Starting phenix.real_space_refine on Fri Mar 22 19:02:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mig_23850/03_2024/7mig_23850_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mig_23850/03_2024/7mig_23850.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mig_23850/03_2024/7mig_23850_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mig_23850/03_2024/7mig_23850_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mig_23850/03_2024/7mig_23850_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mig_23850/03_2024/7mig_23850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mig_23850/03_2024/7mig_23850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mig_23850/03_2024/7mig_23850_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mig_23850/03_2024/7mig_23850_trim_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.263 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 96 5.16 5 C 10964 2.51 5 N 2944 2.21 5 O 3220 1.98 5 F 12 1.80 5 H 17020 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 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 PHE 409": "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 "A TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 507": "OE1" <-> "OE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 40": "OD1" <-> "OD2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 287": "OE1" <-> "OE2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "E TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 356": "OE1" <-> "OE2" Residue "E PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "E PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E GLU 507": "OE1" <-> "OE2" Residue "E GLU 510": "OE1" <-> "OE2" Residue "E TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34272 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 8484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8484 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "A" Number of atoms: 8484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8484 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "B" Number of atoms: 8484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8484 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "E" Number of atoms: 8484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8484 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Inner-chain residues flagged as termini: ['pdbres="GLN C 602 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Inner-chain residues flagged as termini: ['pdbres="GLN B 602 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Time building chain proxies: 15.35, per 1000 atoms: 0.45 Number of scatterers: 34272 At special positions: 0 Unit cell: (124.95, 135.45, 85.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 96 16.00 P 12 15.00 Mg 4 11.99 F 12 9.00 O 3220 8.00 N 2944 7.00 C 10964 6.00 H 17020 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 A 218 " - pdb=" SG CYS A 243 " distance=2.05 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 243 " distance=2.05 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 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: 29.36 Conformation dependent library (CDL) restraints added in 3.7 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: 96 helices and 16 sheets defined 40.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 69 through 77 Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 113 through 129 removed outlier: 7.130A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 169 removed outlier: 4.623A 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 260 Proline residue: C 254 - end of helix removed outlier: 3.507A pdb=" N LEU C 257 " --> pdb=" O PRO C 254 " (cutoff:3.500A) 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 339 through 342 No H-bonds generated for 'chain 'C' and resid 339 through 342' Processing helix chain 'C' and resid 344 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 551 through 554 No H-bonds generated for 'chain 'C' and resid 551 through 554' Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 113 through 129 removed outlier: 7.129A pdb=" N THR A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 169 removed outlier: 4.624A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 250 through 260 Proline residue: A 254 - end of helix removed outlier: 3.507A pdb=" N LEU A 257 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 400 through 412 Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 527 through 530 Processing helix chain 'A' and resid 538 through 547 Processing helix chain 'A' and resid 551 through 554 No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'B' and resid 16 through 29 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'B' and resid 113 through 129 removed outlier: 7.130A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 169 removed outlier: 4.622A pdb=" N PHE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 250 through 260 Proline residue: B 254 - end of helix removed outlier: 3.507A pdb=" N LEU B 257 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 378 through 390 Processing helix chain 'B' and resid 400 through 412 Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 527 through 530 Processing helix chain 'B' and resid 538 through 547 Processing helix chain 'B' and resid 551 through 554 No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'E' and resid 16 through 29 Processing helix chain 'E' and resid 69 through 77 Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'E' and resid 113 through 129 removed outlier: 7.129A pdb=" N THR E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 removed outlier: 4.623A pdb=" N PHE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 238 through 240 No H-bonds generated for 'chain 'E' and resid 238 through 240' Processing helix chain 'E' and resid 250 through 260 Proline residue: E 254 - end of helix removed outlier: 3.507A pdb=" N LEU E 257 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 269 Processing helix chain 'E' and resid 283 through 294 Processing helix chain 'E' and resid 315 through 328 Processing helix chain 'E' and resid 339 through 342 No H-bonds generated for 'chain 'E' and resid 339 through 342' Processing helix chain 'E' and resid 344 through 349 Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 378 through 390 Processing helix chain 'E' and resid 400 through 412 Processing helix chain 'E' and resid 463 through 467 Processing helix chain 'E' and resid 488 through 490 No H-bonds generated for 'chain 'E' and resid 488 through 490' Processing helix chain 'E' and resid 527 through 530 Processing helix chain 'E' and resid 538 through 547 Processing helix chain 'E' and resid 551 through 554 No H-bonds generated for 'chain 'E' and resid 551 through 554' Processing sheet with id= A, first strand: chain 'C' and resid 241 through 244 removed outlier: 6.329A pdb=" N VAL C 214 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL C 244 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N CYS C 216 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY C 8 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 331 through 338 removed outlier: 7.008A pdb=" N GLY C 366 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL C 304 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 368 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL C 369 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 6.613A 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 'A' and resid 241 through 244 removed outlier: 6.329A pdb=" N VAL A 214 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL A 244 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N CYS A 216 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR A 3 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 178 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU A 5 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL A 180 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR A 7 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LEU A 182 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY A 8 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 331 through 338 removed outlier: 7.008A pdb=" N GLY A 366 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL A 304 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU A 368 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL A 369 " --> pdb=" O PRO A 394 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 396 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 433 through 435 Processing sheet with id= H, first strand: chain 'A' and resid 473 through 480 Processing sheet with id= I, first strand: chain 'B' and resid 241 through 244 removed outlier: 6.330A pdb=" N VAL B 214 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 244 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N CYS B 216 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR B 3 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE B 178 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU B 5 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 180 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR B 7 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LEU B 182 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY B 8 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 331 through 338 removed outlier: 7.008A pdb=" N GLY B 366 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL B 304 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 368 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL B 369 " --> pdb=" O PRO B 394 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 396 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 433 through 435 Processing sheet with id= L, first strand: chain 'B' and resid 473 through 480 Processing sheet with id= M, first strand: chain 'E' and resid 241 through 244 removed outlier: 6.329A pdb=" N VAL E 214 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL E 244 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N CYS E 216 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR E 3 " --> pdb=" O CYS E 176 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE E 178 " --> pdb=" O TYR E 3 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU E 5 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 180 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR E 7 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LEU E 182 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY E 8 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 331 through 338 removed outlier: 7.007A pdb=" N GLY E 366 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 304 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU E 368 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL E 369 " --> pdb=" O PRO E 394 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 396 " --> pdb=" O VAL E 369 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 433 through 435 Processing sheet with id= P, first strand: chain 'E' and resid 473 through 480 648 hydrogen bonds defined for protein. 1860 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.64 Time building geometry restraints manager: 30.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.15: 16984 1.15 - 1.33: 3773 1.33 - 1.52: 6665 1.52 - 1.70: 7074 1.70 - 1.89: 152 Bond restraints: 34648 Sorted by residual: bond pdb=" C2' UTP E 602 " pdb=" C3' UTP E 602 " ideal model delta sigma weight residual 1.301 1.527 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C2' UTP A 602 " pdb=" C3' UTP A 602 " ideal model delta sigma weight residual 1.301 1.527 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C2' UTP B 604 " pdb=" C3' UTP B 604 " ideal model delta sigma weight residual 1.301 1.527 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C2' UTP C 604 " pdb=" C3' UTP C 604 " ideal model delta sigma weight residual 1.301 1.526 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' UTP C 604 " pdb=" O4' UTP C 604 " ideal model delta sigma weight residual 1.553 1.391 0.162 2.00e-02 2.50e+03 6.58e+01 ... (remaining 34643 not shown) Histogram of bond angle deviations from ideal: 59.53 - 75.05: 12 75.05 - 90.56: 8 90.56 - 106.08: 1135 106.08 - 121.59: 56083 121.59 - 137.11: 5478 Bond angle restraints: 62716 Sorted by residual: angle pdb=" N PRO B 538 " pdb=" CA PRO B 538 " pdb=" C PRO B 538 " ideal model delta sigma weight residual 110.70 119.96 -9.26 1.22e+00 6.72e-01 5.77e+01 angle pdb=" N PRO E 538 " pdb=" CA PRO E 538 " pdb=" C PRO E 538 " ideal model delta sigma weight residual 110.70 119.95 -9.25 1.22e+00 6.72e-01 5.74e+01 angle pdb=" N PRO C 538 " pdb=" CA PRO C 538 " pdb=" C PRO C 538 " ideal model delta sigma weight residual 110.70 119.94 -9.24 1.22e+00 6.72e-01 5.74e+01 angle pdb=" N PRO A 538 " pdb=" CA PRO A 538 " pdb=" C PRO A 538 " ideal model delta sigma weight residual 110.70 119.90 -9.20 1.22e+00 6.72e-01 5.69e+01 angle pdb=" CA LEU B 497 " pdb=" N LEU B 497 " pdb=" H LEU B 497 " ideal model delta sigma weight residual 114.00 134.76 -20.76 3.00e+00 1.11e-01 4.79e+01 ... (remaining 62711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14229 17.94 - 35.89: 1106 35.89 - 53.83: 522 53.83 - 71.78: 354 71.78 - 89.72: 53 Dihedral angle restraints: 16264 sinusoidal: 9048 harmonic: 7216 Sorted by residual: dihedral pdb=" CB CYS E 218 " pdb=" SG CYS E 218 " pdb=" SG CYS E 243 " pdb=" CB CYS E 243 " ideal model delta sinusoidal sigma weight residual 93.00 -179.28 -87.72 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 243 " pdb=" CB CYS B 243 " ideal model delta sinusoidal sigma weight residual 93.00 -179.30 -87.70 1 1.00e+01 1.00e-02 9.21e+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 93.00 -179.31 -87.69 1 1.00e+01 1.00e-02 9.21e+01 ... (remaining 16261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1584 0.100 - 0.200: 794 0.200 - 0.300: 214 0.300 - 0.400: 36 0.400 - 0.500: 8 Chirality restraints: 2636 Sorted by residual: 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 2.02 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" C1' UTP E 602 " pdb=" C2' UTP E 602 " pdb=" N1 UTP E 602 " pdb=" O4' UTP E 602 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C1' UTP A 602 " pdb=" C2' UTP A 602 " pdb=" N1 UTP A 602 " pdb=" O4' UTP A 602 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.50 2.00e-01 2.50e+01 6.18e+00 ... (remaining 2633 not shown) Planarity restraints: 5044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 387 " -0.128 2.00e-02 2.50e+03 7.45e-02 2.22e+02 pdb=" CG TRP B 387 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 387 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP B 387 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 387 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP B 387 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 387 " 0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 387 " -0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 387 " 0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP B 387 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP B 387 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TRP B 387 " 0.168 2.00e-02 2.50e+03 pdb=" HE3 TRP B 387 " 0.059 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 387 " -0.097 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 387 " 0.102 2.00e-02 2.50e+03 pdb=" HH2 TRP B 387 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 387 " 0.128 2.00e-02 2.50e+03 7.44e-02 2.21e+02 pdb=" CG TRP A 387 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 387 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 387 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 387 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP A 387 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 387 " -0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 387 " 0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 387 " -0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP A 387 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP A 387 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 TRP A 387 " -0.166 2.00e-02 2.50e+03 pdb=" HE3 TRP A 387 " -0.059 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 387 " 0.097 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 387 " -0.102 2.00e-02 2.50e+03 pdb=" HH2 TRP A 387 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 387 " -0.128 2.00e-02 2.50e+03 7.44e-02 2.21e+02 pdb=" CG TRP C 387 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP C 387 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP C 387 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 387 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP C 387 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 387 " 0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 387 " -0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 387 " 0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP C 387 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP C 387 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TRP C 387 " 0.167 2.00e-02 2.50e+03 pdb=" HE3 TRP C 387 " 0.060 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 387 " -0.097 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 387 " 0.101 2.00e-02 2.50e+03 pdb=" HH2 TRP C 387 " -0.083 2.00e-02 2.50e+03 ... (remaining 5041 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.04: 1464 2.04 - 2.68: 46299 2.68 - 3.32: 110296 3.32 - 3.96: 148275 3.96 - 4.60: 218348 Nonbonded interactions: 524682 Sorted by model distance: nonbonded pdb=" HB ILE A 43 " pdb="HG23 VAL E 111 " model vdw 1.405 2.440 nonbonded pdb=" HB ILE A 43 " pdb="HG22 VAL E 111 " model vdw 1.406 2.440 nonbonded pdb="HG23 VAL A 111 " pdb=" HB ILE E 43 " model vdw 1.408 2.440 nonbonded pdb="HG22 VAL A 111 " pdb=" HB ILE E 43 " model vdw 1.409 2.440 nonbonded pdb=" HB ILE C 43 " pdb="HG23 VAL B 111 " model vdw 1.422 2.440 ... (remaining 524677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 556) selection = (chain 'B' and resid 1 through 556) selection = (chain 'C' and resid 1 through 556) selection = (chain 'E' 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.570 Extract box with map and model: 7.540 Check model and map are aligned: 0.550 Set scattering table: 0.340 Process input model: 114.380 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.226 17628 Z= 0.943 Angle : 2.047 19.600 23904 Z= 1.337 Chirality : 0.122 0.500 2636 Planarity : 0.014 0.095 3044 Dihedral : 14.998 89.719 6672 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.63 % Favored : 95.98 % Rotamer: Outliers : 1.48 % Allowed : 6.55 % Favored : 91.97 % Cbeta Deviations : 0.61 % 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 (0.17), residues: 2092 helix: -1.17 (0.15), residues: 896 sheet: -1.17 (0.26), residues: 344 loop : -0.35 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.020 TRP E 285 HIS 0.022 0.005 HIS A 439 PHE 0.079 0.018 PHE B 50 TYR 0.075 0.017 TYR A 265 ARG 0.008 0.002 ARG A 76 *********************** 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 **************************** Evaluate side-chains 528 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 500 time to evaluate : 2.624 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: C 198 GLN cc_start: 0.7344 (mt0) cc_final: 0.7097 (mt0) REVERT: C 265 TYR cc_start: 0.8289 (t80) cc_final: 0.8069 (t80) REVERT: C 335 LYS cc_start: 0.8496 (mttm) cc_final: 0.8253 (mttt) REVERT: C 360 LYS cc_start: 0.7915 (mttt) cc_final: 0.7698 (mtmm) REVERT: C 466 LYS cc_start: 0.8264 (mttt) cc_final: 0.7942 (mtpp) REVERT: A 202 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7500 (ttp-170) REVERT: A 466 LYS cc_start: 0.8213 (mttt) cc_final: 0.7865 (mtmm) REVERT: B 198 GLN cc_start: 0.7259 (mt0) cc_final: 0.6926 (mt0) REVERT: B 322 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7340 (mm-30) REVERT: B 466 LYS cc_start: 0.8191 (mttt) cc_final: 0.7863 (mtpp) REVERT: E 322 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7324 (mm-30) REVERT: E 466 LYS cc_start: 0.8194 (mttt) cc_final: 0.7870 (mtpp) outliers start: 28 outliers final: 5 residues processed: 507 average time/residue: 2.4171 time to fit residues: 1391.6454 Evaluate side-chains 352 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 347 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain E residue 458 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17628 Z= 0.231 Angle : 0.623 5.736 23904 Z= 0.326 Chirality : 0.045 0.167 2636 Planarity : 0.005 0.046 3044 Dihedral : 9.086 78.797 2486 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 11.26 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2092 helix: 0.02 (0.16), residues: 956 sheet: -0.81 (0.27), residues: 344 loop : -0.31 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 358 HIS 0.007 0.002 HIS B 355 PHE 0.014 0.002 PHE B 163 TYR 0.014 0.002 TYR E 42 ARG 0.004 0.001 ARG B 127 *********************** 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 **************************** Evaluate side-chains 418 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 370 time to evaluate : 2.597 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: C 107 LEU cc_start: 0.8186 (mt) cc_final: 0.7912 (mt) REVERT: C 156 SER cc_start: 0.8809 (p) cc_final: 0.8541 (m) REVERT: C 228 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: C 240 GLN cc_start: 0.7837 (mt0) cc_final: 0.7554 (mt0) REVERT: C 259 GLU cc_start: 0.6723 (tm-30) cc_final: 0.6520 (tm-30) REVERT: C 265 TYR cc_start: 0.8404 (t80) cc_final: 0.8007 (t80) REVERT: C 360 LYS cc_start: 0.7993 (mttt) cc_final: 0.7783 (mtmm) REVERT: C 466 LYS cc_start: 0.8309 (mttt) cc_final: 0.8000 (mtpp) REVERT: C 550 ARG cc_start: 0.7154 (mmt180) cc_final: 0.6886 (mtt180) REVERT: A 107 LEU cc_start: 0.8248 (mt) cc_final: 0.8012 (mt) REVERT: A 240 GLN cc_start: 0.7787 (mt0) cc_final: 0.7432 (mt0) REVERT: A 259 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6610 (tm-30) REVERT: A 423 GLU cc_start: 0.7141 (tt0) cc_final: 0.6845 (tt0) REVERT: A 466 LYS cc_start: 0.8274 (mttt) cc_final: 0.7918 (mtmm) REVERT: A 550 ARG cc_start: 0.7179 (mmt180) cc_final: 0.6936 (mtt180) REVERT: B 156 SER cc_start: 0.8804 (p) cc_final: 0.8558 (m) REVERT: B 239 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6975 (mp0) REVERT: B 240 GLN cc_start: 0.7792 (mt0) cc_final: 0.7408 (mt0) REVERT: B 259 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6612 (tm-30) REVERT: B 423 GLU cc_start: 0.7128 (tt0) cc_final: 0.6843 (tt0) REVERT: B 466 LYS cc_start: 0.8268 (mttt) cc_final: 0.7947 (mtpp) REVERT: B 550 ARG cc_start: 0.7165 (mmt180) cc_final: 0.6909 (mtt180) REVERT: E 240 GLN cc_start: 0.7738 (mt0) cc_final: 0.7362 (mt0) REVERT: E 298 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7696 (p) REVERT: E 423 GLU cc_start: 0.7145 (tt0) cc_final: 0.6793 (tt0) REVERT: E 466 LYS cc_start: 0.8262 (mttt) cc_final: 0.7946 (mtpp) outliers start: 48 outliers final: 18 residues processed: 398 average time/residue: 2.6687 time to fit residues: 1195.4265 Evaluate side-chains 337 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 317 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 458 GLN 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: 2.9990 chunk 160 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS C 391 GLN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 HIS ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS E 391 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3978 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= 0.339 Angle : 0.616 6.199 23904 Z= 0.320 Chirality : 0.046 0.142 2636 Planarity : 0.006 0.059 3044 Dihedral : 8.771 78.792 2486 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.07 % Allowed : 13.32 % Favored : 83.62 % 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: -0.04 (0.19), residues: 2092 helix: 0.46 (0.17), residues: 896 sheet: -0.47 (0.27), residues: 340 loop : -0.17 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 124 HIS 0.010 0.002 HIS B 517 PHE 0.015 0.002 PHE B 163 TYR 0.017 0.002 TYR E 42 ARG 0.007 0.001 ARG C 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 **************************** Evaluate side-chains 429 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 371 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: C 107 LEU cc_start: 0.8431 (mt) cc_final: 0.8131 (mt) REVERT: C 123 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7224 (mt-10) REVERT: C 150 THR cc_start: 0.8680 (p) cc_final: 0.8448 (p) REVERT: C 157 MET cc_start: 0.7823 (mmt) cc_final: 0.7542 (mmm) REVERT: C 203 GLU cc_start: 0.7265 (tp30) cc_final: 0.6982 (tp30) REVERT: C 240 GLN cc_start: 0.8005 (mt0) cc_final: 0.7768 (mt0) REVERT: C 298 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7968 (p) REVERT: C 324 SER cc_start: 0.8918 (m) cc_final: 0.8668 (m) REVERT: C 333 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: C 360 LYS cc_start: 0.8034 (mttt) cc_final: 0.7753 (mtmm) REVERT: C 436 MET cc_start: 0.7385 (ttm) cc_final: 0.7110 (ttm) REVERT: C 466 LYS cc_start: 0.8385 (mttt) cc_final: 0.8064 (mtpp) REVERT: C 550 ARG cc_start: 0.7386 (mmt180) cc_final: 0.7132 (mtt180) REVERT: C 554 TYR cc_start: 0.8556 (t80) cc_final: 0.8312 (t80) REVERT: A 107 LEU cc_start: 0.8457 (mt) cc_final: 0.8183 (mt) REVERT: A 203 GLU cc_start: 0.7390 (tp30) cc_final: 0.7175 (tp30) REVERT: A 239 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6991 (mp0) REVERT: A 240 GLN cc_start: 0.8034 (mt0) cc_final: 0.7748 (mt0) REVERT: A 298 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7946 (p) REVERT: A 324 SER cc_start: 0.8904 (m) cc_final: 0.8667 (m) REVERT: A 333 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7083 (tt0) REVERT: A 466 LYS cc_start: 0.8329 (mttt) cc_final: 0.8023 (mtmm) REVERT: A 554 TYR cc_start: 0.8547 (t80) cc_final: 0.8307 (t80) REVERT: B 33 HIS cc_start: 0.8032 (m90) cc_final: 0.7749 (m90) REVERT: B 107 LEU cc_start: 0.8436 (mt) cc_final: 0.8122 (mt) REVERT: B 141 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: B 239 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6981 (mp0) REVERT: B 240 GLN cc_start: 0.7987 (mt0) cc_final: 0.7773 (mt0) REVERT: B 298 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7961 (p) REVERT: B 324 SER cc_start: 0.8900 (m) cc_final: 0.8666 (m) REVERT: B 333 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: B 436 MET cc_start: 0.7313 (ttm) cc_final: 0.7032 (ttm) REVERT: B 466 LYS cc_start: 0.8357 (mttt) cc_final: 0.8044 (mtmm) REVERT: B 483 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6964 (mm-30) REVERT: B 550 ARG cc_start: 0.7429 (mmt180) cc_final: 0.7149 (mtt180) REVERT: E 107 LEU cc_start: 0.8434 (mt) cc_final: 0.8129 (mt) REVERT: E 141 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7447 (mt0) REVERT: E 239 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6998 (mp0) REVERT: E 240 GLN cc_start: 0.8002 (mt0) cc_final: 0.7763 (mt0) REVERT: E 298 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7956 (p) REVERT: E 324 SER cc_start: 0.8903 (m) cc_final: 0.8669 (m) REVERT: E 333 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: E 436 MET cc_start: 0.7370 (ttm) cc_final: 0.7169 (ttm) REVERT: E 466 LYS cc_start: 0.8327 (mttt) cc_final: 0.8015 (mtmm) REVERT: E 554 TYR cc_start: 0.8560 (t80) cc_final: 0.8349 (t80) outliers start: 58 outliers final: 24 residues processed: 407 average time/residue: 2.4208 time to fit residues: 1121.4062 Evaluate side-chains 375 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 341 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 458 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 0.0770 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 177 ASN ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 GLN A 33 HIS A 177 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17628 Z= 0.219 Angle : 0.526 5.434 23904 Z= 0.270 Chirality : 0.042 0.131 2636 Planarity : 0.005 0.056 3044 Dihedral : 7.874 77.367 2486 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.59 % Allowed : 15.43 % Favored : 81.98 % 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: 0.37 (0.19), residues: 2092 helix: 0.89 (0.18), residues: 904 sheet: -0.40 (0.27), residues: 340 loop : -0.01 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.005 0.001 HIS C 355 PHE 0.010 0.001 PHE E 163 TYR 0.014 0.001 TYR E 42 ARG 0.007 0.001 ARG A 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 **************************** Evaluate side-chains 398 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 349 time to evaluate : 2.746 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: C 107 LEU cc_start: 0.8374 (mt) cc_final: 0.8079 (mt) REVERT: C 141 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7426 (mt0) REVERT: C 157 MET cc_start: 0.7784 (mmt) cc_final: 0.7543 (mmm) REVERT: C 203 GLU cc_start: 0.7247 (tp30) cc_final: 0.7003 (tp30) REVERT: C 240 GLN cc_start: 0.8011 (mt0) cc_final: 0.7740 (mt0) REVERT: C 324 SER cc_start: 0.8905 (m) cc_final: 0.8652 (m) REVERT: C 360 LYS cc_start: 0.8033 (mttt) cc_final: 0.7775 (mtmm) REVERT: C 391 GLN cc_start: 0.7497 (mm-40) cc_final: 0.6862 (mp10) REVERT: C 466 LYS cc_start: 0.8358 (mttt) cc_final: 0.8044 (mtpp) REVERT: C 550 ARG cc_start: 0.7410 (mmt180) cc_final: 0.7143 (mtt180) REVERT: C 554 TYR cc_start: 0.8548 (t80) cc_final: 0.8334 (t80) REVERT: A 107 LEU cc_start: 0.8415 (mt) cc_final: 0.8120 (mt) REVERT: A 141 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7406 (mt0) REVERT: A 240 GLN cc_start: 0.8044 (mt0) cc_final: 0.7755 (mt0) REVERT: A 324 SER cc_start: 0.8880 (m) cc_final: 0.8630 (m) REVERT: A 436 MET cc_start: 0.7411 (ttm) cc_final: 0.7170 (ttm) REVERT: A 466 LYS cc_start: 0.8327 (mttt) cc_final: 0.8023 (mtmm) REVERT: A 554 TYR cc_start: 0.8520 (t80) cc_final: 0.8263 (t80) REVERT: B 33 HIS cc_start: 0.8125 (m90) cc_final: 0.7766 (m90) REVERT: B 107 LEU cc_start: 0.8375 (mt) cc_final: 0.8089 (mt) REVERT: B 141 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: B 157 MET cc_start: 0.7807 (mmt) cc_final: 0.7547 (mmm) REVERT: B 240 GLN cc_start: 0.8028 (mt0) cc_final: 0.7743 (mt0) REVERT: B 324 SER cc_start: 0.8884 (m) cc_final: 0.8631 (m) REVERT: B 466 LYS cc_start: 0.8327 (mttt) cc_final: 0.8021 (mtmm) REVERT: B 550 ARG cc_start: 0.7414 (mmt180) cc_final: 0.7166 (mtt180) REVERT: E 107 LEU cc_start: 0.8387 (mt) cc_final: 0.8097 (mt) REVERT: E 141 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: E 239 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6856 (mp0) REVERT: E 240 GLN cc_start: 0.8025 (mt0) cc_final: 0.7732 (mt0) REVERT: E 324 SER cc_start: 0.8899 (m) cc_final: 0.8658 (m) REVERT: E 391 GLN cc_start: 0.7447 (mm-40) cc_final: 0.6665 (mp10) REVERT: E 466 LYS cc_start: 0.8310 (mttt) cc_final: 0.8001 (mtmm) REVERT: E 554 TYR cc_start: 0.8510 (t80) cc_final: 0.8282 (t80) outliers start: 49 outliers final: 19 residues processed: 371 average time/residue: 2.4117 time to fit residues: 1022.1847 Evaluate side-chains 359 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 336 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 458 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN B 87 ASN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17628 Z= 0.245 Angle : 0.528 5.180 23904 Z= 0.268 Chirality : 0.043 0.153 2636 Planarity : 0.004 0.057 3044 Dihedral : 7.842 76.179 2486 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.54 % Allowed : 16.60 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 2092 helix: 1.06 (0.18), residues: 900 sheet: -0.33 (0.27), residues: 340 loop : 0.05 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.006 0.001 HIS E 355 PHE 0.010 0.001 PHE A 457 TYR 0.015 0.001 TYR E 42 ARG 0.007 0.001 ARG C 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 **************************** Evaluate side-chains 391 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 343 time to evaluate : 2.792 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: C 107 LEU cc_start: 0.8447 (mt) cc_final: 0.8139 (mt) REVERT: C 141 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7367 (mt0) REVERT: C 157 MET cc_start: 0.7804 (mmt) cc_final: 0.7515 (mmm) REVERT: C 203 GLU cc_start: 0.7232 (tp30) cc_final: 0.7008 (tp30) REVERT: C 220 ASN cc_start: 0.8287 (m110) cc_final: 0.8075 (m-40) REVERT: C 240 GLN cc_start: 0.8056 (mt0) cc_final: 0.7754 (mt0) REVERT: C 324 SER cc_start: 0.8899 (m) cc_final: 0.8654 (m) REVERT: C 333 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: C 360 LYS cc_start: 0.8024 (mttt) cc_final: 0.7758 (mtmm) REVERT: C 391 GLN cc_start: 0.7454 (mm-40) cc_final: 0.6845 (mp10) REVERT: C 436 MET cc_start: 0.7364 (ttm) cc_final: 0.7092 (ttm) REVERT: C 466 LYS cc_start: 0.8337 (mttt) cc_final: 0.8020 (mtpp) REVERT: C 481 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7293 (ttm-80) REVERT: C 550 ARG cc_start: 0.7465 (mmt180) cc_final: 0.7241 (mtt180) REVERT: C 554 TYR cc_start: 0.8587 (t80) cc_final: 0.8372 (t80) REVERT: A 107 LEU cc_start: 0.8477 (mt) cc_final: 0.8206 (mt) REVERT: A 324 SER cc_start: 0.8901 (m) cc_final: 0.8648 (m) REVERT: A 333 GLU cc_start: 0.7341 (tt0) cc_final: 0.7136 (tm-30) REVERT: A 391 GLN cc_start: 0.7535 (mm-40) cc_final: 0.6764 (mp10) REVERT: A 466 LYS cc_start: 0.8337 (mttt) cc_final: 0.8016 (mtmm) REVERT: A 554 TYR cc_start: 0.8570 (t80) cc_final: 0.8335 (t80) REVERT: B 33 HIS cc_start: 0.8145 (m90) cc_final: 0.7807 (m90) REVERT: B 107 LEU cc_start: 0.8408 (mt) cc_final: 0.8110 (mt) REVERT: B 141 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: B 157 MET cc_start: 0.7848 (mmt) cc_final: 0.7561 (mmm) REVERT: B 324 SER cc_start: 0.8903 (m) cc_final: 0.8648 (m) REVERT: B 341 ASP cc_start: 0.8176 (m-30) cc_final: 0.7756 (m-30) REVERT: B 466 LYS cc_start: 0.8343 (mttt) cc_final: 0.8040 (mtmm) REVERT: B 481 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7263 (ttm-80) REVERT: B 550 ARG cc_start: 0.7477 (mmt180) cc_final: 0.7221 (mtt180) REVERT: E 107 LEU cc_start: 0.8467 (mt) cc_final: 0.8158 (mt) REVERT: E 141 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: E 324 SER cc_start: 0.8898 (m) cc_final: 0.8651 (m) REVERT: E 333 GLU cc_start: 0.7344 (tt0) cc_final: 0.7142 (tm-30) REVERT: E 391 GLN cc_start: 0.7508 (mm-40) cc_final: 0.6822 (mp10) REVERT: E 466 LYS cc_start: 0.8344 (mttt) cc_final: 0.8019 (mtmm) REVERT: E 554 TYR cc_start: 0.8556 (t80) cc_final: 0.8327 (t80) outliers start: 48 outliers final: 21 residues processed: 375 average time/residue: 2.5018 time to fit residues: 1063.8898 Evaluate side-chains 357 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 330 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 458 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 17 optimal weight: 0.2980 chunk 67 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 HIS A 87 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17628 Z= 0.193 Angle : 0.500 4.946 23904 Z= 0.254 Chirality : 0.042 0.134 2636 Planarity : 0.004 0.050 3044 Dihedral : 7.467 74.195 2486 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.64 % Allowed : 16.70 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 2092 helix: 1.25 (0.18), residues: 900 sheet: -0.29 (0.27), residues: 340 loop : 0.10 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.004 0.001 HIS E 355 PHE 0.009 0.001 PHE C 163 TYR 0.013 0.001 TYR A 42 ARG 0.008 0.001 ARG A 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 **************************** Evaluate side-chains 390 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 340 time to evaluate : 3.060 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: C 107 LEU cc_start: 0.8443 (mt) cc_final: 0.8157 (mt) REVERT: C 141 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7302 (mt0) REVERT: C 157 MET cc_start: 0.7810 (mmt) cc_final: 0.7545 (mmm) REVERT: C 203 GLU cc_start: 0.7228 (tp30) cc_final: 0.6997 (tp30) REVERT: C 324 SER cc_start: 0.8862 (m) cc_final: 0.8633 (m) REVERT: C 333 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: C 360 LYS cc_start: 0.8019 (mttt) cc_final: 0.7752 (mtmm) REVERT: C 391 GLN cc_start: 0.7463 (mm-40) cc_final: 0.6941 (mp10) REVERT: C 466 LYS cc_start: 0.8319 (mttt) cc_final: 0.8011 (mtpp) REVERT: C 481 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7191 (ttm-80) REVERT: C 510 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: C 550 ARG cc_start: 0.7368 (mmt180) cc_final: 0.7161 (mtt180) REVERT: C 554 TYR cc_start: 0.8577 (t80) cc_final: 0.8322 (t80) REVERT: A 107 LEU cc_start: 0.8471 (mt) cc_final: 0.8222 (mt) REVERT: A 141 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: A 324 SER cc_start: 0.8845 (m) cc_final: 0.8607 (m) REVERT: A 333 GLU cc_start: 0.7371 (tt0) cc_final: 0.7135 (tm-30) REVERT: A 391 GLN cc_start: 0.7571 (mm-40) cc_final: 0.6761 (mp10) REVERT: A 466 LYS cc_start: 0.8329 (mttt) cc_final: 0.8006 (mtmm) REVERT: A 510 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6305 (mp0) REVERT: A 554 TYR cc_start: 0.8565 (t80) cc_final: 0.8277 (t80) REVERT: B 107 LEU cc_start: 0.8449 (mt) cc_final: 0.8160 (mt) REVERT: B 141 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: B 157 MET cc_start: 0.7804 (mmt) cc_final: 0.7531 (mmm) REVERT: B 240 GLN cc_start: 0.7828 (mt0) cc_final: 0.7450 (mt0) REVERT: B 324 SER cc_start: 0.8840 (m) cc_final: 0.8611 (m) REVERT: B 333 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: B 391 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7033 (mp10) REVERT: B 466 LYS cc_start: 0.8349 (mttt) cc_final: 0.8041 (mtmm) REVERT: B 481 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7226 (ttm-80) REVERT: B 510 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: B 550 ARG cc_start: 0.7468 (mmt180) cc_final: 0.7232 (mtt180) REVERT: E 107 LEU cc_start: 0.8460 (mt) cc_final: 0.8168 (mt) REVERT: E 141 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7408 (mt0) REVERT: E 240 GLN cc_start: 0.7746 (mt0) cc_final: 0.7475 (mt0) REVERT: E 324 SER cc_start: 0.8874 (m) cc_final: 0.8627 (m) REVERT: E 333 GLU cc_start: 0.7372 (tt0) cc_final: 0.7149 (tm-30) REVERT: E 391 GLN cc_start: 0.7545 (mm-40) cc_final: 0.6846 (mp10) REVERT: E 436 MET cc_start: 0.7380 (ttm) cc_final: 0.7159 (ttm) REVERT: E 466 LYS cc_start: 0.8323 (mttt) cc_final: 0.8000 (mtmm) REVERT: E 481 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7147 (ttm170) REVERT: E 510 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6291 (mp0) REVERT: E 535 LYS cc_start: 0.7509 (tttt) cc_final: 0.7178 (tttm) REVERT: E 554 TYR cc_start: 0.8552 (t80) cc_final: 0.8340 (t80) outliers start: 50 outliers final: 24 residues processed: 376 average time/residue: 2.4614 time to fit residues: 1058.7446 Evaluate side-chains 364 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 327 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 510 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17628 Z= 0.208 Angle : 0.534 6.436 23904 Z= 0.279 Chirality : 0.043 0.276 2636 Planarity : 0.004 0.050 3044 Dihedral : 7.458 72.686 2486 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.11 % Allowed : 17.39 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.19), residues: 2092 helix: 1.32 (0.18), residues: 900 sheet: -0.30 (0.27), residues: 340 loop : 0.15 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.005 0.001 HIS E 355 PHE 0.008 0.001 PHE B 163 TYR 0.013 0.001 TYR E 42 ARG 0.008 0.000 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 **************************** Evaluate side-chains 368 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 328 time to evaluate : 2.719 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: C 107 LEU cc_start: 0.8444 (mt) cc_final: 0.8171 (mt) REVERT: C 141 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7308 (mt0) REVERT: C 157 MET cc_start: 0.7814 (mmt) cc_final: 0.7553 (mmm) REVERT: C 203 GLU cc_start: 0.7254 (tp30) cc_final: 0.7008 (tp30) REVERT: C 240 GLN cc_start: 0.7908 (mt0) cc_final: 0.7408 (mt0) REVERT: C 324 SER cc_start: 0.8861 (m) cc_final: 0.8634 (m) REVERT: C 333 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: C 360 LYS cc_start: 0.7986 (mttt) cc_final: 0.7719 (mtmt) REVERT: C 391 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7042 (mp10) REVERT: C 466 LYS cc_start: 0.8318 (mttt) cc_final: 0.8007 (mtpp) REVERT: C 481 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7182 (ttm-80) REVERT: C 510 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: C 550 ARG cc_start: 0.7392 (mmt180) cc_final: 0.7183 (mtt180) REVERT: C 554 TYR cc_start: 0.8582 (t80) cc_final: 0.8352 (t80) REVERT: A 107 LEU cc_start: 0.8480 (mt) cc_final: 0.8208 (mt) REVERT: A 141 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7370 (mt0) REVERT: A 240 GLN cc_start: 0.7782 (mt0) cc_final: 0.7298 (mt0) REVERT: A 324 SER cc_start: 0.8843 (m) cc_final: 0.8606 (m) REVERT: A 333 GLU cc_start: 0.7349 (tt0) cc_final: 0.7092 (tm-30) REVERT: A 391 GLN cc_start: 0.7564 (mm-40) cc_final: 0.6851 (mp10) REVERT: A 466 LYS cc_start: 0.8323 (mttt) cc_final: 0.8008 (mtmm) REVERT: A 481 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7191 (ttm-80) REVERT: A 510 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: A 554 TYR cc_start: 0.8570 (t80) cc_final: 0.8308 (t80) REVERT: B 107 LEU cc_start: 0.8460 (mt) cc_final: 0.8179 (mt) REVERT: B 141 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: B 157 MET cc_start: 0.7777 (mmt) cc_final: 0.7522 (mmm) REVERT: B 324 SER cc_start: 0.8871 (m) cc_final: 0.8626 (m) REVERT: B 333 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: B 391 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7019 (mp10) REVERT: B 466 LYS cc_start: 0.8351 (mttt) cc_final: 0.8039 (mtmm) REVERT: B 481 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7209 (ttm-80) REVERT: B 510 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6311 (mp0) REVERT: B 550 ARG cc_start: 0.7461 (mmt180) cc_final: 0.7239 (mtt180) REVERT: E 107 LEU cc_start: 0.8469 (mt) cc_final: 0.8191 (mt) REVERT: E 141 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7404 (mt0) REVERT: E 324 SER cc_start: 0.8869 (m) cc_final: 0.8624 (m) REVERT: E 333 GLU cc_start: 0.7390 (tt0) cc_final: 0.7146 (tm-30) REVERT: E 391 GLN cc_start: 0.7530 (mm-40) cc_final: 0.6918 (mp10) REVERT: E 466 LYS cc_start: 0.8317 (mttt) cc_final: 0.7989 (mtmm) REVERT: E 481 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7223 (ttm-80) REVERT: E 510 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: E 535 LYS cc_start: 0.7591 (tttt) cc_final: 0.7271 (tttm) REVERT: E 554 TYR cc_start: 0.8555 (t80) cc_final: 0.8293 (t80) outliers start: 40 outliers final: 18 residues processed: 357 average time/residue: 2.4582 time to fit residues: 996.5253 Evaluate side-chains 356 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 324 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 510 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17628 Z= 0.226 Angle : 0.521 6.400 23904 Z= 0.268 Chirality : 0.043 0.230 2636 Planarity : 0.004 0.054 3044 Dihedral : 7.474 70.502 2486 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.38 % Allowed : 17.44 % Favored : 80.18 % 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: 1.29 (0.18), residues: 900 sheet: -0.38 (0.27), residues: 340 loop : 0.11 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 488 HIS 0.005 0.001 HIS C 355 PHE 0.009 0.001 PHE B 59 TYR 0.014 0.001 TYR E 525 ARG 0.008 0.001 ARG C 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 **************************** Evaluate side-chains 377 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 332 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 LEU cc_start: 0.8464 (mt) cc_final: 0.8190 (mt) REVERT: C 141 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7327 (mt0) REVERT: C 157 MET cc_start: 0.7808 (mmt) cc_final: 0.7547 (mmm) REVERT: C 203 GLU cc_start: 0.7148 (tp30) cc_final: 0.6919 (tp30) REVERT: C 240 GLN cc_start: 0.7783 (mt0) cc_final: 0.7429 (mt0) REVERT: C 324 SER cc_start: 0.8894 (m) cc_final: 0.8651 (m) REVERT: C 333 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: C 360 LYS cc_start: 0.7990 (mttt) cc_final: 0.7715 (mtmt) REVERT: C 391 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7058 (mp10) REVERT: C 466 LYS cc_start: 0.8334 (mttt) cc_final: 0.8011 (mtmm) REVERT: C 481 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7172 (ttm-80) REVERT: C 510 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6323 (mp0) REVERT: C 554 TYR cc_start: 0.8574 (t80) cc_final: 0.8342 (t80) REVERT: A 107 LEU cc_start: 0.8484 (mt) cc_final: 0.8218 (mt) REVERT: A 141 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7373 (mt0) REVERT: A 324 SER cc_start: 0.8890 (m) cc_final: 0.8640 (m) REVERT: A 333 GLU cc_start: 0.7380 (tt0) cc_final: 0.7110 (tm-30) REVERT: A 391 GLN cc_start: 0.7588 (mm-40) cc_final: 0.6930 (mp10) REVERT: A 466 LYS cc_start: 0.8321 (mttt) cc_final: 0.8002 (mtmm) REVERT: A 481 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7232 (ttm-80) REVERT: A 510 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: A 554 TYR cc_start: 0.8580 (t80) cc_final: 0.8311 (t80) REVERT: B 107 LEU cc_start: 0.8471 (mt) cc_final: 0.8200 (mt) REVERT: B 141 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7429 (mt0) REVERT: B 157 MET cc_start: 0.7786 (mmt) cc_final: 0.7530 (mmm) REVERT: B 240 GLN cc_start: 0.7775 (mt0) cc_final: 0.7321 (mt0) REVERT: B 324 SER cc_start: 0.8891 (m) cc_final: 0.8647 (m) REVERT: B 333 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: B 391 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7032 (mp10) REVERT: B 466 LYS cc_start: 0.8315 (mttt) cc_final: 0.8015 (mtmm) REVERT: B 481 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7200 (ttm-80) REVERT: B 510 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6294 (mp0) REVERT: B 550 ARG cc_start: 0.7471 (mmt180) cc_final: 0.7259 (mtt180) REVERT: E 107 LEU cc_start: 0.8486 (mt) cc_final: 0.8211 (mt) REVERT: E 141 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7410 (mt0) REVERT: E 155 GLU cc_start: 0.7859 (mp0) cc_final: 0.7556 (mp0) REVERT: E 240 GLN cc_start: 0.7751 (mt0) cc_final: 0.7382 (mt0) REVERT: E 324 SER cc_start: 0.8873 (m) cc_final: 0.8619 (m) REVERT: E 333 GLU cc_start: 0.7388 (tt0) cc_final: 0.7131 (tm-30) REVERT: E 391 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7003 (mp10) REVERT: E 466 LYS cc_start: 0.8312 (mttt) cc_final: 0.7994 (mtmm) REVERT: E 481 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7234 (ttm-80) REVERT: E 510 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: E 554 TYR cc_start: 0.8561 (t80) cc_final: 0.8323 (t80) outliers start: 45 outliers final: 21 residues processed: 364 average time/residue: 2.4497 time to fit residues: 1013.9055 Evaluate side-chains 358 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 323 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 510 GLU 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: 2.9990 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 0.4980 chunk 180 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN B 165 GLN B 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17628 Z= 0.282 Angle : 0.542 6.354 23904 Z= 0.279 Chirality : 0.044 0.219 2636 Planarity : 0.005 0.051 3044 Dihedral : 7.674 67.868 2486 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.43 % Allowed : 17.55 % Favored : 80.02 % 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: 0.56 (0.19), residues: 2092 helix: 1.18 (0.18), residues: 900 sheet: -0.41 (0.27), residues: 340 loop : -0.01 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 488 HIS 0.007 0.001 HIS E 355 PHE 0.009 0.001 PHE E 163 TYR 0.014 0.001 TYR B 525 ARG 0.008 0.001 ARG C 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 **************************** Evaluate side-chains 376 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 330 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 LEU cc_start: 0.8494 (mt) cc_final: 0.8225 (mt) REVERT: C 141 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7388 (mt0) REVERT: C 157 MET cc_start: 0.7841 (mmt) cc_final: 0.7536 (mmm) REVERT: C 169 LYS cc_start: 0.8046 (tttt) cc_final: 0.7804 (tttt) REVERT: C 203 GLU cc_start: 0.7187 (tp30) cc_final: 0.6965 (tp30) REVERT: C 324 SER cc_start: 0.8905 (m) cc_final: 0.8660 (m) REVERT: C 333 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: C 360 LYS cc_start: 0.8015 (mttt) cc_final: 0.7744 (mtmt) REVERT: C 391 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7109 (mp10) REVERT: C 466 LYS cc_start: 0.8324 (mttt) cc_final: 0.7999 (mtmm) REVERT: C 481 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7285 (ttm-80) REVERT: C 510 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6334 (mp0) REVERT: C 554 TYR cc_start: 0.8567 (t80) cc_final: 0.8316 (t80) REVERT: A 107 LEU cc_start: 0.8520 (mt) cc_final: 0.8254 (mt) REVERT: A 141 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: A 324 SER cc_start: 0.8903 (m) cc_final: 0.8654 (m) REVERT: A 333 GLU cc_start: 0.7398 (tt0) cc_final: 0.7133 (tm-30) REVERT: A 391 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7089 (mp10) REVERT: A 466 LYS cc_start: 0.8313 (mttt) cc_final: 0.7996 (mtmm) REVERT: A 481 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7214 (ttm-80) REVERT: A 510 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: A 554 TYR cc_start: 0.8585 (t80) cc_final: 0.8362 (t80) REVERT: B 107 LEU cc_start: 0.8503 (mt) cc_final: 0.8236 (mt) REVERT: B 141 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7442 (mt0) REVERT: B 157 MET cc_start: 0.7781 (mmt) cc_final: 0.7557 (mmm) REVERT: B 324 SER cc_start: 0.8903 (m) cc_final: 0.8659 (m) REVERT: B 333 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: B 391 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7068 (mp10) REVERT: B 466 LYS cc_start: 0.8300 (mttt) cc_final: 0.7991 (mtmm) REVERT: B 481 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7231 (ttm-80) REVERT: B 510 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: B 550 ARG cc_start: 0.7451 (mmt180) cc_final: 0.7248 (mtt180) REVERT: E 107 LEU cc_start: 0.8511 (mt) cc_final: 0.8260 (mt) REVERT: E 141 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7432 (mt0) REVERT: E 155 GLU cc_start: 0.7885 (mp0) cc_final: 0.7553 (mp0) REVERT: E 172 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7798 (ttp80) REVERT: E 240 GLN cc_start: 0.7815 (mt0) cc_final: 0.7361 (mt0) REVERT: E 324 SER cc_start: 0.8900 (m) cc_final: 0.8651 (m) REVERT: E 333 GLU cc_start: 0.7411 (tt0) cc_final: 0.7163 (tm-30) REVERT: E 391 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7033 (mp10) REVERT: E 466 LYS cc_start: 0.8311 (mttt) cc_final: 0.7993 (mtmm) REVERT: E 481 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7319 (ttm-80) REVERT: E 510 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: E 554 TYR cc_start: 0.8583 (t80) cc_final: 0.8340 (t80) outliers start: 46 outliers final: 22 residues processed: 363 average time/residue: 2.6787 time to fit residues: 1094.4123 Evaluate side-chains 363 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 327 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 510 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 129 optimal weight: 0.0050 chunk 103 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 ASN A 177 ASN B 177 ASN E 177 ASN E 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17628 Z= 0.230 Angle : 0.525 7.236 23904 Z= 0.270 Chirality : 0.043 0.221 2636 Planarity : 0.005 0.097 3044 Dihedral : 7.414 65.577 2486 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.96 % Allowed : 18.45 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2092 helix: 1.23 (0.18), residues: 900 sheet: -0.47 (0.27), residues: 340 loop : 0.01 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 488 HIS 0.005 0.001 HIS E 355 PHE 0.008 0.001 PHE C 59 TYR 0.015 0.001 TYR B 525 ARG 0.012 0.001 ARG E 376 ********************** 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 **************************** Evaluate side-chains 369 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 332 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: C 107 LEU cc_start: 0.8501 (mt) cc_final: 0.8233 (mt) REVERT: C 141 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: C 157 MET cc_start: 0.7824 (mmt) cc_final: 0.7451 (mmm) REVERT: C 169 LYS cc_start: 0.8060 (tttt) cc_final: 0.7821 (tttt) REVERT: C 172 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7797 (ttp80) REVERT: C 203 GLU cc_start: 0.7168 (tp30) cc_final: 0.6950 (tp30) REVERT: C 324 SER cc_start: 0.8903 (m) cc_final: 0.8661 (m) REVERT: C 333 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: C 360 LYS cc_start: 0.8016 (mttt) cc_final: 0.7796 (mttp) REVERT: C 391 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7114 (mp10) REVERT: C 436 MET cc_start: 0.7427 (ttm) cc_final: 0.7188 (ttm) REVERT: C 466 LYS cc_start: 0.8309 (mttt) cc_final: 0.8021 (mtmm) REVERT: C 481 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7326 (ttm-80) REVERT: C 510 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: C 554 TYR cc_start: 0.8568 (t80) cc_final: 0.8321 (t80) REVERT: A 107 LEU cc_start: 0.8491 (mt) cc_final: 0.8230 (mt) REVERT: A 141 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: A 240 GLN cc_start: 0.7733 (mt0) cc_final: 0.7480 (mt0) REVERT: A 324 SER cc_start: 0.8903 (m) cc_final: 0.8655 (m) REVERT: A 333 GLU cc_start: 0.7394 (tt0) cc_final: 0.7122 (tm-30) REVERT: A 391 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7082 (mp10) REVERT: A 466 LYS cc_start: 0.8308 (mttt) cc_final: 0.7985 (mtmm) REVERT: A 481 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7172 (ttm-80) REVERT: A 510 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: A 554 TYR cc_start: 0.8585 (t80) cc_final: 0.8319 (t80) REVERT: B 107 LEU cc_start: 0.8513 (mt) cc_final: 0.8243 (mt) REVERT: B 141 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: B 157 MET cc_start: 0.7786 (mmt) cc_final: 0.7564 (mmm) REVERT: B 240 GLN cc_start: 0.7660 (mt0) cc_final: 0.7243 (mt0) REVERT: B 324 SER cc_start: 0.8896 (m) cc_final: 0.8652 (m) REVERT: B 333 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: B 391 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7081 (mp10) REVERT: B 466 LYS cc_start: 0.8293 (mttt) cc_final: 0.7993 (mtmm) REVERT: B 481 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7201 (ttm-80) REVERT: B 510 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: E 107 LEU cc_start: 0.8513 (mt) cc_final: 0.8265 (mt) REVERT: E 141 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7405 (mt0) REVERT: E 155 GLU cc_start: 0.7860 (mp0) cc_final: 0.7531 (mp0) REVERT: E 172 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7794 (ttp80) REVERT: E 240 GLN cc_start: 0.7802 (mt0) cc_final: 0.7423 (mt0) REVERT: E 324 SER cc_start: 0.8894 (m) cc_final: 0.8647 (m) REVERT: E 333 GLU cc_start: 0.7375 (tt0) cc_final: 0.7116 (tm-30) REVERT: E 391 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7023 (mp10) REVERT: E 466 LYS cc_start: 0.8301 (mttt) cc_final: 0.7986 (mtmm) REVERT: E 481 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7358 (ttm-80) REVERT: E 510 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6366 (mp0) REVERT: E 554 TYR cc_start: 0.8578 (t80) cc_final: 0.8351 (t80) outliers start: 37 outliers final: 16 residues processed: 359 average time/residue: 2.7422 time to fit residues: 1104.5566 Evaluate side-chains 360 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 330 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 458 GLN Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 510 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 172 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 ASN A 177 ASN B 177 ASN E 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.152189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.124687 restraints weight = 53114.089| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.70 r_work: 0.3142 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17628 Z= 0.183 Angle : 0.499 6.482 23904 Z= 0.255 Chirality : 0.042 0.183 2636 Planarity : 0.005 0.084 3044 Dihedral : 7.074 61.713 2486 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.85 % Allowed : 18.87 % Favored : 79.28 % 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: 0.77 (0.19), residues: 2092 helix: 1.38 (0.18), residues: 900 sheet: -0.47 (0.26), residues: 340 loop : 0.15 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 488 HIS 0.004 0.001 HIS E 355 PHE 0.008 0.001 PHE E 163 TYR 0.014 0.001 TYR B 525 ARG 0.011 0.000 ARG E 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15800.29 seconds wall clock time: 275 minutes 17.20 seconds (16517.20 seconds total)