 0.7119 (tt0) REVERT: H 161 GLU cc_start: 0.7579 (tp30) cc_final: 0.7097 (tp30) REVERT: H 232 MET cc_start: 0.6977 (mtp) cc_final: 0.6564 (mmp) REVERT: H 292 TYR cc_start: 0.8456 (t80) cc_final: 0.8124 (t80) REVERT: H 365 HIS cc_start: 0.8431 (m170) cc_final: 0.8097 (m-70) REVERT: H 406 VAL cc_start: 0.8004 (t) cc_final: 0.7787 (p) REVERT: H 466 LYS cc_start: 0.8157 (mttt) cc_final: 0.7818 (mtpt) REVERT: H 528 GLU cc_start: 0.7531 (pm20) cc_final: 0.7142 (pm20) REVERT: I 46 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8030 (p0) REVERT: I 161 GLU cc_start: 0.7529 (tp30) cc_final: 0.7041 (tp30) REVERT: I 292 TYR cc_start: 0.8431 (t80) cc_final: 0.8079 (t80) REVERT: I 365 HIS cc_start: 0.8410 (m170) cc_final: 0.8098 (m-70) REVERT: I 406 VAL cc_start: 0.7994 (t) cc_final: 0.7774 (p) REVERT: I 466 LYS cc_start: 0.8135 (mttt) cc_final: 0.7780 (mtpt) REVERT: I 525 TYR cc_start: 0.8365 (p90) cc_final: 0.8093 (p90) REVERT: I 528 GLU cc_start: 0.7532 (pm20) cc_final: 0.7151 (pm20) outliers start: 28 outliers final: 21 residues processed: 412 average time/residue: 0.8160 time to fit residues: 480.7189 Evaluate side-chains 407 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 383 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain G residue 537 SER Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 537 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 116 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17628 Z= 0.199 Angle : 0.507 5.405 23896 Z= 0.255 Chirality : 0.042 0.166 2640 Planarity : 0.005 0.058 3060 Dihedral : 5.579 58.197 2478 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.69 % Allowed : 12.68 % Favored : 85.62 % 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: 0.90 (0.19), residues: 2092 helix: 1.54 (0.18), residues: 892 sheet: -0.38 (0.27), residues: 360 loop : 0.17 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 358 HIS 0.005 0.001 HIS H 116 PHE 0.013 0.001 PHE C 163 TYR 0.022 0.001 TYR I 468 ARG 0.010 0.001 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 421 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 389 time to evaluate : 2.687 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: C 49 THR cc_start: 0.8026 (m) cc_final: 0.7583 (p) REVERT: C 271 ASP cc_start: 0.7257 (t0) cc_final: 0.7000 (t0) REVERT: C 292 TYR cc_start: 0.8374 (t80) cc_final: 0.8107 (t80) REVERT: C 293 ASP cc_start: 0.6341 (m-30) cc_final: 0.6045 (m-30) REVERT: C 365 HIS cc_start: 0.8181 (m90) cc_final: 0.7920 (m170) REVERT: C 467 LEU cc_start: 0.7972 (mt) cc_final: 0.7748 (mt) REVERT: C 468 TYR cc_start: 0.7670 (m-80) cc_final: 0.7265 (m-80) REVERT: C 525 TYR cc_start: 0.8382 (p90) cc_final: 0.7978 (p90) REVERT: C 528 GLU cc_start: 0.7675 (pm20) cc_final: 0.7336 (pm20) REVERT: C 550 ARG cc_start: 0.7559 (tpp80) cc_final: 0.7308 (mmt90) REVERT: G 103 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7502 (tppp) REVERT: G 259 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6572 (mm-30) REVERT: G 365 HIS cc_start: 0.8334 (m170) cc_final: 0.8053 (m-70) REVERT: G 402 MET cc_start: 0.7638 (tmm) cc_final: 0.7141 (tmm) REVERT: G 406 VAL cc_start: 0.7908 (t) cc_final: 0.7664 (p) REVERT: G 452 LYS cc_start: 0.8103 (tttt) cc_final: 0.7386 (ttpt) REVERT: G 466 LYS cc_start: 0.8116 (mttt) cc_final: 0.7771 (mtpt) REVERT: G 481 ARG cc_start: 0.6151 (mtt180) cc_final: 0.5910 (mtm180) REVERT: G 528 GLU cc_start: 0.7584 (pm20) cc_final: 0.7222 (pm20) REVERT: H 84 LYS cc_start: 0.8147 (mtmt) cc_final: 0.7733 (mttt) REVERT: H 103 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7511 (tppp) REVERT: H 232 MET cc_start: 0.6984 (mtp) cc_final: 0.6746 (mmt) REVERT: H 292 TYR cc_start: 0.8484 (t80) cc_final: 0.8150 (t80) REVERT: H 365 HIS cc_start: 0.8345 (m170) cc_final: 0.8092 (m-70) REVERT: H 406 VAL cc_start: 0.8017 (t) cc_final: 0.7789 (p) REVERT: H 466 LYS cc_start: 0.8152 (mttt) cc_final: 0.7802 (mtpt) REVERT: H 528 GLU cc_start: 0.7585 (pm20) cc_final: 0.7260 (pm20) REVERT: I 46 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8084 (p0) REVERT: I 292 TYR cc_start: 0.8444 (t80) cc_final: 0.8081 (t80) REVERT: I 365 HIS cc_start: 0.8347 (m170) cc_final: 0.8053 (m-70) REVERT: I 406 VAL cc_start: 0.8000 (t) cc_final: 0.7772 (p) REVERT: I 466 LYS cc_start: 0.8139 (mttt) cc_final: 0.7781 (mtpt) REVERT: I 528 GLU cc_start: 0.7539 (pm20) cc_final: 0.7203 (pm20) outliers start: 32 outliers final: 28 residues processed: 407 average time/residue: 0.7953 time to fit residues: 467.6020 Evaluate side-chains 411 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 380 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain G residue 537 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 36 SER Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 537 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17628 Z= 0.305 Angle : 0.558 5.365 23896 Z= 0.284 Chirality : 0.044 0.173 2640 Planarity : 0.005 0.067 3060 Dihedral : 6.070 58.006 2478 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.17 % Allowed : 12.68 % Favored : 85.15 % 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: 0.71 (0.19), residues: 2092 helix: 1.27 (0.17), residues: 892 sheet: -0.37 (0.27), residues: 356 loop : 0.14 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 416 HIS 0.006 0.001 HIS C 116 PHE 0.023 0.002 PHE I 163 TYR 0.018 0.002 TYR G 468 ARG 0.012 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 446 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 405 time to evaluate : 2.953 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: C 46 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8402 (p0) REVERT: C 49 THR cc_start: 0.8058 (m) cc_final: 0.7641 (p) REVERT: C 271 ASP cc_start: 0.7369 (t0) cc_final: 0.7087 (t0) REVERT: C 292 TYR cc_start: 0.8419 (t80) cc_final: 0.8130 (t80) REVERT: C 293 ASP cc_start: 0.6371 (m-30) cc_final: 0.6091 (m-30) REVERT: C 466 LYS cc_start: 0.7903 (mttt) cc_final: 0.7647 (mtpt) REVERT: C 467 LEU cc_start: 0.8160 (mt) cc_final: 0.7936 (mt) REVERT: C 528 GLU cc_start: 0.7574 (pm20) cc_final: 0.7269 (pm20) REVERT: G 103 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7548 (tppp) REVERT: G 402 MET cc_start: 0.7602 (tmm) cc_final: 0.7144 (tmm) REVERT: G 406 VAL cc_start: 0.8037 (t) cc_final: 0.7714 (p) REVERT: G 452 LYS cc_start: 0.8186 (tttt) cc_final: 0.7482 (ttpt) REVERT: G 466 LYS cc_start: 0.8106 (mttt) cc_final: 0.7771 (mtpt) REVERT: G 481 ARG cc_start: 0.6290 (mtt180) cc_final: 0.6058 (mtm180) REVERT: G 528 GLU cc_start: 0.7531 (pm20) cc_final: 0.7215 (pm20) REVERT: H 84 LYS cc_start: 0.8174 (mtmt) cc_final: 0.7758 (mttt) REVERT: H 103 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7524 (tppp) REVERT: H 365 HIS cc_start: 0.8392 (m170) cc_final: 0.8151 (m-70) REVERT: H 376 ARG cc_start: 0.6296 (ttp-170) cc_final: 0.6058 (ttp-170) REVERT: H 406 VAL cc_start: 0.8033 (t) cc_final: 0.7809 (p) REVERT: H 452 LYS cc_start: 0.8164 (tttt) cc_final: 0.7860 (tttt) REVERT: H 466 LYS cc_start: 0.8115 (mttt) cc_final: 0.7779 (mtpt) REVERT: H 528 GLU cc_start: 0.7561 (pm20) cc_final: 0.7284 (pm20) REVERT: H 550 ARG cc_start: 0.7495 (mmt90) cc_final: 0.7248 (mmt90) REVERT: I 46 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7927 (p0) REVERT: I 365 HIS cc_start: 0.8414 (m170) cc_final: 0.8117 (m-70) REVERT: I 406 VAL cc_start: 0.7962 (t) cc_final: 0.7729 (p) REVERT: I 466 LYS cc_start: 0.8125 (mttt) cc_final: 0.7775 (mtpt) REVERT: I 525 TYR cc_start: 0.8376 (p90) cc_final: 0.8116 (p90) REVERT: I 528 GLU cc_start: 0.7556 (pm20) cc_final: 0.7271 (pm20) outliers start: 41 outliers final: 32 residues processed: 424 average time/residue: 0.8905 time to fit residues: 539.4176 Evaluate side-chains 433 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 397 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain G residue 537 SER Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 537 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 172 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 189 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17628 Z= 0.207 Angle : 0.512 5.675 23896 Z= 0.259 Chirality : 0.042 0.160 2640 Planarity : 0.005 0.063 3060 Dihedral : 5.585 57.889 2478 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.80 % Allowed : 13.58 % Favored : 84.62 % 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: 0.93 (0.19), residues: 2092 helix: 1.48 (0.18), residues: 888 sheet: -0.32 (0.27), residues: 356 loop : 0.27 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 387 HIS 0.005 0.001 HIS G 116 PHE 0.013 0.001 PHE H 163 TYR 0.020 0.001 TYR G 468 ARG 0.012 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 427 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 393 time to evaluate : 2.800 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: C 49 THR cc_start: 0.7985 (m) cc_final: 0.7637 (p) REVERT: C 161 GLU cc_start: 0.7535 (tp30) cc_final: 0.6995 (tp30) REVERT: C 271 ASP cc_start: 0.7356 (t0) cc_final: 0.7132 (t0) REVERT: C 292 TYR cc_start: 0.8386 (t80) cc_final: 0.8107 (t80) REVERT: C 293 ASP cc_start: 0.6381 (m-30) cc_final: 0.6098 (m-30) REVERT: C 365 HIS cc_start: 0.8267 (m90) cc_final: 0.8001 (m170) REVERT: C 376 ARG cc_start: 0.6398 (ttp80) cc_final: 0.6006 (ttp80) REVERT: C 466 LYS cc_start: 0.7931 (mttt) cc_final: 0.7719 (mttm) REVERT: C 467 LEU cc_start: 0.8144 (mt) cc_final: 0.7918 (mt) REVERT: G 103 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7510 (mtmm) REVERT: G 376 ARG cc_start: 0.6299 (ttp-170) cc_final: 0.5869 (ttp80) REVERT: G 402 MET cc_start: 0.7607 (tmm) cc_final: 0.7150 (tmm) REVERT: G 406 VAL cc_start: 0.8009 (t) cc_final: 0.7691 (p) REVERT: G 452 LYS cc_start: 0.8173 (tttt) cc_final: 0.7479 (ttpt) REVERT: G 466 LYS cc_start: 0.8103 (mttt) cc_final: 0.7768 (mtpt) REVERT: G 481 ARG cc_start: 0.6124 (mtt180) cc_final: 0.5863 (mtm180) REVERT: G 528 GLU cc_start: 0.7542 (pm20) cc_final: 0.7229 (pm20) REVERT: G 550 ARG cc_start: 0.7514 (mmt90) cc_final: 0.7242 (mmt90) REVERT: H 84 LYS cc_start: 0.8147 (mtmt) cc_final: 0.7748 (mttt) REVERT: H 103 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7507 (tppp) REVERT: H 232 MET cc_start: 0.7227 (mtp) cc_final: 0.6948 (mmt) REVERT: H 365 HIS cc_start: 0.8353 (m170) cc_final: 0.8105 (m-70) REVERT: H 376 ARG cc_start: 0.6261 (ttp-170) cc_final: 0.5856 (ttp80) REVERT: H 406 VAL cc_start: 0.8032 (t) cc_final: 0.7811 (p) REVERT: H 452 LYS cc_start: 0.8147 (tttt) cc_final: 0.7859 (tttt) REVERT: H 466 LYS cc_start: 0.8122 (mttt) cc_final: 0.7796 (mtpt) REVERT: H 525 TYR cc_start: 0.8390 (p90) cc_final: 0.8180 (p90) REVERT: H 528 GLU cc_start: 0.7564 (pm20) cc_final: 0.7260 (pm20) REVERT: H 550 ARG cc_start: 0.7497 (mmt90) cc_final: 0.7231 (mmt90) REVERT: I 46 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7990 (p0) REVERT: I 365 HIS cc_start: 0.8423 (m170) cc_final: 0.8125 (m-70) REVERT: I 406 VAL cc_start: 0.7986 (t) cc_final: 0.7758 (p) REVERT: I 466 LYS cc_start: 0.8131 (mttt) cc_final: 0.7788 (mtpt) REVERT: I 528 GLU cc_start: 0.7591 (pm20) cc_final: 0.7305 (pm20) outliers start: 34 outliers final: 29 residues processed: 409 average time/residue: 0.7985 time to fit residues: 468.6352 Evaluate side-chains 422 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 390 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain G residue 537 SER Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 537 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 0.0970 chunk 139 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17628 Z= 0.201 Angle : 0.515 10.189 23896 Z= 0.259 Chirality : 0.042 0.161 2640 Planarity : 0.005 0.070 3060 Dihedral : 5.346 58.068 2475 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.69 % Allowed : 13.79 % Favored : 84.51 % 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: 1.04 (0.19), residues: 2092 helix: 1.58 (0.18), residues: 888 sheet: -0.26 (0.28), residues: 356 loop : 0.33 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP G 387 HIS 0.005 0.001 HIS H 116 PHE 0.013 0.001 PHE G 163 TYR 0.016 0.001 TYR G 468 ARG 0.012 0.001 ARG G 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 427 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 395 time to evaluate : 2.751 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: C 49 THR cc_start: 0.7967 (m) cc_final: 0.7644 (p) REVERT: C 161 GLU cc_start: 0.7536 (tp30) cc_final: 0.6983 (tp30) REVERT: C 240 GLN cc_start: 0.7851 (mt0) cc_final: 0.7604 (mt0) REVERT: C 271 ASP cc_start: 0.7501 (t0) cc_final: 0.7239 (t0) REVERT: C 292 TYR cc_start: 0.8366 (t80) cc_final: 0.8097 (t80) REVERT: C 293 ASP cc_start: 0.6388 (m-30) cc_final: 0.6100 (m-30) REVERT: C 365 HIS cc_start: 0.8268 (m90) cc_final: 0.8008 (m170) REVERT: C 376 ARG cc_start: 0.6468 (ttp80) cc_final: 0.6087 (ttp80) REVERT: C 466 LYS cc_start: 0.7940 (mttt) cc_final: 0.7730 (mttm) REVERT: G 103 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7525 (tppp) REVERT: G 376 ARG cc_start: 0.6335 (ttp-170) cc_final: 0.5916 (ttp80) REVERT: G 402 MET cc_start: 0.7600 (tmm) cc_final: 0.7147 (tmm) REVERT: G 406 VAL cc_start: 0.8079 (t) cc_final: 0.7784 (p) REVERT: G 452 LYS cc_start: 0.8177 (tttt) cc_final: 0.7469 (ttpt) REVERT: G 466 LYS cc_start: 0.8098 (mttt) cc_final: 0.7875 (mttm) REVERT: G 481 ARG cc_start: 0.6177 (mtt180) cc_final: 0.5921 (mtm180) REVERT: G 528 GLU cc_start: 0.7540 (pm20) cc_final: 0.7220 (pm20) REVERT: G 550 ARG cc_start: 0.7518 (mmt90) cc_final: 0.7266 (mmt90) REVERT: H 84 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7714 (mttt) REVERT: H 103 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7528 (tppp) REVERT: H 232 MET cc_start: 0.7144 (mtp) cc_final: 0.6742 (mmt) REVERT: H 365 HIS cc_start: 0.8389 (m170) cc_final: 0.8145 (m-70) REVERT: H 376 ARG cc_start: 0.6252 (ttp-170) cc_final: 0.5813 (ttp80) REVERT: H 383 GLN cc_start: 0.7535 (mt0) cc_final: 0.7039 (mt0) REVERT: H 406 VAL cc_start: 0.8030 (t) cc_final: 0.7812 (p) REVERT: H 452 LYS cc_start: 0.8147 (tttt) cc_final: 0.7873 (tttt) REVERT: H 466 LYS cc_start: 0.8127 (mttt) cc_final: 0.7891 (mttm) REVERT: H 528 GLU cc_start: 0.7591 (pm20) cc_final: 0.7278 (pm20) REVERT: H 550 ARG cc_start: 0.7501 (mmt90) cc_final: 0.7231 (mmt90) REVERT: I 46 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7924 (p0) REVERT: I 294 ARG cc_start: 0.7243 (ptp90) cc_final: 0.7002 (mtm110) REVERT: I 365 HIS cc_start: 0.8424 (m170) cc_final: 0.8121 (m-70) REVERT: I 406 VAL cc_start: 0.7924 (t) cc_final: 0.7701 (p) REVERT: I 466 LYS cc_start: 0.8131 (mttt) cc_final: 0.7832 (mttp) REVERT: I 528 GLU cc_start: 0.7592 (pm20) cc_final: 0.7282 (pm20) outliers start: 32 outliers final: 28 residues processed: 409 average time/residue: 0.8359 time to fit residues: 493.6652 Evaluate side-chains 423 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 392 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain G residue 537 SER Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 537 SER Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 36 SER Chi-restraints excluded: chain I residue 46 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 537 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.160870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.130014 restraints weight = 54035.624| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.99 r_work: 0.3226 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17628 Z= 0.222 Angle : 0.523 9.042 23896 Z= 0.262 Chirality : 0.042 0.159 2640 Planarity : 0.005 0.065 3060 Dihedral : 5.229 43.813 2472 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.74 % Allowed : 13.79 % Favored : 84.46 % 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: 1.03 (0.19), residues: 2092 helix: 1.57 (0.18), residues: 888 sheet: -0.25 (0.27), residues: 356 loop : 0.31 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 387 HIS 0.005 0.001 HIS G 116 PHE 0.016 0.001 PHE I 163 TYR 0.018 0.001 TYR C 468 ARG 0.012 0.001 ARG I 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10233.13 seconds wall clock time: 182 minutes 22.02 seconds (10942.02 seconds total)