Starting phenix.real_space_refine on Tue Mar 19 09:47:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/03_2024/3jd2_6635_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/03_2024/3jd2_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_6635/03_2024/3jd2_6635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/03_2024/3jd2_6635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/03_2024/3jd2_6635_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/03_2024/3jd2_6635_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.71, per 1000 atoms: 0.53 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: 9.21 Conformation dependent library (CDL) restraints added in 4.7 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: 5.42 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: 7.38 Time building geometry restraints manager: 10.15 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: 14410 16.86 - 33.71: 320 33.71 - 50.57: 162 50.57 - 67.43: 66 67.43 - 84.28: 24 Dihedral angle restraints: 14982 sinusoidal: 6504 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 14979 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: 0.900 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: 5.020 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 66.410 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.320 ------------------------------------------------------------------------------- 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 : 10.879 84.282 9582 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 % Allowed : 0.48 % Favored : 98.80 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 72 HIS 0.007 0.002 HIS B 391 PHE 0.025 0.003 PHE B 399 TYR 0.025 0.003 TYR A 382 ARG 0.007 0.001 ARG D 396 *********************** 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 : 2.895 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: A 500 PHE cc_start: 0.7108 (m-10) cc_final: 0.6127 (m-10) REVERT: B 500 PHE cc_start: 0.7200 (m-10) cc_final: 0.5813 (m-10) REVERT: C 500 PHE cc_start: 0.7076 (m-10) cc_final: 0.5977 (t80) REVERT: D 500 PHE cc_start: 0.7103 (m-10) cc_final: 0.6126 (m-10) REVERT: E 500 PHE cc_start: 0.7191 (m-10) cc_final: 0.5805 (m-10) REVERT: F 500 PHE cc_start: 0.7073 (m-10) cc_final: 0.5975 (t80) outliers start: 18 outliers final: 12 residues processed: 505 average time/residue: 0.4527 time to fit residues: 326.1856 Evaluate side-chains 249 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 237 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 373 LEU 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: 5.9990 chunk 230 optimal weight: 20.0000 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: 5.0086 ------------------------------------------------------------------------------- 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 330 GLN 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 330 GLN 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: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24360 Z= 0.291 Angle : 0.579 4.922 32994 Z= 0.305 Chirality : 0.046 0.154 3588 Planarity : 0.005 0.050 4224 Dihedral : 11.924 78.917 4014 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.44 % Allowed : 5.49 % Favored : 93.07 % 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: -3.37 (0.14), residues: 2964 helix: -1.71 (0.12), residues: 1368 sheet: -2.57 (0.21), residues: 456 loop : -2.55 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 281 HIS 0.004 0.001 HIS C 391 PHE 0.024 0.003 PHE F 16 TYR 0.020 0.002 TYR F 382 ARG 0.004 0.001 ARG B 46 *********************** 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 316 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 280 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8257 (mp10) REVERT: A 269 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8280 (ptmt) REVERT: A 500 PHE cc_start: 0.6757 (m-10) cc_final: 0.6265 (t80) REVERT: B 84 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8313 (mp10) REVERT: B 500 PHE cc_start: 0.6673 (m-10) cc_final: 0.6197 (t80) REVERT: C 500 PHE cc_start: 0.6791 (m-10) cc_final: 0.6281 (t80) REVERT: D 84 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8259 (mp10) REVERT: D 181 ASP cc_start: 0.8274 (t70) cc_final: 0.7645 (t70) REVERT: D 269 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8282 (ptmt) REVERT: E 84 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8319 (mp10) outliers start: 36 outliers final: 22 residues processed: 301 average time/residue: 0.3191 time to fit residues: 155.1015 Evaluate side-chains 259 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 469 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.0770 chunk 222 optimal weight: 0.0980 chunk 181 optimal weight: 0.0670 chunk 73 optimal weight: 40.0000 chunk 267 optimal weight: 7.9990 chunk 288 optimal weight: 9.9990 chunk 238 optimal weight: 0.5980 chunk 265 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 330 GLN B 437 GLN D 40 GLN D 330 GLN E 437 GLN F 330 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24360 Z= 0.113 Angle : 0.451 4.929 32994 Z= 0.236 Chirality : 0.041 0.151 3588 Planarity : 0.004 0.049 4224 Dihedral : 10.973 89.498 4002 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.92 % Allowed : 7.17 % Favored : 91.91 % 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: -1.75 (0.15), residues: 2964 helix: -0.20 (0.14), residues: 1356 sheet: -1.90 (0.23), residues: 432 loop : -1.93 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 281 HIS 0.003 0.000 HIS D 85 PHE 0.018 0.001 PHE E 16 TYR 0.007 0.001 TYR C 382 ARG 0.003 0.000 ARG D 419 *********************** 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 347 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 324 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LYS cc_start: 0.8480 (ttpt) cc_final: 0.8276 (ptmt) REVERT: A 500 PHE cc_start: 0.6728 (m-10) cc_final: 0.6387 (t80) REVERT: B 84 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8141 (mp10) REVERT: B 500 PHE cc_start: 0.6767 (m-10) cc_final: 0.6333 (t80) REVERT: C 78 TYR cc_start: 0.8341 (m-80) cc_final: 0.7919 (m-80) REVERT: C 407 TYR cc_start: 0.8399 (m-80) cc_final: 0.8192 (m-10) REVERT: C 500 PHE cc_start: 0.6717 (m-10) cc_final: 0.6381 (t80) REVERT: D 269 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8279 (ptmt) REVERT: F 78 TYR cc_start: 0.8333 (m-80) cc_final: 0.7915 (m-80) REVERT: F 407 TYR cc_start: 0.8400 (m-80) cc_final: 0.8193 (m-10) outliers start: 23 outliers final: 15 residues processed: 335 average time/residue: 0.3698 time to fit residues: 191.6105 Evaluate side-chains 255 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 240 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 179 optimal weight: 40.0000 chunk 268 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 254 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 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 437 GLN B 437 GLN B 463 GLN C 40 GLN C 56 ASN C 205 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 437 GLN E 40 GLN E 56 ASN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN E 463 GLN F 40 GLN F 56 ASN F 205 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3308 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= 0.352 Angle : 0.565 5.133 32994 Z= 0.294 Chirality : 0.046 0.155 3588 Planarity : 0.005 0.055 4224 Dihedral : 10.485 73.417 4002 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.84 % Allowed : 8.21 % Favored : 89.94 % 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: -0.06 (0.14), residues: 1368 sheet: -1.77 (0.24), residues: 444 loop : -1.69 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 281 HIS 0.004 0.001 HIS B 85 PHE 0.023 0.002 PHE D 122 TYR 0.017 0.002 TYR F 382 ARG 0.004 0.000 ARG D 19 *********************** 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 296 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 250 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8604 (m-80) cc_final: 0.8321 (m-80) REVERT: A 269 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8264 (ptmt) REVERT: A 330 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: A 500 PHE cc_start: 0.6684 (m-10) cc_final: 0.6245 (t80) REVERT: B 163 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8123 (t70) REVERT: D 78 TYR cc_start: 0.8598 (m-80) cc_final: 0.8314 (m-80) REVERT: D 269 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8272 (ptmt) REVERT: D 330 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: E 163 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8123 (t70) outliers start: 46 outliers final: 32 residues processed: 276 average time/residue: 0.3380 time to fit residues: 149.3002 Evaluate side-chains 263 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 431 VAL 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: 2.9990 chunk 4 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 242 optimal weight: 0.6980 chunk 196 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 145 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 56 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24360 Z= 0.159 Angle : 0.457 4.539 32994 Z= 0.240 Chirality : 0.042 0.150 3588 Planarity : 0.004 0.051 4224 Dihedral : 9.903 71.387 4002 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.32 % Allowed : 9.38 % Favored : 89.30 % 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: -0.86 (0.16), residues: 2964 helix: 0.60 (0.14), residues: 1332 sheet: -1.58 (0.24), residues: 444 loop : -1.44 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 281 HIS 0.003 0.001 HIS E 85 PHE 0.014 0.001 PHE D 122 TYR 0.011 0.001 TYR D 382 ARG 0.004 0.000 ARG D 19 *********************** 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 286 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 253 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8469 (m-80) cc_final: 0.8257 (m-80) REVERT: A 269 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8250 (ptmt) REVERT: B 181 ASP cc_start: 0.8379 (t70) cc_final: 0.8019 (t0) REVERT: C 233 MET cc_start: 0.7913 (mmm) cc_final: 0.7495 (mmp) REVERT: D 78 TYR cc_start: 0.8471 (m-80) cc_final: 0.8256 (m-80) REVERT: D 269 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8259 (ptmt) outliers start: 33 outliers final: 19 residues processed: 270 average time/residue: 0.3230 time to fit residues: 141.3982 Evaluate side-chains 255 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 236 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 431 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 364 ASN A 437 GLN B 437 GLN C 437 GLN D 40 GLN D 364 ASN D 437 GLN E 40 GLN E 437 GLN F 437 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24360 Z= 0.213 Angle : 0.485 6.088 32994 Z= 0.252 Chirality : 0.043 0.149 3588 Planarity : 0.004 0.051 4224 Dihedral : 9.567 73.558 4002 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.48 % Allowed : 9.94 % Favored : 88.58 % 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: -0.60 (0.16), residues: 2964 helix: 0.87 (0.14), residues: 1332 sheet: -1.39 (0.24), residues: 450 loop : -1.41 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 281 HIS 0.003 0.001 HIS B 85 PHE 0.017 0.002 PHE D 122 TYR 0.013 0.001 TYR A 382 ARG 0.003 0.000 ARG D 19 *********************** 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 287 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 250 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8096 (t0) REVERT: A 233 MET cc_start: 0.8270 (mmm) cc_final: 0.7757 (mmp) REVERT: B 181 ASP cc_start: 0.8360 (t70) cc_final: 0.8154 (t0) REVERT: C 238 MET cc_start: 0.5868 (pmm) cc_final: 0.5500 (pmm) REVERT: D 163 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8114 (t0) REVERT: D 233 MET cc_start: 0.8272 (mmm) cc_final: 0.7778 (mmp) outliers start: 37 outliers final: 29 residues processed: 278 average time/residue: 0.3242 time to fit residues: 147.6310 Evaluate side-chains 263 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 232 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 431 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 158 optimal weight: 0.0070 chunk 283 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 172 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 437 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24360 Z= 0.115 Angle : 0.435 5.429 32994 Z= 0.226 Chirality : 0.041 0.141 3588 Planarity : 0.004 0.045 4224 Dihedral : 9.127 71.920 4002 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.16 % Allowed : 10.46 % Favored : 88.38 % 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: 0.00 (0.16), residues: 2964 helix: 1.45 (0.15), residues: 1332 sheet: -1.02 (0.25), residues: 432 loop : -1.24 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 281 HIS 0.002 0.000 HIS A 298 PHE 0.025 0.001 PHE C 500 TYR 0.007 0.001 TYR E 382 ARG 0.004 0.000 ARG D 19 *********************** 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 303 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 274 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8225 (t0) REVERT: A 319 CYS cc_start: 0.6488 (t) cc_final: 0.6244 (m) REVERT: B 78 TYR cc_start: 0.8422 (m-80) cc_final: 0.8114 (m-80) REVERT: B 163 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8225 (t0) REVERT: B 181 ASP cc_start: 0.8348 (t70) cc_final: 0.7819 (t0) REVERT: C 78 TYR cc_start: 0.8441 (m-80) cc_final: 0.8151 (m-80) REVERT: D 163 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8222 (t0) REVERT: D 319 CYS cc_start: 0.6500 (t) cc_final: 0.6217 (m) REVERT: E 78 TYR cc_start: 0.8421 (m-80) cc_final: 0.8115 (m-80) REVERT: E 163 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8218 (t0) REVERT: F 78 TYR cc_start: 0.8438 (m-80) cc_final: 0.8148 (m-80) outliers start: 29 outliers final: 23 residues processed: 294 average time/residue: 0.3241 time to fit residues: 154.5818 Evaluate side-chains 278 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 251 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU 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: 8.9990 chunk 169 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 222 optimal weight: 8.9990 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 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN B 40 GLN B 437 GLN D 437 GLN E 40 GLN E 437 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24360 Z= 0.230 Angle : 0.493 6.195 32994 Z= 0.257 Chirality : 0.043 0.146 3588 Planarity : 0.004 0.048 4224 Dihedral : 9.206 72.757 4002 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.68 % Allowed : 10.66 % Favored : 87.66 % 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: -0.04 (0.16), residues: 2964 helix: 1.38 (0.15), residues: 1332 sheet: -1.04 (0.25), residues: 444 loop : -1.22 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 281 HIS 0.003 0.001 HIS B 85 PHE 0.018 0.002 PHE D 122 TYR 0.013 0.001 TYR A 382 ARG 0.004 0.000 ARG D 419 *********************** 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 286 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 244 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8120 (t0) REVERT: B 11 LYS cc_start: 0.7094 (pttt) cc_final: 0.6622 (mttp) REVERT: B 78 TYR cc_start: 0.8542 (m-80) cc_final: 0.8237 (m-80) REVERT: B 163 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8275 (t0) REVERT: B 181 ASP cc_start: 0.8313 (t70) cc_final: 0.8090 (t0) REVERT: C 78 TYR cc_start: 0.8564 (m-80) cc_final: 0.8216 (m-80) REVERT: D 163 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8101 (t0) REVERT: E 11 LYS cc_start: 0.7087 (pttt) cc_final: 0.6620 (mttp) REVERT: E 78 TYR cc_start: 0.8541 (m-80) cc_final: 0.8238 (m-80) REVERT: E 163 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8276 (t0) REVERT: E 330 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7798 (tp40) REVERT: F 78 TYR cc_start: 0.8558 (m-80) cc_final: 0.8211 (m-80) outliers start: 42 outliers final: 32 residues processed: 271 average time/residue: 0.3279 time to fit residues: 144.3037 Evaluate side-chains 274 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 237 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.9990 chunk 271 optimal weight: 0.0970 chunk 247 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 158 optimal weight: 0.0060 chunk 115 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 263 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN B 40 GLN B 437 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN E 40 GLN E 437 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4327 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= 0.110 Angle : 0.434 5.515 32994 Z= 0.226 Chirality : 0.041 0.139 3588 Planarity : 0.004 0.043 4224 Dihedral : 8.730 72.834 4002 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.32 % Allowed : 11.26 % Favored : 87.42 % 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: 1.83 (0.15), residues: 1332 sheet: -0.71 (0.25), residues: 432 loop : -1.12 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 281 HIS 0.002 0.000 HIS F 189 PHE 0.019 0.001 PHE C 500 TYR 0.007 0.001 TYR F 183 ARG 0.007 0.000 ARG D 419 *********************** 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 299 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 266 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8236 (t0) REVERT: A 319 CYS cc_start: 0.6415 (t) cc_final: 0.6137 (m) REVERT: B 11 LYS cc_start: 0.6937 (pttt) cc_final: 0.6563 (mttp) REVERT: B 78 TYR cc_start: 0.8396 (m-80) cc_final: 0.8137 (m-80) REVERT: B 163 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8251 (t0) REVERT: B 181 ASP cc_start: 0.8293 (t70) cc_final: 0.7920 (t0) REVERT: B 330 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7631 (tp40) REVERT: C 78 TYR cc_start: 0.8429 (m-80) cc_final: 0.8123 (m-80) REVERT: C 319 CYS cc_start: 0.6430 (t) cc_final: 0.6148 (m) REVERT: D 163 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8232 (t0) REVERT: D 319 CYS cc_start: 0.6390 (t) cc_final: 0.6111 (m) REVERT: E 11 LYS cc_start: 0.6977 (pttt) cc_final: 0.6615 (mttp) REVERT: E 78 TYR cc_start: 0.8403 (m-80) cc_final: 0.8147 (m-80) REVERT: E 163 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8240 (t0) REVERT: E 330 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7648 (tp40) REVERT: F 78 TYR cc_start: 0.8425 (m-80) cc_final: 0.8123 (m-80) REVERT: F 319 CYS cc_start: 0.6407 (t) cc_final: 0.6142 (m) outliers start: 33 outliers final: 27 residues processed: 286 average time/residue: 0.3226 time to fit residues: 150.7554 Evaluate side-chains 284 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 251 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 181 ASP Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 431 VAL 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: 20.0000 chunk 170 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 292 optimal weight: 20.0000 chunk 269 optimal weight: 7.9990 chunk 233 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 B 40 GLN B 437 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN E 40 GLN E 437 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24360 Z= 0.301 Angle : 0.529 5.556 32994 Z= 0.276 Chirality : 0.045 0.149 3588 Planarity : 0.004 0.052 4224 Dihedral : 9.174 74.243 3998 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.68 % Allowed : 10.74 % Favored : 87.58 % 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: 0.06 (0.16), residues: 2964 helix: 1.39 (0.14), residues: 1344 sheet: -0.86 (0.25), residues: 444 loop : -1.16 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 281 HIS 0.004 0.001 HIS B 85 PHE 0.022 0.002 PHE A 122 TYR 0.014 0.001 TYR A 382 ARG 0.006 0.000 ARG D 419 ********************** 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 285 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 243 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8132 (t0) REVERT: A 319 CYS cc_start: 0.6567 (t) cc_final: 0.6268 (m) REVERT: B 11 LYS cc_start: 0.7115 (pttt) cc_final: 0.6627 (mttp) REVERT: B 78 TYR cc_start: 0.8581 (m-80) cc_final: 0.8233 (m-80) REVERT: B 163 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8326 (t0) REVERT: B 181 ASP cc_start: 0.8487 (t70) cc_final: 0.8237 (t0) REVERT: D 163 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8130 (t0) REVERT: D 319 CYS cc_start: 0.6555 (t) cc_final: 0.6291 (m) REVERT: E 11 LYS cc_start: 0.7140 (pttt) cc_final: 0.6696 (mttp) REVERT: E 78 TYR cc_start: 0.8580 (m-80) cc_final: 0.8231 (m-80) REVERT: E 163 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8305 (t0) REVERT: E 330 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7752 (tp40) outliers start: 42 outliers final: 31 residues processed: 272 average time/residue: 0.3330 time to fit residues: 146.4395 Evaluate side-chains 269 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 233 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 272 THR 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: 10.0000 chunk 71 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 233 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 29 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 40 GLN B 437 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN E 40 GLN E 437 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.079494 restraints weight = 46801.532| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.57 r_work: 0.2911 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 : 0.005 0.050 24360 Z= 0.316 Angle : 0.552 7.373 32994 Z= 0.287 Chirality : 0.046 0.150 3588 Planarity : 0.005 0.056 4224 Dihedral : 9.570 77.717 3998 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.60 % Allowed : 11.14 % Favored : 87.26 % 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: -0.15 (0.16), residues: 2964 helix: 1.20 (0.14), residues: 1338 sheet: -0.94 (0.25), residues: 450 loop : -1.25 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 281 HIS 0.004 0.001 HIS E 85 PHE 0.023 0.002 PHE A 122 TYR 0.015 0.001 TYR A 382 ARG 0.006 0.000 ARG D 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4584.53 seconds wall clock time: 84 minutes 29.08 seconds (5069.08 seconds total)