Starting phenix.real_space_refine on Sat Feb 17 07:28:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/02_2024/6pk4_20354_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/02_2024/6pk4_20354.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/02_2024/6pk4_20354_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/02_2024/6pk4_20354_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/02_2024/6pk4_20354_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/02_2024/6pk4_20354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/02_2024/6pk4_20354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/02_2024/6pk4_20354_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk4_20354/02_2024/6pk4_20354_updated.pdb" } resolution = 3.5 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= 0.023 sd= 0.773 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 96 5.16 5 C 11332 2.51 5 N 3084 2.21 5 O 3340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 68": "OD1" <-> "OD2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 68": "OD1" <-> "OD2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17876 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "B" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "C" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "D" Number of atoms: 4409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4409 Classifications: {'peptide': 559} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 528} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU A 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU A 155 " occ=0.75 residue: pdb=" N CYS A 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS A 243 " occ=0.75 residue: pdb=" N GLU B 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU B 155 " occ=0.75 residue: pdb=" N CYS B 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS B 243 " occ=0.75 residue: pdb=" N GLU C 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU C 155 " occ=0.75 residue: pdb=" N CYS C 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS C 243 " occ=0.75 residue: pdb=" N GLU D 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU D 155 " occ=0.75 residue: pdb=" N CYS D 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS D 243 " occ=0.75 Time building chain proxies: 10.40, per 1000 atoms: 0.58 Number of scatterers: 17876 At special positions: 0 Unit cell: (137.55, 87.15, 124.95, 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 96 16.00 P 24 15.00 O 3340 8.00 N 3084 7.00 C 11332 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.19 Conformation dependent library (CDL) restraints added in 3.6 seconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 24 sheets defined 37.4% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.606A pdb=" N SER A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.502A pdb=" N ASN A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 100 " --> pdb=" O HIS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 116 No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 118 through 130 removed outlier: 4.044A pdb=" N MET A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 Proline residue: A 158 - end of helix removed outlier: 4.576A pdb=" N GLU A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN A 165 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 169 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 195 through 207 removed outlier: 3.539A pdb=" N GLY A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 251 through 259 removed outlier: 4.023A pdb=" N VAL A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 269 removed outlier: 3.899A pdb=" N LYS A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 removed outlier: 3.656A pdb=" N ASP A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 removed outlier: 4.356A pdb=" N ALA A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.891A pdb=" N GLU A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 removed outlier: 4.781A pdb=" N GLN A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 412 removed outlier: 3.619A pdb=" N VAL A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.703A pdb=" N LEU A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.503A pdb=" N GLN A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 547 removed outlier: 3.615A pdb=" N GLY A 542 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 557 removed outlier: 3.674A pdb=" N LEU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 30 removed outlier: 3.607A pdb=" N SER B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 90 through 101 removed outlier: 3.502A pdb=" N ASN B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 100 " --> pdb=" O HIS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 118 through 130 removed outlier: 4.044A pdb=" N MET B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 169 Proline residue: B 158 - end of helix removed outlier: 4.577A pdb=" N GLU B 161 " --> pdb=" O PRO B 158 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN B 165 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 169 " --> pdb=" O PHE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 195 through 207 removed outlier: 3.538A pdb=" N GLY B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 251 through 259 removed outlier: 4.023A pdb=" N VAL B 255 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 269 removed outlier: 3.899A pdb=" N LYS B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 3.656A pdb=" N ASP B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 327 removed outlier: 4.357A pdb=" N ALA B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 351 through 362 removed outlier: 3.892A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 390 removed outlier: 4.781A pdb=" N GLN B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 412 removed outlier: 3.619A pdb=" N VAL B 406 " --> pdb=" O MET B 402 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 removed outlier: 3.702A pdb=" N LEU B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.503A pdb=" N GLN B 491 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 547 removed outlier: 3.615A pdb=" N GLY B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 removed outlier: 3.674A pdb=" N LEU B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 removed outlier: 3.606A pdb=" N SER C 22 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.501A pdb=" N ASN C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS C 100 " --> pdb=" O HIS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 116 No H-bonds generated for 'chain 'C' and resid 113 through 116' Processing helix chain 'C' and resid 118 through 130 removed outlier: 4.044A pdb=" N MET C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 169 Proline residue: C 158 - end of helix removed outlier: 4.577A pdb=" N GLU C 161 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN C 165 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 169 " --> pdb=" O PHE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 195 through 207 removed outlier: 3.538A pdb=" N GLY C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 251 through 259 removed outlier: 4.022A pdb=" N VAL C 255 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 269 removed outlier: 3.899A pdb=" N LYS C 267 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 removed outlier: 3.656A pdb=" N ASP C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 292 " --> pdb=" O MET C 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 removed outlier: 4.357A pdb=" N ALA C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 324 " --> pdb=" O ALA C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 344 through 349 Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.891A pdb=" N GLU C 356 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 390 removed outlier: 4.781A pdb=" N GLN C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 412 removed outlier: 3.619A pdb=" N VAL C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 410 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 removed outlier: 3.703A pdb=" N LEU C 467 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 3.503A pdb=" N GLN C 491 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 547 removed outlier: 3.614A pdb=" N GLY C 542 " --> pdb=" O PRO C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 557 removed outlier: 3.674A pdb=" N LEU C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.606A pdb=" N SER D 22 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.501A pdb=" N ASN D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS D 100 " --> pdb=" O HIS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 116 No H-bonds generated for 'chain 'D' and resid 113 through 116' Processing helix chain 'D' and resid 118 through 130 removed outlier: 4.045A pdb=" N MET D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 169 Proline residue: D 158 - end of helix removed outlier: 4.577A pdb=" N GLU D 161 " --> pdb=" O PRO D 158 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN D 165 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS D 169 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 195 through 207 removed outlier: 3.539A pdb=" N GLY D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 251 through 259 removed outlier: 4.023A pdb=" N VAL D 255 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU D 258 " --> pdb=" O PRO D 254 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 269 removed outlier: 3.899A pdb=" N LYS D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 removed outlier: 3.656A pdb=" N ASP D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 292 " --> pdb=" O MET D 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 327 removed outlier: 4.357A pdb=" N ALA D 320 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 351 through 362 removed outlier: 3.892A pdb=" N GLU D 356 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 390 removed outlier: 4.780A pdb=" N GLN D 383 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 412 removed outlier: 3.619A pdb=" N VAL D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 410 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 removed outlier: 3.703A pdb=" N LEU D 467 " --> pdb=" O ILE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.503A pdb=" N GLN D 491 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 547 removed outlier: 3.614A pdb=" N GLY D 542 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 557 removed outlier: 3.674A pdb=" N LEU D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 175 through 177 removed outlier: 6.718A pdb=" N TYR A 3 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 35 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 180 through 182 removed outlier: 6.201A pdb=" N VAL A 215 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 303 through 305 Processing sheet with id= D, first strand: chain 'A' and resid 367 through 369 removed outlier: 3.831A pdb=" N LEU A 396 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE A 520 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 522 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 513 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 482 through 484 removed outlier: 3.501A pdb=" N ASP A 420 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 473 through 480 removed outlier: 3.862A pdb=" N HIS A 478 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 451 " --> pdb=" O HIS A 478 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 480 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 449 " --> pdb=" O HIS A 480 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.718A pdb=" N TYR B 3 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 35 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 180 through 182 removed outlier: 6.200A pdb=" N VAL B 215 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 303 through 305 Processing sheet with id= J, first strand: chain 'B' and resid 367 through 369 removed outlier: 3.831A pdb=" N LEU B 396 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE B 520 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 522 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 513 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 482 through 484 removed outlier: 3.501A pdb=" N ASP B 420 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 473 through 480 removed outlier: 3.861A pdb=" N HIS B 478 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 451 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS B 480 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 449 " --> pdb=" O HIS B 480 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.718A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 35 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 180 through 182 removed outlier: 6.201A pdb=" N VAL C 215 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 303 through 305 Processing sheet with id= P, first strand: chain 'C' and resid 367 through 369 removed outlier: 3.832A pdb=" N LEU C 396 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE C 520 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 522 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 513 " --> pdb=" O SER C 498 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 482 through 484 removed outlier: 3.501A pdb=" N ASP C 420 " --> pdb=" O VAL C 430 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 473 through 480 removed outlier: 3.861A pdb=" N HIS C 478 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY C 451 " --> pdb=" O HIS C 478 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 480 " --> pdb=" O ARG C 449 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 449 " --> pdb=" O HIS C 480 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 175 through 177 removed outlier: 6.718A pdb=" N TYR D 3 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 35 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 180 through 182 removed outlier: 6.201A pdb=" N VAL D 215 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 303 through 305 Processing sheet with id= V, first strand: chain 'D' and resid 367 through 369 removed outlier: 3.832A pdb=" N LEU D 396 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE D 520 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 522 " --> pdb=" O ILE D 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 513 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 482 through 484 removed outlier: 3.501A pdb=" N ASP D 420 " --> pdb=" O VAL D 430 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 473 through 480 removed outlier: 3.861A pdb=" N HIS D 478 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY D 451 " --> pdb=" O HIS D 478 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS D 480 " --> pdb=" O ARG D 449 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 449 " --> pdb=" O HIS D 480 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1308 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: 5.62 Time building geometry restraints manager: 7.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 2726 1.25 - 1.39: 4536 1.39 - 1.53: 10173 1.53 - 1.68: 673 1.68 - 1.82: 152 Bond restraints: 18260 Sorted by residual: bond pdb=" C4' UTP A 601 " pdb=" O4' UTP A 601 " ideal model delta sigma weight residual 1.320 1.534 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C4' UTP C 601 " pdb=" O4' UTP C 601 " ideal model delta sigma weight residual 1.320 1.534 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C4' UTP D 601 " pdb=" O4' UTP D 601 " ideal model delta sigma weight residual 1.320 1.533 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C4' UTP B 601 " pdb=" O4' UTP B 601 " ideal model delta sigma weight residual 1.320 1.533 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C1' UTP D 601 " pdb=" O4' UTP D 601 " ideal model delta sigma weight residual 1.553 1.351 0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 18255 not shown) Histogram of bond angle deviations from ideal: 97.54 - 105.84: 564 105.84 - 114.14: 10544 114.14 - 122.45: 11026 122.45 - 130.75: 2526 130.75 - 139.05: 100 Bond angle restraints: 24760 Sorted by residual: angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 120.55 19.32 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 120.58 19.29 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 120.60 19.27 1.00e+00 1.00e+00 3.71e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 120.61 19.26 1.00e+00 1.00e+00 3.71e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 120.57 16.26 1.00e+00 1.00e+00 2.64e+02 ... (remaining 24755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 10296 16.92 - 33.84: 568 33.84 - 50.75: 176 50.75 - 67.67: 36 67.67 - 84.59: 4 Dihedral angle restraints: 11080 sinusoidal: 4660 harmonic: 6420 Sorted by residual: dihedral pdb=" CA VAL B 58 " pdb=" C VAL B 58 " pdb=" N PHE B 59 " pdb=" CA PHE B 59 " ideal model delta harmonic sigma weight residual 180.00 136.26 43.74 0 5.00e+00 4.00e-02 7.65e+01 dihedral pdb=" CA VAL C 58 " pdb=" C VAL C 58 " pdb=" N PHE C 59 " pdb=" CA PHE C 59 " ideal model delta harmonic sigma weight residual 180.00 136.29 43.71 0 5.00e+00 4.00e-02 7.64e+01 dihedral pdb=" CA VAL D 58 " pdb=" C VAL D 58 " pdb=" N PHE D 59 " pdb=" CA PHE D 59 " ideal model delta harmonic sigma weight residual 180.00 136.31 43.69 0 5.00e+00 4.00e-02 7.64e+01 ... (remaining 11077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2587 0.137 - 0.274: 121 0.274 - 0.411: 28 0.411 - 0.548: 8 0.548 - 0.685: 8 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CB ILE B 301 " pdb=" CA ILE B 301 " pdb=" CG1 ILE B 301 " pdb=" CG2 ILE B 301 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CB ILE D 301 " pdb=" CA ILE D 301 " pdb=" CG1 ILE D 301 " pdb=" CG2 ILE D 301 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CB ILE A 301 " pdb=" CA ILE A 301 " pdb=" CG1 ILE A 301 " pdb=" CG2 ILE A 301 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 2749 not shown) Planarity restraints: 3172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 66 " 0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU A 66 " -0.088 2.00e-02 2.50e+03 pdb=" O GLU A 66 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL A 67 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 66 " -0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU D 66 " 0.088 2.00e-02 2.50e+03 pdb=" O GLU D 66 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL D 67 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 66 " -0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU C 66 " 0.088 2.00e-02 2.50e+03 pdb=" O GLU C 66 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL C 67 " -0.029 2.00e-02 2.50e+03 ... (remaining 3169 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 40 2.08 - 2.79: 4513 2.79 - 3.49: 23299 3.49 - 4.20: 41898 4.20 - 4.90: 71259 Nonbonded interactions: 141009 Sorted by model distance: nonbonded pdb=" O LEU B 69 " pdb=" N LEU B 71 " model vdw 1.380 2.520 nonbonded pdb=" O LEU A 69 " pdb=" N LEU A 71 " model vdw 1.381 2.520 nonbonded pdb=" O LEU D 69 " pdb=" N LEU D 71 " model vdw 1.381 2.520 nonbonded pdb=" O LEU C 69 " pdb=" N LEU C 71 " model vdw 1.381 2.520 nonbonded pdb=" OD1 ASP A 70 " pdb=" O1B ATP A 602 " model vdw 1.413 3.040 ... (remaining 141004 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' } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 7.510 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 51.930 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 0.214 18260 Z= 0.721 Angle : 1.371 19.319 24760 Z= 0.817 Chirality : 0.085 0.685 2752 Planarity : 0.009 0.072 3172 Dihedral : 12.048 84.590 6960 Min Nonbonded Distance : 1.380 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.90 % Allowed : 7.54 % Favored : 91.56 % Rotamer: Outliers : 1.44 % Allowed : 5.35 % Favored : 93.21 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 1.13 % 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: -4.81 (0.14), residues: 2228 helix: -3.89 (0.11), residues: 768 sheet: -3.32 (0.22), residues: 380 loop : -2.47 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 124 HIS 0.007 0.002 HIS A 235 PHE 0.033 0.003 PHE A 482 TYR 0.058 0.005 TYR B 94 ARG 0.008 0.001 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 492 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 SER cc_start: 0.8461 (p) cc_final: 0.8160 (p) REVERT: A 122 GLN cc_start: 0.8238 (pt0) cc_final: 0.7859 (pp30) REVERT: A 139 GLU cc_start: 0.8098 (tt0) cc_final: 0.7109 (mp0) REVERT: A 186 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5886 (mm) REVERT: A 335 MET cc_start: 0.7627 (ptp) cc_final: 0.7103 (ptp) REVERT: B 12 SER cc_start: 0.8459 (p) cc_final: 0.8158 (p) REVERT: B 122 GLN cc_start: 0.8237 (pt0) cc_final: 0.7859 (pp30) REVERT: B 139 GLU cc_start: 0.8089 (tt0) cc_final: 0.7095 (mp0) REVERT: B 186 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5886 (mm) REVERT: B 335 MET cc_start: 0.7631 (ptp) cc_final: 0.7109 (ptp) REVERT: C 122 GLN cc_start: 0.8255 (pt0) cc_final: 0.7859 (pp30) REVERT: C 139 GLU cc_start: 0.8134 (tt0) cc_final: 0.7197 (mp0) REVERT: C 186 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5880 (mm) REVERT: C 322 GLU cc_start: 0.8246 (pt0) cc_final: 0.7891 (pt0) REVERT: C 335 MET cc_start: 0.7652 (ptp) cc_final: 0.7118 (ptp) REVERT: D 122 GLN cc_start: 0.8252 (pt0) cc_final: 0.7858 (pp30) REVERT: D 139 GLU cc_start: 0.8135 (tt0) cc_final: 0.7198 (mp0) REVERT: D 186 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5863 (mm) REVERT: D 322 GLU cc_start: 0.8241 (pt0) cc_final: 0.7904 (pt0) REVERT: D 335 MET cc_start: 0.7648 (ptp) cc_final: 0.7112 (ptp) outliers start: 28 outliers final: 20 residues processed: 516 average time/residue: 0.3371 time to fit residues: 250.3851 Evaluate side-chains 260 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 236 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 313 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 99 ASN A 192 GLN A 526 HIS B 95 GLN B 99 ASN B 192 GLN B 526 HIS C 95 GLN C 99 ASN C 192 GLN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 99 ASN D 192 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18260 Z= 0.215 Angle : 0.770 9.277 24760 Z= 0.396 Chirality : 0.056 0.675 2752 Planarity : 0.007 0.059 3172 Dihedral : 10.951 86.264 2628 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.92 % Favored : 93.90 % Rotamer: Outliers : 3.60 % Allowed : 13.32 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -3.70 (0.15), residues: 2228 helix: -2.58 (0.14), residues: 828 sheet: -2.57 (0.24), residues: 360 loop : -2.16 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 124 HIS 0.005 0.001 HIS B 330 PHE 0.018 0.002 PHE A 520 TYR 0.017 0.002 TYR D 53 ARG 0.009 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 289 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8152 (pt0) cc_final: 0.7782 (pp30) REVERT: A 139 GLU cc_start: 0.8073 (tt0) cc_final: 0.7065 (mp0) REVERT: A 157 MET cc_start: 0.8584 (mmm) cc_final: 0.7795 (mmm) REVERT: A 301 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7489 (mp) REVERT: A 335 MET cc_start: 0.7642 (ptp) cc_final: 0.7052 (ptp) REVERT: A 362 CYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7151 (p) REVERT: A 409 PHE cc_start: 0.8176 (t80) cc_final: 0.7909 (t80) REVERT: B 122 GLN cc_start: 0.8154 (pt0) cc_final: 0.7785 (pp30) REVERT: B 139 GLU cc_start: 0.8074 (tt0) cc_final: 0.7064 (mp0) REVERT: B 157 MET cc_start: 0.8582 (mmm) cc_final: 0.7790 (mmm) REVERT: B 301 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7304 (mp) REVERT: B 335 MET cc_start: 0.7643 (ptp) cc_final: 0.7054 (ptp) REVERT: B 362 CYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7148 (p) REVERT: B 409 PHE cc_start: 0.8159 (t80) cc_final: 0.7912 (t80) REVERT: C 75 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7821 (tm-30) REVERT: C 122 GLN cc_start: 0.8190 (pt0) cc_final: 0.7789 (pp30) REVERT: C 139 GLU cc_start: 0.8124 (tt0) cc_final: 0.7142 (mp0) REVERT: C 157 MET cc_start: 0.8576 (mmm) cc_final: 0.7792 (mmm) REVERT: C 191 GLU cc_start: 0.7507 (mp0) cc_final: 0.7242 (mp0) REVERT: C 209 LEU cc_start: 0.8978 (mp) cc_final: 0.8762 (mm) REVERT: C 301 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7323 (mp) REVERT: C 335 MET cc_start: 0.7652 (ptp) cc_final: 0.7052 (ptp) REVERT: D 75 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7868 (tm-30) REVERT: D 122 GLN cc_start: 0.8194 (pt0) cc_final: 0.7790 (pp30) REVERT: D 139 GLU cc_start: 0.8117 (tt0) cc_final: 0.7144 (mp0) REVERT: D 157 MET cc_start: 0.8579 (mmm) cc_final: 0.7795 (mmm) REVERT: D 209 LEU cc_start: 0.8970 (mp) cc_final: 0.8760 (mm) REVERT: D 301 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7314 (mp) REVERT: D 335 MET cc_start: 0.7645 (ptp) cc_final: 0.7047 (ptp) outliers start: 70 outliers final: 18 residues processed: 329 average time/residue: 0.2946 time to fit residues: 147.0898 Evaluate side-chains 248 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 496 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18260 Z= 0.328 Angle : 0.736 8.655 24760 Z= 0.375 Chirality : 0.053 0.614 2752 Planarity : 0.005 0.057 3172 Dihedral : 10.047 82.125 2596 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.17 % Favored : 91.65 % Rotamer: Outliers : 6.22 % Allowed : 13.53 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.16), residues: 2228 helix: -1.55 (0.16), residues: 840 sheet: -2.35 (0.26), residues: 348 loop : -1.92 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 124 HIS 0.004 0.001 HIS C 480 PHE 0.023 0.002 PHE B 520 TYR 0.019 0.003 TYR D 94 ARG 0.012 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 251 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8160 (mmmt) REVERT: A 122 GLN cc_start: 0.8204 (pt0) cc_final: 0.7897 (pp30) REVERT: A 139 GLU cc_start: 0.8224 (tt0) cc_final: 0.7170 (mp0) REVERT: A 186 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6246 (mm) REVERT: A 335 MET cc_start: 0.7564 (ptp) cc_final: 0.6896 (ptp) REVERT: A 362 CYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7265 (p) REVERT: A 510 GLU cc_start: 0.7861 (tp30) cc_final: 0.7618 (tp30) REVERT: B 122 GLN cc_start: 0.8208 (pt0) cc_final: 0.7900 (pp30) REVERT: B 139 GLU cc_start: 0.8220 (tt0) cc_final: 0.7169 (mp0) REVERT: B 186 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6247 (mm) REVERT: B 335 MET cc_start: 0.7571 (ptp) cc_final: 0.6905 (ptp) REVERT: B 362 CYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7262 (p) REVERT: B 510 GLU cc_start: 0.7856 (tp30) cc_final: 0.7617 (tp30) REVERT: C 75 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8021 (tm-30) REVERT: C 122 GLN cc_start: 0.8191 (pt0) cc_final: 0.7865 (pp30) REVERT: C 139 GLU cc_start: 0.8184 (tt0) cc_final: 0.7157 (mp0) REVERT: C 155 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: C 177 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7625 (t0) REVERT: C 186 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6230 (mm) REVERT: C 191 GLU cc_start: 0.7796 (mp0) cc_final: 0.7428 (mp0) REVERT: C 209 LEU cc_start: 0.9049 (mp) cc_final: 0.8815 (mp) REVERT: C 335 MET cc_start: 0.7609 (ptp) cc_final: 0.6785 (ptp) REVERT: D 75 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8006 (tm-30) REVERT: D 122 GLN cc_start: 0.8185 (pt0) cc_final: 0.7861 (pp30) REVERT: D 139 GLU cc_start: 0.8222 (tt0) cc_final: 0.7197 (mp0) REVERT: D 186 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6291 (mm) REVERT: D 191 GLU cc_start: 0.7651 (mp0) cc_final: 0.7362 (mp0) REVERT: D 335 MET cc_start: 0.7588 (ptp) cc_final: 0.6744 (ptp) outliers start: 121 outliers final: 52 residues processed: 340 average time/residue: 0.2835 time to fit residues: 148.7885 Evaluate side-chains 267 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 207 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 190 optimal weight: 0.0010 chunk 57 optimal weight: 2.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 167 GLN A 192 GLN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS B 167 GLN B 192 GLN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN C 177 ASN C 192 GLN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN D 192 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18260 Z= 0.264 Angle : 0.693 9.356 24760 Z= 0.347 Chirality : 0.050 0.472 2752 Planarity : 0.005 0.056 3172 Dihedral : 9.787 88.527 2596 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.36 % Favored : 92.46 % Rotamer: Outliers : 5.04 % Allowed : 17.59 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.17), residues: 2228 helix: -1.05 (0.18), residues: 844 sheet: -2.33 (0.25), residues: 348 loop : -1.76 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 124 HIS 0.005 0.001 HIS D 330 PHE 0.017 0.002 PHE B 520 TYR 0.014 0.002 TYR B 3 ARG 0.005 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 225 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLN cc_start: 0.8100 (pt0) cc_final: 0.7812 (pp30) REVERT: A 139 GLU cc_start: 0.8233 (tt0) cc_final: 0.7145 (mp0) REVERT: A 142 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8706 (tt) REVERT: A 157 MET cc_start: 0.8589 (mmm) cc_final: 0.7755 (mmm) REVERT: A 186 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6214 (mm) REVERT: A 335 MET cc_start: 0.7672 (ptp) cc_final: 0.7428 (pmm) REVERT: A 510 GLU cc_start: 0.7872 (tp30) cc_final: 0.7633 (tp30) REVERT: B 122 GLN cc_start: 0.8101 (pt0) cc_final: 0.7814 (pp30) REVERT: B 139 GLU cc_start: 0.8228 (tt0) cc_final: 0.7147 (mp0) REVERT: B 142 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8717 (tt) REVERT: B 155 GLU cc_start: 0.7859 (pm20) cc_final: 0.7513 (pm20) REVERT: B 157 MET cc_start: 0.8589 (mmm) cc_final: 0.7733 (mmm) REVERT: B 186 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6211 (mm) REVERT: B 335 MET cc_start: 0.7675 (ptp) cc_final: 0.7425 (pmm) REVERT: B 510 GLU cc_start: 0.7891 (tp30) cc_final: 0.7638 (tp30) REVERT: C 75 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7938 (tm-30) REVERT: C 122 GLN cc_start: 0.8130 (pt0) cc_final: 0.7799 (pp30) REVERT: C 139 GLU cc_start: 0.8233 (tt0) cc_final: 0.7147 (mp0) REVERT: C 161 GLU cc_start: 0.8595 (tp30) cc_final: 0.8278 (tp30) REVERT: C 177 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7557 (t0) REVERT: C 186 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6156 (mm) REVERT: C 191 GLU cc_start: 0.7723 (mp0) cc_final: 0.7513 (mp0) REVERT: C 335 MET cc_start: 0.7623 (ptp) cc_final: 0.6964 (ptp) REVERT: C 509 MET cc_start: 0.7310 (mmp) cc_final: 0.6772 (mmp) REVERT: D 75 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8035 (tm-30) REVERT: D 122 GLN cc_start: 0.8129 (pt0) cc_final: 0.7802 (pp30) REVERT: D 139 GLU cc_start: 0.8226 (tt0) cc_final: 0.7156 (mp0) REVERT: D 142 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8701 (tt) REVERT: D 155 GLU cc_start: 0.7893 (pm20) cc_final: 0.7571 (pm20) REVERT: D 161 GLU cc_start: 0.8578 (tp30) cc_final: 0.8267 (tp30) REVERT: D 186 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6188 (mm) REVERT: D 335 MET cc_start: 0.7566 (ptp) cc_final: 0.6941 (ptp) REVERT: D 509 MET cc_start: 0.7327 (mmp) cc_final: 0.6786 (mmp) outliers start: 98 outliers final: 65 residues processed: 297 average time/residue: 0.3098 time to fit residues: 144.5561 Evaluate side-chains 284 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 211 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 190 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS C 167 GLN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18260 Z= 0.225 Angle : 0.674 9.390 24760 Z= 0.336 Chirality : 0.047 0.300 2752 Planarity : 0.004 0.056 3172 Dihedral : 9.323 79.474 2596 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.78 % Favored : 93.04 % Rotamer: Outliers : 4.63 % Allowed : 18.78 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.17), residues: 2228 helix: -0.80 (0.18), residues: 844 sheet: -2.38 (0.25), residues: 356 loop : -1.65 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 124 HIS 0.004 0.001 HIS B 330 PHE 0.016 0.001 PHE A 520 TYR 0.019 0.002 TYR D 468 ARG 0.004 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 244 time to evaluate : 2.070 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 122 GLN cc_start: 0.8076 (pt0) cc_final: 0.7801 (pp30) REVERT: A 139 GLU cc_start: 0.8216 (tt0) cc_final: 0.7117 (mp0) REVERT: A 155 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: A 161 GLU cc_start: 0.8574 (tp30) cc_final: 0.8241 (tp30) REVERT: A 234 CYS cc_start: 0.8180 (m) cc_final: 0.7940 (m) REVERT: A 335 MET cc_start: 0.7678 (ptp) cc_final: 0.7469 (pmm) REVERT: A 510 GLU cc_start: 0.7985 (tp30) cc_final: 0.7732 (tp30) REVERT: B 122 GLN cc_start: 0.8024 (pt0) cc_final: 0.7776 (pp30) REVERT: B 139 GLU cc_start: 0.8211 (tt0) cc_final: 0.7110 (mp0) REVERT: B 155 GLU cc_start: 0.7994 (pm20) cc_final: 0.7709 (pm20) REVERT: B 161 GLU cc_start: 0.8591 (tp30) cc_final: 0.8268 (tp30) REVERT: B 234 CYS cc_start: 0.8184 (m) cc_final: 0.7932 (m) REVERT: B 335 MET cc_start: 0.7684 (ptp) cc_final: 0.7470 (pmm) REVERT: B 510 GLU cc_start: 0.7991 (tp30) cc_final: 0.7743 (tp30) REVERT: C 75 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7928 (tm-30) REVERT: C 122 GLN cc_start: 0.8153 (pt0) cc_final: 0.7854 (pp30) REVERT: C 139 GLU cc_start: 0.8236 (tt0) cc_final: 0.7162 (mp0) REVERT: C 155 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: C 157 MET cc_start: 0.8531 (mmm) cc_final: 0.7689 (mmm) REVERT: C 161 GLU cc_start: 0.8595 (tp30) cc_final: 0.8257 (tp30) REVERT: C 177 ASN cc_start: 0.7843 (t0) cc_final: 0.7403 (t0) REVERT: C 191 GLU cc_start: 0.7683 (mp0) cc_final: 0.7466 (mp0) REVERT: D 122 GLN cc_start: 0.8096 (pt0) cc_final: 0.7804 (pp30) REVERT: D 139 GLU cc_start: 0.8216 (tt0) cc_final: 0.7137 (mp0) REVERT: D 155 GLU cc_start: 0.8015 (pm20) cc_final: 0.7733 (pm20) REVERT: D 157 MET cc_start: 0.8531 (mmm) cc_final: 0.7664 (mmm) REVERT: D 161 GLU cc_start: 0.8561 (tp30) cc_final: 0.8250 (tp30) REVERT: D 234 CYS cc_start: 0.8171 (m) cc_final: 0.7927 (m) REVERT: D 335 MET cc_start: 0.7683 (ptp) cc_final: 0.7446 (pmm) outliers start: 90 outliers final: 63 residues processed: 305 average time/residue: 0.2857 time to fit residues: 136.0239 Evaluate side-chains 288 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 223 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 70 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18260 Z= 0.186 Angle : 0.660 10.178 24760 Z= 0.322 Chirality : 0.046 0.258 2752 Planarity : 0.004 0.054 3172 Dihedral : 8.986 78.743 2596 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.16 % Favored : 94.66 % Rotamer: Outliers : 3.96 % Allowed : 20.22 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -1.82 (0.18), residues: 2228 helix: -0.42 (0.18), residues: 816 sheet: -2.06 (0.26), residues: 364 loop : -1.44 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 124 HIS 0.004 0.001 HIS C 480 PHE 0.020 0.001 PHE B 50 TYR 0.016 0.001 TYR D 468 ARG 0.003 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 244 time to evaluate : 2.321 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: A 2 LYS cc_start: 0.8528 (mmtm) cc_final: 0.8213 (mmmt) REVERT: A 122 GLN cc_start: 0.7970 (pt0) cc_final: 0.7738 (pp30) REVERT: A 139 GLU cc_start: 0.8172 (tt0) cc_final: 0.7046 (mp0) REVERT: A 155 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: A 157 MET cc_start: 0.8512 (mmm) cc_final: 0.7681 (mmm) REVERT: A 161 GLU cc_start: 0.8546 (tp30) cc_final: 0.8223 (tp30) REVERT: A 186 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.6058 (mm) REVERT: A 234 CYS cc_start: 0.8071 (m) cc_final: 0.7852 (m) REVERT: A 298 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7661 (tp) REVERT: A 335 MET cc_start: 0.7695 (ptp) cc_final: 0.7492 (pmm) REVERT: A 510 GLU cc_start: 0.7968 (tp30) cc_final: 0.7745 (tp30) REVERT: B 122 GLN cc_start: 0.7953 (pt0) cc_final: 0.7714 (pp30) REVERT: B 139 GLU cc_start: 0.8167 (tt0) cc_final: 0.7051 (mp0) REVERT: B 155 GLU cc_start: 0.8071 (pm20) cc_final: 0.7778 (pm20) REVERT: B 157 MET cc_start: 0.8517 (mmm) cc_final: 0.7672 (mmm) REVERT: B 161 GLU cc_start: 0.8552 (tp30) cc_final: 0.8212 (tp30) REVERT: B 186 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6056 (mm) REVERT: B 234 CYS cc_start: 0.8075 (m) cc_final: 0.7860 (m) REVERT: B 298 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7668 (tp) REVERT: B 510 GLU cc_start: 0.7975 (tp30) cc_final: 0.7775 (tp30) REVERT: C 122 GLN cc_start: 0.8025 (pt0) cc_final: 0.7759 (pp30) REVERT: C 139 GLU cc_start: 0.8261 (tt0) cc_final: 0.7194 (mp0) REVERT: C 161 GLU cc_start: 0.8539 (tp30) cc_final: 0.8212 (tp30) REVERT: C 186 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.6025 (mm) REVERT: C 191 GLU cc_start: 0.7676 (mp0) cc_final: 0.7462 (mp0) REVERT: C 298 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.7637 (tp) REVERT: D 122 GLN cc_start: 0.8016 (pt0) cc_final: 0.7770 (pp30) REVERT: D 139 GLU cc_start: 0.8167 (tt0) cc_final: 0.7067 (mp0) REVERT: D 161 GLU cc_start: 0.8536 (tp30) cc_final: 0.8207 (tp30) REVERT: D 186 LEU cc_start: 0.6286 (OUTLIER) cc_final: 0.6064 (mm) REVERT: D 298 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7664 (tp) outliers start: 77 outliers final: 56 residues processed: 300 average time/residue: 0.2735 time to fit residues: 129.5835 Evaluate side-chains 281 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 216 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 120 optimal weight: 0.0980 chunk 179 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 129 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN D 87 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18260 Z= 0.197 Angle : 0.660 9.030 24760 Z= 0.323 Chirality : 0.047 0.252 2752 Planarity : 0.004 0.054 3172 Dihedral : 8.636 76.826 2596 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.27 % Allowed : 21.14 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -1.62 (0.18), residues: 2228 helix: -0.33 (0.19), residues: 816 sheet: -1.86 (0.27), residues: 364 loop : -1.29 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 124 HIS 0.003 0.001 HIS B 330 PHE 0.020 0.001 PHE A 50 TYR 0.011 0.001 TYR A 42 ARG 0.002 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 230 time to evaluate : 2.097 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: A 1 MET cc_start: 0.7851 (tpt) cc_final: 0.7379 (tpp) REVERT: A 122 GLN cc_start: 0.7933 (pt0) cc_final: 0.7682 (pp30) REVERT: A 139 GLU cc_start: 0.8234 (tt0) cc_final: 0.7067 (mp0) REVERT: A 157 MET cc_start: 0.8526 (mmm) cc_final: 0.7690 (mmm) REVERT: A 161 GLU cc_start: 0.8507 (tp30) cc_final: 0.8209 (tp30) REVERT: A 186 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.6032 (mm) REVERT: A 298 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7541 (tp) REVERT: A 335 MET cc_start: 0.7752 (ptp) cc_final: 0.7535 (pmm) REVERT: A 510 GLU cc_start: 0.7969 (tp30) cc_final: 0.7608 (tp30) REVERT: B 122 GLN cc_start: 0.7937 (pt0) cc_final: 0.7687 (pp30) REVERT: B 139 GLU cc_start: 0.8234 (tt0) cc_final: 0.7076 (mp0) REVERT: B 157 MET cc_start: 0.8551 (mmm) cc_final: 0.7715 (mmm) REVERT: B 161 GLU cc_start: 0.8511 (tp30) cc_final: 0.8198 (tp30) REVERT: B 186 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.6030 (mm) REVERT: B 298 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7518 (tp) REVERT: B 510 GLU cc_start: 0.7973 (tp30) cc_final: 0.7766 (tp30) REVERT: C 122 GLN cc_start: 0.8006 (pt0) cc_final: 0.7745 (pp30) REVERT: C 139 GLU cc_start: 0.8276 (tt0) cc_final: 0.7227 (mp0) REVERT: C 157 MET cc_start: 0.8456 (mmm) cc_final: 0.7623 (mmt) REVERT: C 161 GLU cc_start: 0.8533 (tp30) cc_final: 0.8230 (tp30) REVERT: C 186 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5983 (mm) REVERT: C 191 GLU cc_start: 0.7746 (mp0) cc_final: 0.7535 (mp0) REVERT: C 298 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7537 (tp) REVERT: D 1 MET cc_start: 0.7984 (tpt) cc_final: 0.7778 (tpp) REVERT: D 122 GLN cc_start: 0.7942 (pt0) cc_final: 0.7687 (pp30) REVERT: D 139 GLU cc_start: 0.8240 (tt0) cc_final: 0.7183 (mp0) REVERT: D 153 ASP cc_start: 0.8038 (p0) cc_final: 0.7236 (p0) REVERT: D 157 MET cc_start: 0.8472 (mmm) cc_final: 0.8071 (mmm) REVERT: D 161 GLU cc_start: 0.8500 (tp30) cc_final: 0.8195 (tp30) REVERT: D 186 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.6053 (mm) REVERT: D 298 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7507 (tp) outliers start: 83 outliers final: 65 residues processed: 294 average time/residue: 0.2624 time to fit residues: 122.2067 Evaluate side-chains 288 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 215 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 144 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 192 optimal weight: 30.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18260 Z= 0.228 Angle : 0.679 8.346 24760 Z= 0.331 Chirality : 0.047 0.239 2752 Planarity : 0.004 0.054 3172 Dihedral : 8.402 85.020 2592 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.17 % Allowed : 21.81 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -1.48 (0.18), residues: 2228 helix: -0.23 (0.19), residues: 820 sheet: -1.84 (0.26), residues: 364 loop : -1.16 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 124 HIS 0.004 0.001 HIS D 55 PHE 0.016 0.002 PHE B 50 TYR 0.011 0.002 TYR A 42 ARG 0.003 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 218 time to evaluate : 2.064 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: A 1 MET cc_start: 0.7818 (tpt) cc_final: 0.7426 (tpp) REVERT: A 122 GLN cc_start: 0.7941 (pt0) cc_final: 0.7697 (pp30) REVERT: A 139 GLU cc_start: 0.8296 (tt0) cc_final: 0.7165 (mp0) REVERT: A 153 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7585 (p0) REVERT: A 157 MET cc_start: 0.8524 (mmm) cc_final: 0.7761 (mmm) REVERT: A 161 GLU cc_start: 0.8484 (tp30) cc_final: 0.8196 (tp30) REVERT: A 186 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5950 (mm) REVERT: A 298 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7469 (tp) REVERT: A 510 GLU cc_start: 0.7969 (tp30) cc_final: 0.7615 (tp30) REVERT: B 122 GLN cc_start: 0.7910 (pt0) cc_final: 0.7688 (pp30) REVERT: B 139 GLU cc_start: 0.8275 (tt0) cc_final: 0.7174 (mp0) REVERT: B 157 MET cc_start: 0.8585 (mmm) cc_final: 0.7746 (mmm) REVERT: B 161 GLU cc_start: 0.8491 (tp30) cc_final: 0.8201 (tp30) REVERT: B 186 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5957 (mm) REVERT: B 298 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7493 (tp) REVERT: B 510 GLU cc_start: 0.7975 (tp30) cc_final: 0.7773 (tp30) REVERT: C 122 GLN cc_start: 0.8041 (pt0) cc_final: 0.7790 (pp30) REVERT: C 139 GLU cc_start: 0.8275 (tt0) cc_final: 0.7190 (mp0) REVERT: C 161 GLU cc_start: 0.8521 (tp30) cc_final: 0.8247 (tp30) REVERT: C 186 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5978 (mm) REVERT: C 191 GLU cc_start: 0.7757 (mp0) cc_final: 0.7535 (mp0) REVERT: C 298 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7501 (tp) REVERT: D 1 MET cc_start: 0.8015 (tpt) cc_final: 0.7803 (tpp) REVERT: D 122 GLN cc_start: 0.7910 (pt0) cc_final: 0.7685 (pp30) REVERT: D 157 MET cc_start: 0.8488 (mmm) cc_final: 0.8113 (mmm) REVERT: D 161 GLU cc_start: 0.8479 (tp30) cc_final: 0.8179 (tp30) REVERT: D 186 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5992 (mm) REVERT: D 298 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7493 (tp) outliers start: 81 outliers final: 63 residues processed: 276 average time/residue: 0.2801 time to fit residues: 119.5824 Evaluate side-chains 279 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 207 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 292 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18260 Z= 0.314 Angle : 0.719 10.440 24760 Z= 0.352 Chirality : 0.048 0.230 2752 Planarity : 0.004 0.053 3172 Dihedral : 8.400 86.243 2592 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.27 % Allowed : 21.45 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -1.41 (0.18), residues: 2228 helix: -0.13 (0.19), residues: 820 sheet: -2.13 (0.25), residues: 376 loop : -0.99 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 124 HIS 0.004 0.001 HIS D 116 PHE 0.016 0.002 PHE B 520 TYR 0.012 0.002 TYR B 307 ARG 0.018 0.001 ARG D 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 219 time to evaluate : 2.160 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: A 1 MET cc_start: 0.7707 (tpt) cc_final: 0.7379 (tpp) REVERT: A 54 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 122 GLN cc_start: 0.7960 (pt0) cc_final: 0.7743 (pp30) REVERT: A 157 MET cc_start: 0.8531 (mmm) cc_final: 0.7815 (mmm) REVERT: A 161 GLU cc_start: 0.8534 (tp30) cc_final: 0.8244 (tp30) REVERT: A 186 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5971 (mm) REVERT: A 298 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7472 (tp) REVERT: A 510 GLU cc_start: 0.7942 (tp30) cc_final: 0.7728 (tp30) REVERT: B 122 GLN cc_start: 0.7960 (pt0) cc_final: 0.7745 (pp30) REVERT: B 157 MET cc_start: 0.8542 (mmm) cc_final: 0.7693 (mmm) REVERT: B 161 GLU cc_start: 0.8541 (tp30) cc_final: 0.8252 (tp30) REVERT: B 186 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5961 (mm) REVERT: B 298 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7509 (tp) REVERT: B 510 GLU cc_start: 0.7993 (tp30) cc_final: 0.7752 (tp30) REVERT: C 122 GLN cc_start: 0.8014 (pt0) cc_final: 0.7750 (pp30) REVERT: C 157 MET cc_start: 0.8528 (mmm) cc_final: 0.8216 (mmm) REVERT: C 161 GLU cc_start: 0.8541 (tp30) cc_final: 0.8253 (tp30) REVERT: C 186 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5957 (mm) REVERT: C 191 GLU cc_start: 0.7842 (mp0) cc_final: 0.7505 (mp0) REVERT: C 298 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7807 (tp) REVERT: D 122 GLN cc_start: 0.8005 (pt0) cc_final: 0.7782 (pp30) REVERT: D 161 GLU cc_start: 0.8492 (tp30) cc_final: 0.8202 (tp30) REVERT: D 186 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.6019 (mm) REVERT: D 298 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7509 (tp) outliers start: 83 outliers final: 72 residues processed: 279 average time/residue: 0.2774 time to fit residues: 122.9861 Evaluate side-chains 284 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 204 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.3980 chunk 127 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 chunk 219 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 138 optimal weight: 0.0570 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18260 Z= 0.185 Angle : 0.700 12.343 24760 Z= 0.337 Chirality : 0.047 0.231 2752 Planarity : 0.004 0.052 3172 Dihedral : 8.061 86.677 2592 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.42 % Allowed : 23.66 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % 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: -1.27 (0.18), residues: 2228 helix: -0.06 (0.19), residues: 828 sheet: -1.98 (0.25), residues: 376 loop : -0.90 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 285 HIS 0.003 0.001 HIS B 330 PHE 0.015 0.001 PHE C 525 TYR 0.009 0.001 TYR D 468 ARG 0.014 0.000 ARG C 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 223 time to evaluate : 2.318 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: A 1 MET cc_start: 0.7640 (tpt) cc_final: 0.7337 (tpp) REVERT: A 54 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 122 GLN cc_start: 0.7788 (pt0) cc_final: 0.7487 (pp30) REVERT: A 126 MET cc_start: 0.8827 (mmm) cc_final: 0.8555 (mmm) REVERT: A 153 ASP cc_start: 0.7847 (p0) cc_final: 0.7516 (p0) REVERT: A 155 GLU cc_start: 0.8149 (pm20) cc_final: 0.7594 (pm20) REVERT: A 157 MET cc_start: 0.8478 (mmm) cc_final: 0.7783 (mmm) REVERT: A 161 GLU cc_start: 0.8411 (tp30) cc_final: 0.8139 (tp30) REVERT: A 298 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7283 (tp) REVERT: A 510 GLU cc_start: 0.7989 (tp30) cc_final: 0.7608 (tp30) REVERT: B 122 GLN cc_start: 0.7801 (pt0) cc_final: 0.7564 (pp30) REVERT: B 157 MET cc_start: 0.8539 (mmm) cc_final: 0.7664 (mmm) REVERT: B 161 GLU cc_start: 0.8424 (tp30) cc_final: 0.8149 (tp30) REVERT: B 298 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7319 (tp) REVERT: B 510 GLU cc_start: 0.7975 (tp30) cc_final: 0.7584 (tp30) REVERT: C 1 MET cc_start: 0.7735 (tpt) cc_final: 0.7533 (tpp) REVERT: C 122 GLN cc_start: 0.7846 (pt0) cc_final: 0.7618 (pp30) REVERT: C 157 MET cc_start: 0.8474 (mmm) cc_final: 0.7739 (mmt) REVERT: C 177 ASN cc_start: 0.7825 (t0) cc_final: 0.7442 (t0) REVERT: C 191 GLU cc_start: 0.7803 (mp0) cc_final: 0.7558 (mp0) REVERT: C 237 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8319 (t0) REVERT: C 298 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7571 (tp) REVERT: D 122 GLN cc_start: 0.7817 (pt0) cc_final: 0.7545 (pp30) REVERT: D 126 MET cc_start: 0.8820 (mmm) cc_final: 0.8604 (mmm) REVERT: D 157 MET cc_start: 0.8438 (mmm) cc_final: 0.7580 (mmt) REVERT: D 298 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7310 (tp) outliers start: 47 outliers final: 40 residues processed: 256 average time/residue: 0.2763 time to fit residues: 111.2488 Evaluate side-chains 255 residues out of total 1944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 210 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 365 ASP Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 73 optimal weight: 0.0170 chunk 179 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.122754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.098092 restraints weight = 40024.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.101914 restraints weight = 21007.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.104557 restraints weight = 13724.349| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18260 Z= 0.185 Angle : 0.680 12.024 24760 Z= 0.327 Chirality : 0.047 0.243 2752 Planarity : 0.004 0.053 3172 Dihedral : 7.860 87.481 2592 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.57 % Allowed : 23.15 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2228 helix: -0.01 (0.19), residues: 828 sheet: -1.98 (0.25), residues: 384 loop : -0.86 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 285 HIS 0.007 0.001 HIS D 55 PHE 0.014 0.001 PHE C 409 TYR 0.011 0.001 TYR B 307 ARG 0.015 0.000 ARG D 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3550.20 seconds wall clock time: 66 minutes 32.14 seconds (3992.14 seconds total)