Starting phenix.real_space_refine (version: dev) on Fri Feb 24 23:36:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd3_6632/02_2023/3jd3_6632_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd3_6632/02_2023/3jd3_6632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd3_6632/02_2023/3jd3_6632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd3_6632/02_2023/3jd3_6632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd3_6632/02_2023/3jd3_6632_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd3_6632/02_2023/3jd3_6632_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24006 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "B" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "C" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "D" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "E" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "F" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1B NAI A 603 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI A 603 " occ=0.35 residue: pdb=" C1B NAI B 603 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI B 603 " occ=0.35 residue: pdb=" C1B NAI C 601 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI C 601 " occ=0.35 residue: pdb=" C1B NAI D 603 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI D 603 " occ=0.35 residue: pdb=" C1B NAI E 603 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI E 603 " occ=0.35 residue: pdb=" C1B NAI F 601 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI F 601 " occ=0.35 Time building chain proxies: 13.50, per 1000 atoms: 0.56 Number of scatterers: 24006 At special positions: 0 Unit cell: (110.294, 116.67, 162.573, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 42 15.00 O 4626 8.00 N 4188 7.00 C 15036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.48 Conformation dependent library (CDL) restraints added in 3.5 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 25 sheets defined 50.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.695A pdb=" N PHE A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 17 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 51 removed outlier: 4.463A pdb=" N VAL A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) 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 101 through 118 Processing helix chain 'A' and resid 140 through 155 removed outlier: 3.806A pdb=" N ARG A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.564A pdb=" N TRP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.529A pdb=" N HIS A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.828A pdb=" N ARG A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 297 removed outlier: 4.154A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.971A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 removed outlier: 3.991A pdb=" N ASN A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLY A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 420 removed outlier: 3.586A pdb=" N TYR A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N MET A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER A 412 " --> pdb=" O HIS A 408 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 441 Processing helix chain 'A' and resid 445 through 471 removed outlier: 3.866A pdb=" N ALA A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 496 removed outlier: 3.509A pdb=" N ARG A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.695A pdb=" N PHE B 16 " --> pdb=" O MET B 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 17 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 51 removed outlier: 4.463A pdb=" N VAL B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) 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 101 through 118 Processing helix chain 'B' and resid 140 through 155 removed outlier: 3.806A pdb=" N ARG B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 154 " --> pdb=" O MET B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.564A pdb=" N TRP B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.529A pdb=" N HIS B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 225 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 233 No H-bonds generated for 'chain 'B' and resid 230 through 233' Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.828A pdb=" N ARG B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 297 removed outlier: 4.154A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.971A pdb=" N LYS B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.991A pdb=" N ASN B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLY B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL B 378 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 386 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 389 " --> pdb=" O TRP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 420 removed outlier: 3.586A pdb=" N TYR B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET B 411 " --> pdb=" O TYR B 407 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER B 412 " --> pdb=" O HIS B 408 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 445 through 471 removed outlier: 3.865A pdb=" N ALA B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 496 removed outlier: 3.508A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 31 removed outlier: 3.695A pdb=" N PHE C 16 " --> pdb=" O MET C 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 17 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 51 removed outlier: 4.463A pdb=" N VAL C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) 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 101 through 118 Processing helix chain 'C' and resid 140 through 155 removed outlier: 3.807A pdb=" N ARG C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 154 " --> pdb=" O MET C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 183 removed outlier: 3.565A pdb=" N TRP C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.529A pdb=" N HIS C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C 225 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 233 No H-bonds generated for 'chain 'C' and resid 230 through 233' Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 256 through 266 removed outlier: 3.827A pdb=" N ARG C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 297 removed outlier: 4.154A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.971A pdb=" N LYS C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 390 removed outlier: 3.991A pdb=" N ASN C 374 " --> pdb=" O ASP C 370 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 375 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 376 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL C 378 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 386 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 389 " --> pdb=" O TRP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 420 removed outlier: 3.586A pdb=" N TYR C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET C 411 " --> pdb=" O TYR C 407 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER C 412 " --> pdb=" O HIS C 408 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 441 Processing helix chain 'C' and resid 445 through 471 removed outlier: 3.865A pdb=" N ALA C 454 " --> pdb=" O HIS C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 496 removed outlier: 3.509A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 31 removed outlier: 3.695A pdb=" N PHE D 16 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE D 17 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 51 removed outlier: 4.464A pdb=" N VAL D 45 " --> pdb=" O LYS D 41 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 101 through 118 Processing helix chain 'D' and resid 140 through 155 removed outlier: 3.806A pdb=" N ARG D 147 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS D 154 " --> pdb=" O MET D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.564A pdb=" N TRP D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 214 through 226 removed outlier: 3.529A pdb=" N HIS D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 225 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 233 No H-bonds generated for 'chain 'D' and resid 230 through 233' Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 256 through 266 removed outlier: 3.829A pdb=" N ARG D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 297 removed outlier: 4.154A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.971A pdb=" N LYS D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 390 removed outlier: 3.991A pdb=" N ASN D 374 " --> pdb=" O ASP D 370 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLY D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL D 378 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 386 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 389 " --> pdb=" O TRP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 420 removed outlier: 3.586A pdb=" N TYR D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N MET D 411 " --> pdb=" O TYR D 407 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER D 412 " --> pdb=" O HIS D 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 441 Processing helix chain 'D' and resid 445 through 471 removed outlier: 3.865A pdb=" N ALA D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 496 removed outlier: 3.510A pdb=" N ARG D 491 " --> pdb=" O GLU D 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 31 removed outlier: 3.696A pdb=" N PHE E 16 " --> pdb=" O MET E 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE E 17 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 51 removed outlier: 4.464A pdb=" N VAL E 45 " --> pdb=" O LYS E 41 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) 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 101 through 118 Processing helix chain 'E' and resid 140 through 155 removed outlier: 3.806A pdb=" N ARG E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS E 154 " --> pdb=" O MET E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 183 removed outlier: 3.563A pdb=" N TRP E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 214 through 226 removed outlier: 3.529A pdb=" N HIS E 221 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN E 225 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 233 No H-bonds generated for 'chain 'E' and resid 230 through 233' Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 256 through 266 removed outlier: 3.828A pdb=" N ARG E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 297 removed outlier: 4.154A pdb=" N LEU E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 316 No H-bonds generated for 'chain 'E' and resid 314 through 316' Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 354 through 362 removed outlier: 3.971A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 390 removed outlier: 3.991A pdb=" N ASN E 374 " --> pdb=" O ASP E 370 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY E 377 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL E 378 " --> pdb=" O ASN E 374 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 386 " --> pdb=" O TYR E 382 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 389 " --> pdb=" O TRP E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 420 removed outlier: 3.586A pdb=" N TYR E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET E 411 " --> pdb=" O TYR E 407 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER E 412 " --> pdb=" O HIS E 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS E 420 " --> pdb=" O SER E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 441 Processing helix chain 'E' and resid 445 through 471 removed outlier: 3.865A pdb=" N ALA E 454 " --> pdb=" O HIS E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 496 removed outlier: 3.509A pdb=" N ARG E 491 " --> pdb=" O GLU E 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 31 removed outlier: 3.696A pdb=" N PHE F 16 " --> pdb=" O MET F 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE F 17 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 51 removed outlier: 4.464A pdb=" N VAL F 45 " --> pdb=" O LYS F 41 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG F 50 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 101 through 118 Processing helix chain 'F' and resid 140 through 155 removed outlier: 3.807A pdb=" N ARG F 147 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU F 152 " --> pdb=" O PHE F 148 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS F 154 " --> pdb=" O MET F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 183 removed outlier: 3.564A pdb=" N TRP F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 214 through 226 removed outlier: 3.529A pdb=" N HIS F 221 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN F 225 " --> pdb=" O HIS F 221 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 233 No H-bonds generated for 'chain 'F' and resid 230 through 233' Processing helix chain 'F' and resid 242 through 244 No H-bonds generated for 'chain 'F' and resid 242 through 244' Processing helix chain 'F' and resid 256 through 266 removed outlier: 3.828A pdb=" N ARG F 261 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE F 266 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 297 removed outlier: 4.154A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 354 through 362 removed outlier: 3.971A pdb=" N LYS F 358 " --> pdb=" O PRO F 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 390 removed outlier: 3.991A pdb=" N ASN F 374 " --> pdb=" O ASP F 370 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY F 376 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL F 378 " --> pdb=" O ASN F 374 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F 386 " --> pdb=" O TYR F 382 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU F 389 " --> pdb=" O TRP F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 420 removed outlier: 3.586A pdb=" N TYR F 407 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET F 411 " --> pdb=" O TYR F 407 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER F 412 " --> pdb=" O HIS F 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS F 420 " --> pdb=" O SER F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 441 Processing helix chain 'F' and resid 445 through 471 removed outlier: 3.865A pdb=" N ALA F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 496 removed outlier: 3.509A pdb=" N ARG F 491 " --> pdb=" O GLU F 487 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 57 through 61 removed outlier: 3.537A pdb=" N GLY A 77 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY A 124 " --> pdb=" O HIS A 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.803A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA A 127 " --> pdb=" O ARG A 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.641A pdb=" N VAL A 273 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.207A pdb=" N MET A 366 " --> pdb=" O ILE A 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 57 through 61 removed outlier: 3.537A pdb=" N GLY B 77 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY B 124 " --> pdb=" O HIS B 82 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.803A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA B 127 " --> pdb=" O ARG B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.641A pdb=" N VAL B 273 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 343 through 345 removed outlier: 6.206A pdb=" N MET B 366 " --> pdb=" O ILE B 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 57 through 61 removed outlier: 3.537A pdb=" N GLY C 77 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY C 124 " --> pdb=" O HIS C 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.803A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA C 127 " --> pdb=" O ARG C 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 272 through 275 removed outlier: 3.641A pdb=" N VAL C 273 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 278 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 343 through 345 removed outlier: 6.207A pdb=" N MET C 366 " --> pdb=" O ILE C 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 57 through 61 removed outlier: 3.536A pdb=" N GLY D 77 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY D 124 " --> pdb=" O HIS D 82 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.803A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA D 127 " --> pdb=" O ARG D 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 272 through 275 removed outlier: 3.640A pdb=" N VAL D 273 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 343 through 345 removed outlier: 6.206A pdb=" N MET D 366 " --> pdb=" O ILE D 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 57 through 61 removed outlier: 3.536A pdb=" N GLY E 77 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY E 124 " --> pdb=" O HIS E 82 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= S, first strand: chain 'E' and resid 163 through 167 removed outlier: 6.803A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA E 127 " --> pdb=" O ARG E 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 272 through 275 removed outlier: 3.642A pdb=" N VAL E 273 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 343 through 345 removed outlier: 6.207A pdb=" N MET E 366 " --> pdb=" O ILE E 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 57 through 61 removed outlier: 3.536A pdb=" N GLY F 77 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY F 124 " --> pdb=" O HIS F 82 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 163 through 167 removed outlier: 6.803A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA F 127 " --> pdb=" O ARG F 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 272 through 275 removed outlier: 3.641A pdb=" N VAL F 273 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 343 through 345 removed outlier: 6.207A pdb=" N MET F 366 " --> pdb=" O ILE F 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y 860 hydrogen bonds defined for protein. 2562 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: 8.01 Time building geometry restraints manager: 11.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7771 1.34 - 1.45: 3883 1.45 - 1.57: 12646 1.57 - 1.69: 72 1.69 - 1.80: 192 Bond restraints: 24564 Sorted by residual: bond pdb=" C3N NAI E 602 " pdb=" C7N NAI E 602 " ideal model delta sigma weight residual 1.473 1.577 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C3N NAI F 603 " pdb=" C7N NAI F 603 " ideal model delta sigma weight residual 1.473 1.577 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C3N NAI C 603 " pdb=" C7N NAI C 603 " ideal model delta sigma weight residual 1.473 1.577 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C3N NAI B 602 " pdb=" C7N NAI B 602 " ideal model delta sigma weight residual 1.473 1.576 -0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C3N NAI A 602 " pdb=" C7N NAI A 602 " ideal model delta sigma weight residual 1.473 1.576 -0.103 2.00e-02 2.50e+03 2.68e+01 ... (remaining 24559 not shown) Histogram of bond angle deviations from ideal: 94.64 - 102.94: 248 102.94 - 111.24: 10571 111.24 - 119.54: 10330 119.54 - 127.84: 11929 127.84 - 136.13: 240 Bond angle restraints: 33318 Sorted by residual: angle pdb=" O2A NAI E 602 " pdb=" PA NAI E 602 " pdb=" O5B NAI E 602 " ideal model delta sigma weight residual 105.34 121.04 -15.70 3.00e+00 1.11e-01 2.74e+01 angle pdb=" O2A NAI F 603 " pdb=" PA NAI F 603 " pdb=" O5B NAI F 603 " ideal model delta sigma weight residual 105.34 121.04 -15.70 3.00e+00 1.11e-01 2.74e+01 angle pdb=" O2A NAI C 603 " pdb=" PA NAI C 603 " pdb=" O5B NAI C 603 " ideal model delta sigma weight residual 105.34 121.03 -15.69 3.00e+00 1.11e-01 2.74e+01 angle pdb=" O2A NAI A 602 " pdb=" PA NAI A 602 " pdb=" O5B NAI A 602 " ideal model delta sigma weight residual 105.34 121.03 -15.69 3.00e+00 1.11e-01 2.74e+01 angle pdb=" O2A NAI B 602 " pdb=" PA NAI B 602 " pdb=" O5B NAI B 602 " ideal model delta sigma weight residual 105.34 121.02 -15.68 3.00e+00 1.11e-01 2.73e+01 ... (remaining 33313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 14370 35.85 - 71.70: 66 71.70 - 107.54: 12 107.54 - 143.39: 6 143.39 - 179.24: 12 Dihedral angle restraints: 14466 sinusoidal: 5988 harmonic: 8478 Sorted by residual: dihedral pdb=" C5' GTP A 601 " pdb=" O5' GTP A 601 " pdb=" PA GTP A 601 " pdb=" O3A GTP A 601 " ideal model delta sinusoidal sigma weight residual 69.27 -109.97 179.24 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP F 602 " pdb=" O5' GTP F 602 " pdb=" PA GTP F 602 " pdb=" O3A GTP F 602 " ideal model delta sinusoidal sigma weight residual 69.27 -109.97 179.23 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP C 602 " pdb=" O5' GTP C 602 " pdb=" PA GTP C 602 " pdb=" O3A GTP C 602 " ideal model delta sinusoidal sigma weight residual 69.27 -109.97 179.23 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 14463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3197 0.081 - 0.161: 367 0.161 - 0.242: 26 0.242 - 0.323: 16 0.323 - 0.403: 6 Chirality restraints: 3612 Sorted by residual: chirality pdb=" C3B NAI A 602 " pdb=" C2B NAI A 602 " pdb=" C4B NAI A 602 " pdb=" O3B NAI A 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.31 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" C3B NAI E 602 " pdb=" C2B NAI E 602 " pdb=" C4B NAI E 602 " pdb=" O3B NAI E 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.31 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C3B NAI B 602 " pdb=" C2B NAI B 602 " pdb=" C4B NAI B 602 " pdb=" O3B NAI B 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.31 -0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 3609 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1B NAI B 602 " -0.030 2.00e-02 2.50e+03 1.32e-02 4.78e+00 pdb=" C2A NAI B 602 " 0.007 2.00e-02 2.50e+03 pdb=" C4A NAI B 602 " 0.012 2.00e-02 2.50e+03 pdb=" C5A NAI B 602 " 0.006 2.00e-02 2.50e+03 pdb=" C6A NAI B 602 " -0.003 2.00e-02 2.50e+03 pdb=" C8A NAI B 602 " 0.011 2.00e-02 2.50e+03 pdb=" N1A NAI B 602 " -0.004 2.00e-02 2.50e+03 pdb=" N3A NAI B 602 " 0.010 2.00e-02 2.50e+03 pdb=" N6A NAI B 602 " -0.021 2.00e-02 2.50e+03 pdb=" N7A NAI B 602 " 0.011 2.00e-02 2.50e+03 pdb=" N9A NAI B 602 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NAI E 602 " -0.030 2.00e-02 2.50e+03 1.32e-02 4.77e+00 pdb=" C2A NAI E 602 " 0.007 2.00e-02 2.50e+03 pdb=" C4A NAI E 602 " 0.012 2.00e-02 2.50e+03 pdb=" C5A NAI E 602 " 0.006 2.00e-02 2.50e+03 pdb=" C6A NAI E 602 " -0.003 2.00e-02 2.50e+03 pdb=" C8A NAI E 602 " 0.010 2.00e-02 2.50e+03 pdb=" N1A NAI E 602 " -0.004 2.00e-02 2.50e+03 pdb=" N3A NAI E 602 " 0.010 2.00e-02 2.50e+03 pdb=" N6A NAI E 602 " -0.021 2.00e-02 2.50e+03 pdb=" N7A NAI E 602 " 0.011 2.00e-02 2.50e+03 pdb=" N9A NAI E 602 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NAI A 602 " 0.030 2.00e-02 2.50e+03 1.31e-02 4.74e+00 pdb=" C2A NAI A 602 " -0.007 2.00e-02 2.50e+03 pdb=" C4A NAI A 602 " -0.012 2.00e-02 2.50e+03 pdb=" C5A NAI A 602 " -0.006 2.00e-02 2.50e+03 pdb=" C6A NAI A 602 " 0.003 2.00e-02 2.50e+03 pdb=" C8A NAI A 602 " -0.010 2.00e-02 2.50e+03 pdb=" N1A NAI A 602 " 0.004 2.00e-02 2.50e+03 pdb=" N3A NAI A 602 " -0.010 2.00e-02 2.50e+03 pdb=" N6A NAI A 602 " 0.021 2.00e-02 2.50e+03 pdb=" N7A NAI A 602 " -0.012 2.00e-02 2.50e+03 pdb=" N9A NAI A 602 " -0.001 2.00e-02 2.50e+03 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 856 2.68 - 3.23: 26911 3.23 - 3.79: 38325 3.79 - 4.34: 54709 4.34 - 4.90: 84524 Nonbonded interactions: 205325 Sorted by model distance: nonbonded pdb=" OG1 THR D 272 " pdb=" O ILE D 280 " model vdw 2.125 2.440 nonbonded pdb=" OG1 THR A 272 " pdb=" O ILE A 280 " model vdw 2.125 2.440 nonbonded pdb=" OG1 THR F 272 " pdb=" O ILE F 280 " model vdw 2.125 2.440 nonbonded pdb=" OG1 THR C 272 " pdb=" O ILE C 280 " model vdw 2.125 2.440 nonbonded pdb=" OG1 THR E 272 " pdb=" O ILE E 280 " model vdw 2.125 2.440 ... (remaining 205320 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 6 through 501 or resid 603)) selection = (chain 'B' and (resid 6 through 501 or resid 603)) selection = (chain 'C' and (resid 6 through 501 or resid 603)) selection = (chain 'D' and (resid 6 through 501 or resid 603)) selection = (chain 'E' and (resid 6 through 501 or resid 603)) selection = (chain 'F' and (resid 6 through 501 or resid 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 114 5.16 5 C 15036 2.51 5 N 4188 2.21 5 O 4626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.35 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.990 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: 0.020 Extract box with map and model: 6.070 Check model and map are aligned: 0.390 Process input model: 61.960 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.011 0.104 24564 Z= 0.715 Angle : 1.017 15.703 33318 Z= 0.488 Chirality : 0.058 0.403 3612 Planarity : 0.005 0.053 4230 Dihedral : 11.398 179.239 9066 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -5.32 (0.12), residues: 2964 helix: -3.56 (0.10), residues: 1368 sheet: -3.50 (0.22), residues: 354 loop : -3.31 (0.15), residues: 1242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 2.987 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 outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.4057 time to fit residues: 311.3533 Evaluate side-chains 259 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 3.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 9.9990 chunk 222 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 81 GLN A 82 HIS A 85 HIS A 205 GLN A 225 ASN A 388 ASN A 463 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 81 GLN B 82 HIS B 193 ASN B 205 GLN B 225 ASN B 388 ASN B 463 GLN C 56 ASN C 81 GLN C 82 HIS C 205 GLN C 225 ASN C 388 ASN C 414 GLN C 437 GLN D 56 ASN D 81 GLN D 82 HIS D 85 HIS D 205 GLN D 225 ASN D 388 ASN D 463 GLN ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN E 81 GLN E 82 HIS E 193 ASN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN E 388 ASN E 463 GLN F 56 ASN F 81 GLN F 82 HIS F 205 GLN F 225 ASN F 388 ASN F 414 GLN F 437 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 24564 Z= 0.322 Angle : 0.692 6.707 33318 Z= 0.355 Chirality : 0.046 0.173 3612 Planarity : 0.005 0.041 4230 Dihedral : 14.185 175.230 3474 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.41 (0.14), residues: 2964 helix: -1.68 (0.12), residues: 1428 sheet: -3.02 (0.23), residues: 354 loop : -2.58 (0.17), residues: 1182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 343 time to evaluate : 3.008 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 outliers start: 57 outliers final: 38 residues processed: 382 average time/residue: 0.3616 time to fit residues: 221.5529 Evaluate side-chains 287 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 249 time to evaluate : 2.958 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2303 time to fit residues: 20.1421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 222 optimal weight: 40.0000 chunk 181 optimal weight: 50.0000 chunk 73 optimal weight: 8.9990 chunk 267 optimal weight: 20.0000 chunk 288 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 265 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS B 205 GLN B 437 GLN C 85 HIS ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN D 437 GLN ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS E 205 GLN E 437 GLN F 85 HIS ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 24564 Z= 0.254 Angle : 0.624 7.661 33318 Z= 0.317 Chirality : 0.044 0.155 3612 Planarity : 0.004 0.038 4230 Dihedral : 13.897 172.936 3474 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.43 (0.15), residues: 2964 helix: -0.72 (0.13), residues: 1470 sheet: -2.97 (0.23), residues: 366 loop : -2.19 (0.18), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 299 time to evaluate : 3.334 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 outliers start: 30 outliers final: 17 residues processed: 320 average time/residue: 0.3367 time to fit residues: 176.1317 Evaluate side-chains 246 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 229 time to evaluate : 2.786 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2883 time to fit residues: 12.4788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 179 optimal weight: 40.0000 chunk 268 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN D 330 GLN D 437 GLN ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 437 GLN F 330 GLN F 437 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 24564 Z= 0.244 Angle : 0.593 6.550 33318 Z= 0.300 Chirality : 0.043 0.151 3612 Planarity : 0.004 0.037 4230 Dihedral : 13.685 170.827 3474 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.79 (0.15), residues: 2964 helix: -0.19 (0.13), residues: 1464 sheet: -2.67 (0.23), residues: 360 loop : -1.88 (0.19), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 276 time to evaluate : 3.199 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 outliers start: 46 outliers final: 23 residues processed: 300 average time/residue: 0.3505 time to fit residues: 170.3977 Evaluate side-chains 272 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 249 time to evaluate : 3.036 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2400 time to fit residues: 14.4160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 117 optimal weight: 50.0000 chunk 242 optimal weight: 6.9990 chunk 196 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 145 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 437 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 330 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 ASN D 437 GLN ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN F 205 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 24564 Z= 0.270 Angle : 0.596 7.107 33318 Z= 0.302 Chirality : 0.043 0.155 3612 Planarity : 0.004 0.035 4230 Dihedral : 13.559 169.036 3474 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.49 (0.15), residues: 2964 helix: 0.07 (0.13), residues: 1452 sheet: -2.40 (0.24), residues: 360 loop : -1.79 (0.18), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 269 time to evaluate : 3.168 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 outliers start: 38 outliers final: 26 residues processed: 282 average time/residue: 0.3379 time to fit residues: 155.3638 Evaluate side-chains 269 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 2.841 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2316 time to fit residues: 15.0464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 284 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 chunk 131 optimal weight: 50.0000 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 24564 Z= 0.239 Angle : 0.580 6.727 33318 Z= 0.291 Chirality : 0.043 0.148 3612 Planarity : 0.004 0.037 4230 Dihedral : 13.195 164.864 3474 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.18 (0.15), residues: 2964 helix: 0.22 (0.13), residues: 1464 sheet: -1.96 (0.24), residues: 420 loop : -1.55 (0.19), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 262 time to evaluate : 3.200 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 outliers start: 22 outliers final: 13 residues processed: 276 average time/residue: 0.3540 time to fit residues: 158.8243 Evaluate side-chains 250 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 237 time to evaluate : 2.993 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2267 time to fit residues: 9.3779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 207 optimal weight: 0.1980 chunk 160 optimal weight: 0.0870 chunk 239 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 chunk 283 optimal weight: 0.0030 chunk 177 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 130 optimal weight: 50.0000 overall best weight: 2.2572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 HIS D 387 ASN ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 24564 Z= 0.160 Angle : 0.542 7.204 33318 Z= 0.272 Chirality : 0.042 0.173 3612 Planarity : 0.004 0.038 4230 Dihedral : 12.375 178.829 3474 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.81 (0.15), residues: 2964 helix: 0.53 (0.14), residues: 1464 sheet: -1.73 (0.24), residues: 420 loop : -1.42 (0.19), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 285 time to evaluate : 3.256 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 outliers start: 13 outliers final: 5 residues processed: 293 average time/residue: 0.3528 time to fit residues: 168.2018 Evaluate side-chains 233 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 228 time to evaluate : 3.134 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2275 time to fit residues: 6.2407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 180 optimal weight: 50.0000 chunk 193 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 26 optimal weight: 50.0000 chunk 222 optimal weight: 40.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 24564 Z= 0.283 Angle : 0.603 7.341 33318 Z= 0.306 Chirality : 0.043 0.171 3612 Planarity : 0.004 0.035 4230 Dihedral : 11.875 169.320 3474 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.92 (0.15), residues: 2964 helix: 0.43 (0.14), residues: 1464 sheet: -1.75 (0.24), residues: 420 loop : -1.46 (0.19), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 241 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 260 average time/residue: 0.3214 time to fit residues: 138.9428 Evaluate side-chains 249 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 223 time to evaluate : 3.036 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2140 time to fit residues: 14.2659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 9.9990 chunk 271 optimal weight: 30.0000 chunk 247 optimal weight: 0.0570 chunk 264 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 81 optimal weight: 50.0000 chunk 238 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 overall best weight: 1.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 24564 Z= 0.162 Angle : 0.550 8.644 33318 Z= 0.278 Chirality : 0.042 0.156 3612 Planarity : 0.004 0.037 4230 Dihedral : 11.311 169.450 3474 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.65 (0.16), residues: 2964 helix: 0.63 (0.14), residues: 1470 sheet: -1.61 (0.24), residues: 420 loop : -1.32 (0.19), residues: 1074 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 256 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 259 average time/residue: 0.3502 time to fit residues: 148.5371 Evaluate side-chains 235 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 3.093 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2348 time to fit residues: 4.6190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 30.0000 chunk 279 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 292 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 24 optimal weight: 30.0000 chunk 180 optimal weight: 0.6980 chunk 143 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24564 Z= 0.198 Angle : 0.565 7.915 33318 Z= 0.286 Chirality : 0.042 0.217 3612 Planarity : 0.004 0.036 4230 Dihedral : 11.273 175.697 3474 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.16), residues: 2964 helix: 0.69 (0.14), residues: 1470 sheet: -1.55 (0.25), residues: 420 loop : -1.30 (0.19), residues: 1074 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 250 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 252 average time/residue: 0.3495 time to fit residues: 143.7710 Evaluate side-chains 238 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 232 time to evaluate : 3.011 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2822 time to fit residues: 6.8517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.103870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.076963 restraints weight = 60634.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079799 restraints weight = 31275.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081582 restraints weight = 20671.138| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24564 Z= 0.189 Angle : 0.566 8.122 33318 Z= 0.287 Chirality : 0.042 0.207 3612 Planarity : 0.004 0.037 4230 Dihedral : 11.166 179.765 3474 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.42 (0.16), residues: 2964 helix: 0.91 (0.14), residues: 1422 sheet: -1.59 (0.24), residues: 426 loop : -1.21 (0.19), residues: 1116 =============================================================================== Job complete usr+sys time: 4382.62 seconds wall clock time: 83 minutes 53.52 seconds (5033.52 seconds total)