Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 21:16:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/04_2023/3jd2_6635_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/04_2023/3jd2_6635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/04_2023/3jd2_6635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/04_2023/3jd2_6635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/04_2023/3jd2_6635_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/04_2023/3jd2_6635_updated.pdb" } resolution = 3.3 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 114 5.16 5 C 14976 2.51 5 N 4158 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23814 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: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1B NAI A 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI A 602 " occ=0.35 residue: pdb=" C1B NAI B 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI B 602 " 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 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI D 602 " occ=0.35 residue: pdb=" C1B NAI E 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI E 602 " 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: 12.20, per 1000 atoms: 0.51 Number of scatterers: 23814 At special positions: 0 Unit cell: (114.92, 118.3, 165.62, 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 24 15.00 O 4542 8.00 N 4158 7.00 C 14976 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: 9.43 Conformation dependent library (CDL) restraints added in 3.4 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: 120 helices and 30 sheets defined 48.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.510A pdb=" N GLU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 51 removed outlier: 4.093A pdb=" N ARG A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.634A pdb=" N TYR A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.842A pdb=" N GLU A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.700A pdb=" N TRP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) 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 227 removed outlier: 3.567A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.513A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 236' Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.511A pdb=" N HIS A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.557A pdb=" N LYS A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.744A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 removed outlier: 4.341A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 419 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 434 through 440 removed outlier: 3.513A pdb=" N ASP A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.984A pdb=" N ALA A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 477 through 496 removed outlier: 3.766A pdb=" N ARG A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.510A pdb=" N GLU B 14 " --> pdb=" O PHE B 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 51 removed outlier: 4.093A pdb=" N ARG B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.635A pdb=" N TYR B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.842A pdb=" N GLU B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.699A pdb=" N TRP B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) 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 227 removed outlier: 3.568A pdb=" N ILE B 223 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 225 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 236 removed outlier: 3.513A pdb=" N SER B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 236 " --> pdb=" O TYR B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 236' Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.511A pdb=" N HIS B 258 " --> pdb=" O ASN B 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.556A pdb=" N LYS B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.744A pdb=" N LYS B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 4.341A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL B 378 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 419 Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 434 through 440 removed outlier: 3.513A pdb=" N ASP B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 459 removed outlier: 3.985A pdb=" N ALA B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 477 through 496 removed outlier: 3.767A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 496 " --> pdb=" O VAL B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.510A pdb=" N GLU C 14 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 51 removed outlier: 4.093A pdb=" N ARG C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 removed outlier: 3.634A pdb=" N TYR C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.842A pdb=" N GLU C 142 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.700A pdb=" N TRP C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) 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 227 removed outlier: 3.566A pdb=" N ILE C 223 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 225 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 236 removed outlier: 3.513A pdb=" N SER C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 230 through 236' Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.511A pdb=" N HIS C 258 " --> pdb=" O ASN C 254 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.557A pdb=" N LYS C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 363 removed outlier: 3.744A pdb=" N LYS C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 390 removed outlier: 4.340A pdb=" N ALA C 375 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY C 376 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL C 378 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 419 Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'C' and resid 434 through 440 removed outlier: 3.513A pdb=" N ASP C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 459 removed outlier: 3.985A pdb=" N ALA C 454 " --> pdb=" O HIS C 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 470 Processing helix chain 'C' and resid 477 through 496 removed outlier: 3.767A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C 496 " --> pdb=" O VAL C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.510A pdb=" N GLU D 14 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 24 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 51 removed outlier: 4.093A pdb=" N ARG D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 117 removed outlier: 3.634A pdb=" N TYR D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 135 No H-bonds generated for 'chain 'D' and resid 133 through 135' Processing helix chain 'D' and resid 138 through 153 removed outlier: 3.842A pdb=" N GLU D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 186 removed outlier: 3.700A pdb=" N TRP D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) 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 227 removed outlier: 3.567A pdb=" N ILE D 223 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN D 225 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 236 removed outlier: 3.513A pdb=" N SER D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 230 through 236' Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.511A pdb=" N HIS D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.557A pdb=" N LYS D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 363 removed outlier: 3.744A pdb=" N LYS D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 390 removed outlier: 4.341A pdb=" N ALA D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL D 378 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 419 Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 434 through 440 removed outlier: 3.513A pdb=" N ASP D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 459 removed outlier: 3.984A pdb=" N ALA D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'D' and resid 477 through 496 removed outlier: 3.766A pdb=" N ARG D 491 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 492 " --> pdb=" O LYS D 488 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 496 " --> pdb=" O VAL D 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.510A pdb=" N GLU E 14 " --> pdb=" O PHE E 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 24 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 51 removed outlier: 4.093A pdb=" N ARG E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 117 removed outlier: 3.635A pdb=" N TYR E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA E 116 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 138 through 153 removed outlier: 3.842A pdb=" N GLU E 142 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 186 removed outlier: 3.699A pdb=" N TRP E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) 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 227 removed outlier: 3.568A pdb=" N ILE E 223 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN E 225 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 236 removed outlier: 3.513A pdb=" N SER E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 236 " --> pdb=" O TYR E 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 230 through 236' Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.511A pdb=" N HIS E 258 " --> pdb=" O ASN E 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR E 262 " --> pdb=" O HIS E 258 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.556A pdb=" N LYS E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 363 removed outlier: 3.744A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 390 removed outlier: 4.341A pdb=" N ALA E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY E 377 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL E 378 " --> pdb=" O ASN E 374 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 380 " --> pdb=" O GLY E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 419 Processing helix chain 'E' and resid 422 through 424 No H-bonds generated for 'chain 'E' and resid 422 through 424' Processing helix chain 'E' and resid 434 through 440 removed outlier: 3.513A pdb=" N ASP E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 459 removed outlier: 3.985A pdb=" N ALA E 454 " --> pdb=" O HIS E 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'E' and resid 477 through 496 removed outlier: 3.767A pdb=" N ARG E 491 " --> pdb=" O GLU E 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR E 493 " --> pdb=" O VAL E 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU E 495 " --> pdb=" O ARG E 491 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 496 " --> pdb=" O VAL E 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.510A pdb=" N GLU F 14 " --> pdb=" O PHE F 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 51 removed outlier: 4.093A pdb=" N ARG F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 117 removed outlier: 3.634A pdb=" N TYR F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 135 No H-bonds generated for 'chain 'F' and resid 133 through 135' Processing helix chain 'F' and resid 138 through 153 removed outlier: 3.842A pdb=" N GLU F 142 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 152 " --> pdb=" O PHE F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 186 removed outlier: 3.700A pdb=" N TRP F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) 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 227 removed outlier: 3.566A pdb=" N ILE F 223 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN F 225 " --> pdb=" O HIS F 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 236 removed outlier: 3.513A pdb=" N SER F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 236 " --> pdb=" O TYR F 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 230 through 236' Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.511A pdb=" N HIS F 258 " --> pdb=" O ASN F 254 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR F 262 " --> pdb=" O HIS F 258 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE F 266 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 296 removed outlier: 3.557A pdb=" N LYS F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 removed outlier: 3.744A pdb=" N LYS F 358 " --> pdb=" O PRO F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 390 removed outlier: 4.340A pdb=" N ALA F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY F 376 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL F 378 " --> pdb=" O ASN F 374 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL F 380 " --> pdb=" O GLY F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 419 Processing helix chain 'F' and resid 422 through 424 No H-bonds generated for 'chain 'F' and resid 422 through 424' Processing helix chain 'F' and resid 434 through 440 removed outlier: 3.513A pdb=" N ASP F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 459 removed outlier: 3.985A pdb=" N ALA F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 458 " --> pdb=" O ALA F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'F' and resid 477 through 496 removed outlier: 3.767A pdb=" N ARG F 491 " --> pdb=" O GLU F 487 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR F 493 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU F 495 " --> pdb=" O ARG F 491 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F 496 " --> pdb=" O VAL F 492 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 57 through 60 removed outlier: 3.696A pdb=" N ARG A 79 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 63 through 66 Processing sheet with id= C, first strand: chain 'A' and resid 89 through 92 Processing sheet with id= D, first strand: chain 'A' and resid 321 through 324 removed outlier: 6.726A pdb=" N ILE A 343 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA A 345 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET A 366 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU A 346 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE A 368 " --> pdb=" O GLU A 346 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 246 through 249 removed outlier: 6.387A pdb=" N LYS A 269 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL A 249 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE A 271 " --> pdb=" O VAL A 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 57 through 60 removed outlier: 3.696A pdb=" N ARG B 79 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 63 through 66 Processing sheet with id= H, first strand: chain 'B' and resid 89 through 92 Processing sheet with id= I, first strand: chain 'B' and resid 321 through 324 removed outlier: 6.726A pdb=" N ILE B 343 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ALA B 345 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET B 366 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU B 346 " --> pdb=" O MET B 366 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE B 368 " --> pdb=" O GLU B 346 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 246 through 249 removed outlier: 6.387A pdb=" N LYS B 269 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL B 249 " --> pdb=" O LYS B 269 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE B 271 " --> pdb=" O VAL B 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 57 through 60 removed outlier: 3.696A pdb=" N ARG C 79 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 63 through 66 Processing sheet with id= M, first strand: chain 'C' and resid 89 through 92 Processing sheet with id= N, first strand: chain 'C' and resid 321 through 324 removed outlier: 6.726A pdb=" N ILE C 343 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA C 345 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET C 366 " --> pdb=" O ILE C 344 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU C 346 " --> pdb=" O MET C 366 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE C 368 " --> pdb=" O GLU C 346 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 246 through 249 removed outlier: 6.388A pdb=" N LYS C 269 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL C 249 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE C 271 " --> pdb=" O VAL C 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.696A pdb=" N ARG D 79 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 63 through 66 Processing sheet with id= R, first strand: chain 'D' and resid 89 through 92 Processing sheet with id= S, first strand: chain 'D' and resid 321 through 324 removed outlier: 6.726A pdb=" N ILE D 343 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA D 345 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET D 366 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU D 346 " --> pdb=" O MET D 366 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE D 368 " --> pdb=" O GLU D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 246 through 249 removed outlier: 6.387A pdb=" N LYS D 269 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL D 249 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE D 271 " --> pdb=" O VAL D 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 57 through 60 removed outlier: 3.696A pdb=" N ARG E 79 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 63 through 66 Processing sheet with id= W, first strand: chain 'E' and resid 89 through 92 Processing sheet with id= X, first strand: chain 'E' and resid 321 through 324 removed outlier: 6.726A pdb=" N ILE E 343 " --> pdb=" O LEU E 322 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ALA E 345 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET E 366 " --> pdb=" O ILE E 344 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU E 346 " --> pdb=" O MET E 366 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE E 368 " --> pdb=" O GLU E 346 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 246 through 249 removed outlier: 6.387A pdb=" N LYS E 269 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL E 249 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE E 271 " --> pdb=" O VAL E 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 57 through 60 removed outlier: 3.696A pdb=" N ARG F 79 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 63 through 66 Processing sheet with id= AB, first strand: chain 'F' and resid 89 through 92 Processing sheet with id= AC, first strand: chain 'F' and resid 321 through 324 removed outlier: 6.726A pdb=" N ILE F 343 " --> pdb=" O LEU F 322 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA F 345 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET F 366 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU F 346 " --> pdb=" O MET F 366 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE F 368 " --> pdb=" O GLU F 346 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 246 through 249 removed outlier: 6.388A pdb=" N LYS F 269 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL F 249 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE F 271 " --> pdb=" O VAL F 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 840 hydrogen bonds defined for protein. 2484 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: 7.46 Time building geometry restraints manager: 10.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7714 1.33 - 1.45: 3666 1.45 - 1.57: 12740 1.57 - 1.69: 48 1.69 - 1.81: 192 Bond restraints: 24360 Sorted by residual: bond pdb=" C3N NAI C 601 " pdb=" C7N NAI C 601 " ideal model delta sigma weight residual 1.473 1.592 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C3N NAI F 601 " pdb=" C7N NAI F 601 " ideal model delta sigma weight residual 1.473 1.592 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C3N NAI A 602 " pdb=" C7N NAI A 602 " ideal model delta sigma weight residual 1.473 1.591 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C3N NAI D 602 " pdb=" C7N NAI D 602 " ideal model delta sigma weight residual 1.473 1.591 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C3N NAI B 602 " pdb=" C7N NAI B 602 " ideal model delta sigma weight residual 1.473 1.591 -0.118 2.00e-02 2.50e+03 3.46e+01 ... (remaining 24355 not shown) Histogram of bond angle deviations from ideal: 94.66 - 103.54: 394 103.54 - 112.42: 12410 112.42 - 121.30: 14322 121.30 - 130.18: 5698 130.18 - 139.06: 170 Bond angle restraints: 32994 Sorted by residual: angle pdb=" O2A NAI E 601 " pdb=" PA NAI E 601 " pdb=" O5B NAI E 601 " ideal model delta sigma weight residual 105.34 121.02 -15.68 3.00e+00 1.11e-01 2.73e+01 angle pdb=" O2A NAI B 601 " pdb=" PA NAI B 601 " pdb=" O5B NAI B 601 " ideal model delta sigma weight residual 105.34 121.02 -15.68 3.00e+00 1.11e-01 2.73e+01 angle pdb=" O2A NAI D 601 " pdb=" PA NAI D 601 " pdb=" O5B NAI D 601 " ideal model delta sigma weight residual 105.34 121.00 -15.66 3.00e+00 1.11e-01 2.72e+01 angle pdb=" O2A NAI A 601 " pdb=" PA NAI A 601 " pdb=" O5B NAI A 601 " ideal model delta sigma weight residual 105.34 121.00 -15.66 3.00e+00 1.11e-01 2.72e+01 angle pdb=" O2A NAI F 602 " pdb=" PA NAI F 602 " pdb=" O5B NAI F 602 " ideal model delta sigma weight residual 105.34 120.98 -15.64 3.00e+00 1.11e-01 2.72e+01 ... (remaining 32989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 14014 16.86 - 33.71: 266 33.71 - 50.57: 72 50.57 - 67.43: 12 67.43 - 84.28: 18 Dihedral angle restraints: 14382 sinusoidal: 5904 harmonic: 8478 Sorted by residual: dihedral pdb=" CA ALA F 375 " pdb=" C ALA F 375 " pdb=" N GLY F 376 " pdb=" CA GLY F 376 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ALA C 375 " pdb=" C ALA C 375 " pdb=" N GLY C 376 " pdb=" CA GLY C 376 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ALA A 375 " pdb=" C ALA A 375 " pdb=" N GLY A 376 " pdb=" CA GLY A 376 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 14379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3142 0.080 - 0.161: 386 0.161 - 0.241: 20 0.241 - 0.321: 28 0.321 - 0.401: 12 Chirality restraints: 3588 Sorted by residual: chirality pdb=" C3B NAI B 601 " pdb=" C2B NAI B 601 " pdb=" C4B NAI B 601 " pdb=" O3B NAI B 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C3B NAI E 601 " pdb=" C2B NAI E 601 " pdb=" C4B NAI E 601 " pdb=" O3B NAI E 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C3B NAI A 601 " pdb=" C2B NAI A 601 " pdb=" C4B NAI A 601 " pdb=" O3B NAI A 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.40 2.00e-01 2.50e+01 3.99e+00 ... (remaining 3585 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 336 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO D 337 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 337 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 337 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 336 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 337 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 336 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO E 337 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " -0.036 5.00e-02 4.00e+02 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4326 2.75 - 3.29: 22948 3.29 - 3.83: 37039 3.83 - 4.36: 47532 4.36 - 4.90: 78925 Nonbonded interactions: 190770 Sorted by model distance: nonbonded pdb=" O THR B 239 " pdb=" NZ LYS B 245 " model vdw 2.219 2.520 nonbonded pdb=" O THR E 239 " pdb=" NZ LYS E 245 " model vdw 2.219 2.520 nonbonded pdb=" O THR F 239 " pdb=" NZ LYS F 245 " model vdw 2.219 2.520 nonbonded pdb=" O THR C 239 " pdb=" NZ LYS C 245 " model vdw 2.219 2.520 nonbonded pdb=" O THR A 239 " pdb=" NZ LYS A 245 " model vdw 2.220 2.520 ... (remaining 190765 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.35 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 6.000 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 58.080 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 0.119 24360 Z= 0.722 Angle : 1.045 15.681 32994 Z= 0.484 Chirality : 0.061 0.401 3588 Planarity : 0.005 0.065 4224 Dihedral : 8.836 84.282 8982 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.81 % Allowed : 5.60 % Favored : 93.59 % Rotamer Outliers : 0.72 % 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: -5.54 (0.11), residues: 2964 helix: -3.94 (0.08), residues: 1374 sheet: -3.14 (0.21), residues: 450 loop : -3.25 (0.15), residues: 1140 *********************** 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 505 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 487 time to evaluate : 2.684 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: 18 outliers final: 12 residues processed: 505 average time/residue: 0.4539 time to fit residues: 327.5745 Evaluate side-chains 249 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 237 time to evaluate : 2.789 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2216 time to fit residues: 8.7732 ------------------------------------------------------------------------------- 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: 30.0000 chunk 222 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 150 optimal weight: 30.0000 chunk 119 optimal weight: 6.9990 chunk 230 optimal weight: 40.0000 chunk 89 optimal weight: 6.9990 chunk 140 optimal weight: 0.0470 chunk 171 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 56 ASN A 57 HIS A 84 GLN A 225 ASN A 437 GLN B 40 GLN B 56 ASN B 57 HIS B 84 GLN B 209 HIS B 225 ASN B 437 GLN C 56 ASN C 57 HIS C 84 GLN C 209 HIS C 225 ASN C 437 GLN D 40 GLN D 56 ASN D 57 HIS D 84 GLN D 225 ASN D 437 GLN E 40 GLN E 56 ASN E 57 HIS E 84 GLN E 209 HIS E 225 ASN E 437 GLN F 56 ASN F 57 HIS F 84 GLN F 209 HIS F 225 ASN F 437 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 24360 Z= 0.298 Angle : 0.584 4.933 32994 Z= 0.308 Chirality : 0.046 0.154 3588 Planarity : 0.005 0.050 4224 Dihedral : 8.125 87.996 3390 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 1.36 % 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: -3.32 (0.14), residues: 2964 helix: -1.66 (0.12), residues: 1368 sheet: -2.56 (0.21), residues: 456 loop : -2.53 (0.17), residues: 1140 *********************** 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 315 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 281 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 22 residues processed: 300 average time/residue: 0.3415 time to fit residues: 166.6885 Evaluate side-chains 248 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 3.089 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2260 time to fit residues: 13.4979 ------------------------------------------------------------------------------- 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: 0.9990 chunk 82 optimal weight: 5.9990 chunk 222 optimal weight: 20.0000 chunk 181 optimal weight: 0.9990 chunk 73 optimal weight: 40.0000 chunk 267 optimal weight: 9.9990 chunk 288 optimal weight: 9.9990 chunk 238 optimal weight: 0.3980 chunk 265 optimal weight: 8.9990 chunk 91 optimal weight: 0.0470 chunk 214 optimal weight: 6.9990 overall best weight: 1.6884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 330 GLN B 56 ASN B 437 GLN C 56 ASN D 56 ASN D 330 GLN E 56 ASN E 437 GLN F 56 ASN F 205 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 24360 Z= 0.146 Angle : 0.463 4.533 32994 Z= 0.244 Chirality : 0.042 0.152 3588 Planarity : 0.004 0.048 4224 Dihedral : 7.291 75.508 3390 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.60 % 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: -1.80 (0.15), residues: 2964 helix: -0.25 (0.14), residues: 1356 sheet: -1.97 (0.23), residues: 438 loop : -1.90 (0.18), residues: 1170 *********************** 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 303 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 288 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 298 average time/residue: 0.3690 time to fit residues: 173.2374 Evaluate side-chains 248 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 241 time to evaluate : 2.790 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2149 time to fit residues: 6.6986 ------------------------------------------------------------------------------- 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: 10.0000 chunk 201 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 127 optimal weight: 0.0980 chunk 179 optimal weight: 40.0000 chunk 268 optimal weight: 4.9990 chunk 284 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 254 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 437 GLN C 205 GLN C 330 GLN C 437 GLN D 437 GLN E 437 GLN F 437 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 24360 Z= 0.263 Angle : 0.511 4.444 32994 Z= 0.268 Chirality : 0.044 0.151 3588 Planarity : 0.004 0.052 4224 Dihedral : 7.425 75.374 3390 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 1.40 % 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: -1.31 (0.15), residues: 2964 helix: 0.14 (0.14), residues: 1368 sheet: -1.72 (0.23), residues: 444 loop : -1.64 (0.18), residues: 1152 *********************** 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 280 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 245 time to evaluate : 3.024 Fit side-chains outliers start: 35 outliers final: 16 residues processed: 261 average time/residue: 0.3547 time to fit residues: 147.9390 Evaluate side-chains 248 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 2.805 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2545 time to fit residues: 10.9098 ------------------------------------------------------------------------------- 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: 5.9990 chunk 161 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 196 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 145 optimal weight: 8.9990 chunk 255 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 437 GLN C 40 GLN C 437 GLN D 40 GLN D 437 GLN F 40 GLN F 437 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 24360 Z= 0.339 Angle : 0.564 5.518 32994 Z= 0.293 Chirality : 0.046 0.156 3588 Planarity : 0.005 0.057 4224 Dihedral : 7.423 78.803 3390 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.92 % 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: -1.22 (0.15), residues: 2964 helix: 0.30 (0.14), residues: 1350 sheet: -1.74 (0.24), residues: 450 loop : -1.66 (0.18), residues: 1164 *********************** 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 275 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 3.048 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 260 average time/residue: 0.3364 time to fit residues: 143.2073 Evaluate side-chains 245 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 232 time to evaluate : 2.968 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2384 time to fit residues: 9.3622 ------------------------------------------------------------------------------- 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: 5.9990 chunk 255 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 437 GLN B 437 GLN C 437 GLN D 40 GLN D 437 GLN E 437 GLN F 437 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 24360 Z= 0.247 Angle : 0.511 5.257 32994 Z= 0.265 Chirality : 0.044 0.151 3588 Planarity : 0.004 0.056 4224 Dihedral : 7.024 80.054 3390 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.92 % 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: -0.82 (0.16), residues: 2964 helix: 0.66 (0.14), residues: 1332 sheet: -1.59 (0.24), residues: 450 loop : -1.44 (0.18), residues: 1182 *********************** 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 258 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 235 time to evaluate : 2.813 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 243 average time/residue: 0.3185 time to fit residues: 129.0275 Evaluate side-chains 240 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 2.969 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2252 time to fit residues: 8.6273 ------------------------------------------------------------------------------- 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: 10.0000 chunk 32 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 160 optimal weight: 0.0980 chunk 239 optimal weight: 6.9990 chunk 158 optimal weight: 8.9990 chunk 283 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 437 GLN C 437 GLN D 437 GLN E 437 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 24360 Z= 0.165 Angle : 0.461 4.649 32994 Z= 0.240 Chirality : 0.042 0.148 3588 Planarity : 0.004 0.051 4224 Dihedral : 6.574 80.497 3390 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 0.76 % 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: -0.34 (0.16), residues: 2964 helix: 1.19 (0.15), residues: 1314 sheet: -1.30 (0.24), residues: 444 loop : -1.35 (0.18), residues: 1206 *********************** 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 276 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 257 time to evaluate : 3.096 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 274 average time/residue: 0.3454 time to fit residues: 153.6569 Evaluate side-chains 239 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 230 time to evaluate : 2.940 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2522 time to fit residues: 8.1734 ------------------------------------------------------------------------------- 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: 6.9990 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 180 optimal weight: 0.0870 chunk 193 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 222 optimal weight: 30.0000 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 437 GLN D 437 GLN E 437 GLN F 364 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 24360 Z= 0.146 Angle : 0.456 5.849 32994 Z= 0.237 Chirality : 0.042 0.142 3588 Planarity : 0.004 0.047 4224 Dihedral : 6.295 80.559 3390 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.48 % 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: -0.05 (0.16), residues: 2964 helix: 1.47 (0.15), residues: 1332 sheet: -1.06 (0.24), residues: 444 loop : -1.35 (0.18), residues: 1188 *********************** 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 261 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 249 time to evaluate : 2.702 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 254 average time/residue: 0.3618 time to fit residues: 147.9992 Evaluate side-chains 239 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 2.802 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2904 time to fit residues: 5.7666 ------------------------------------------------------------------------------- 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: 5.9990 chunk 271 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 264 optimal weight: 5.9990 chunk 158 optimal weight: 0.0770 chunk 115 optimal weight: 0.8980 chunk 207 optimal weight: 0.0020 chunk 81 optimal weight: 6.9990 chunk 238 optimal weight: 0.0470 chunk 249 optimal weight: 0.5980 chunk 263 optimal weight: 10.0000 overall best weight: 0.3244 ------------------------------------------------------------------------------- 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 B 437 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN D 437 GLN E 437 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 24360 Z= 0.116 Angle : 0.445 10.057 32994 Z= 0.227 Chirality : 0.041 0.156 3588 Planarity : 0.004 0.062 4224 Dihedral : 5.905 80.402 3390 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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: 0.41 (0.16), residues: 2964 helix: 1.79 (0.15), residues: 1350 sheet: -0.54 (0.26), residues: 426 loop : -1.22 (0.18), residues: 1188 *********************** 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 273 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 268 time to evaluate : 3.193 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 270 average time/residue: 0.3508 time to fit residues: 153.4600 Evaluate side-chains 240 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 2.858 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3177 time to fit residues: 4.8911 ------------------------------------------------------------------------------- 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: 8.9990 chunk 279 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 194 optimal weight: 10.0000 chunk 292 optimal weight: 8.9990 chunk 269 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 143 optimal weight: 0.0040 overall best weight: 3.2998 ------------------------------------------------------------------------------- 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 B 437 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN E 437 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 24360 Z= 0.205 Angle : 0.483 8.686 32994 Z= 0.250 Chirality : 0.043 0.142 3588 Planarity : 0.004 0.051 4224 Dihedral : 6.054 80.998 3390 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 0.24 (0.16), residues: 2964 helix: 1.61 (0.14), residues: 1368 sheet: -0.58 (0.25), residues: 438 loop : -1.31 (0.18), residues: 1158 ********************** 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 245 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 240 time to evaluate : 3.299 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 242 average time/residue: 0.3500 time to fit residues: 137.2871 Evaluate side-chains 237 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 3.089 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2126 time to fit residues: 5.2642 ------------------------------------------------------------------------------- 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: 10.0000 chunk 248 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 29 optimal weight: 30.0000 chunk 43 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 B 437 GLN D 437 GLN E 437 GLN F 364 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.113161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081192 restraints weight = 46579.610| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.57 r_work: 0.2929 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 24360 Z= 0.233 Angle : 0.503 7.606 32994 Z= 0.260 Chirality : 0.044 0.145 3588 Planarity : 0.004 0.052 4224 Dihedral : 6.307 81.599 3390 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.36 % 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: 0.18 (0.16), residues: 2964 helix: 1.56 (0.14), residues: 1344 sheet: -0.62 (0.25), residues: 444 loop : -1.27 (0.18), residues: 1176 =============================================================================== Job complete usr+sys time: 4327.71 seconds wall clock time: 80 minutes 35.22 seconds (4835.22 seconds total)