Starting phenix.real_space_refine on Fri Feb 16 06:44:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a11_15065/02_2024/8a11_15065_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a11_15065/02_2024/8a11_15065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a11_15065/02_2024/8a11_15065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a11_15065/02_2024/8a11_15065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a11_15065/02_2024/8a11_15065_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a11_15065/02_2024/8a11_15065_updated.pdb" } resolution = 3.52 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= 0.050 sd= 0.669 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 10 5.49 5 S 72 5.16 5 C 9209 2.51 5 N 2557 2.21 5 O 2782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A ASP 219": "OD1" <-> "OD2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C ASP 142": "OD1" <-> "OD2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C ASP 482": "OD1" <-> "OD2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 415": "OE1" <-> "OE2" Residue "D PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 450": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14630 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3605 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 445} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3639 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 448} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3639 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 448} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3621 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 446} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 8.41, per 1000 atoms: 0.57 Number of scatterers: 14630 At special positions: 0 Unit cell: (123.571, 135.128, 96.901, 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 72 16.00 P 10 15.00 O 2782 8.00 N 2557 7.00 C 9209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.01 Conformation dependent library (CDL) restraints added in 2.9 seconds 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 11 sheets defined 46.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 26 through 29 No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 87 through 103 removed outlier: 3.597A pdb=" N GLU A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.658A pdb=" N GLU A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 306 through 320 Processing helix chain 'A' and resid 322 through 345 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 415 through 439 removed outlier: 4.100A pdb=" N GLN A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 4.089A pdb=" N ALA A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 472 removed outlier: 4.431A pdb=" N ALA A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA A 460 " --> pdb=" O LYS A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 22 removed outlier: 3.702A pdb=" N MET B 21 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 29 No H-bonds generated for 'chain 'B' and resid 26 through 29' Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 87 through 103 Processing helix chain 'B' and resid 120 through 131 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.691A pdb=" N GLU B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 235 through 238 No H-bonds generated for 'chain 'B' and resid 235 through 238' Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'B' and resid 322 through 344 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.678A pdb=" N VAL B 376 " --> pdb=" O ARG B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.527A pdb=" N SER B 410 " --> pdb=" O PRO B 406 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 439 Processing helix chain 'B' and resid 445 through 453 removed outlier: 5.007A pdb=" N ALA B 453 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 473 removed outlier: 4.215A pdb=" N ALA B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 22 Processing helix chain 'C' and resid 26 through 29 No H-bonds generated for 'chain 'C' and resid 26 through 29' Processing helix chain 'C' and resid 31 through 45 Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 87 through 103 Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 162 through 166 Processing helix chain 'C' and resid 184 through 193 removed outlier: 3.948A pdb=" N GLU C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.566A pdb=" N ASN C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 306 through 320 removed outlier: 4.035A pdb=" N ALA C 310 " --> pdb=" O ASN C 306 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 345 Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 408 through 411 No H-bonds generated for 'chain 'C' and resid 408 through 411' Processing helix chain 'C' and resid 415 through 439 Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.972A pdb=" N ALA C 453 " --> pdb=" O LYS C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 472 Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 26 through 29 No H-bonds generated for 'chain 'D' and resid 26 through 29' Processing helix chain 'D' and resid 31 through 45 Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 87 through 103 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 120 through 131 Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 162 through 166 Processing helix chain 'D' and resid 184 through 193 removed outlier: 3.996A pdb=" N ARG D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.549A pdb=" N VAL D 296 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 319 removed outlier: 3.773A pdb=" N ALA D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 345 removed outlier: 4.093A pdb=" N LEU D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 406 through 411 Processing helix chain 'D' and resid 415 through 439 Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 455 through 472 Processing sheet with id= A, first strand: chain 'A' and resid 111 through 114 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 362 removed outlier: 3.916A pdb=" N ASN A 385 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 273 through 276 removed outlier: 7.123A pdb=" N ILE A 284 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 197 through 201 removed outlier: 6.536A pdb=" N TYR B 224 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA B 200 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET B 226 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 250 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 359 through 361 Processing sheet with id= F, first strand: chain 'B' and resid 273 through 276 removed outlier: 7.068A pdb=" N ILE B 284 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= H, first strand: chain 'C' and resid 359 through 362 removed outlier: 3.667A pdb=" N VAL C 361 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 273 through 276 removed outlier: 6.996A pdb=" N ILE C 284 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 111 through 114 Processing sheet with id= K, first strand: chain 'D' and resid 358 through 362 removed outlier: 3.956A pdb=" N ASN D 385 " --> pdb=" O ARG D 402 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1731 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: 3.95 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4751 1.34 - 1.46: 1966 1.46 - 1.57: 8107 1.57 - 1.69: 15 1.69 - 1.81: 104 Bond restraints: 14943 Sorted by residual: bond pdb=" OP4 LLP A 257 " pdb=" P LLP A 257 " ideal model delta sigma weight residual 1.730 1.544 0.186 2.00e-02 2.50e+03 8.62e+01 bond pdb=" OP4 LLP C 257 " pdb=" P LLP C 257 " ideal model delta sigma weight residual 1.730 1.545 0.185 2.00e-02 2.50e+03 8.57e+01 bond pdb=" OP4 LLP D 257 " pdb=" P LLP D 257 " ideal model delta sigma weight residual 1.730 1.545 0.185 2.00e-02 2.50e+03 8.57e+01 bond pdb=" OP4 LLP B 257 " pdb=" P LLP B 257 " ideal model delta sigma weight residual 1.730 1.545 0.185 2.00e-02 2.50e+03 8.54e+01 bond pdb=" NZ LLP A 257 " pdb=" C4' LLP A 257 " ideal model delta sigma weight residual 1.313 1.433 -0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 14938 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.25: 540 107.25 - 113.93: 8317 113.93 - 120.61: 6151 120.61 - 127.29: 5103 127.29 - 133.97: 146 Bond angle restraints: 20257 Sorted by residual: angle pdb=" CE LLP C 257 " pdb=" NZ LLP C 257 " pdb=" C4' LLP C 257 " ideal model delta sigma weight residual 120.00 109.23 10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" NZ LLP B 257 " pdb=" C4' LLP B 257 " pdb=" C4 LLP B 257 " ideal model delta sigma weight residual 120.00 109.37 10.63 3.00e+00 1.11e-01 1.25e+01 angle pdb=" NZ LLP D 257 " pdb=" C4' LLP D 257 " pdb=" C4 LLP D 257 " ideal model delta sigma weight residual 120.00 109.43 10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" NZ LLP C 257 " pdb=" C4' LLP C 257 " pdb=" C4 LLP C 257 " ideal model delta sigma weight residual 120.00 109.43 10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CE LLP B 257 " pdb=" NZ LLP B 257 " pdb=" C4' LLP B 257 " ideal model delta sigma weight residual 120.00 109.60 10.40 3.00e+00 1.11e-01 1.20e+01 ... (remaining 20252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.82: 8651 22.82 - 45.65: 296 45.65 - 68.47: 18 68.47 - 91.30: 23 91.30 - 114.12: 3 Dihedral angle restraints: 8991 sinusoidal: 3614 harmonic: 5377 Sorted by residual: dihedral pdb=" C5 LLP A 257 " pdb=" C5' LLP A 257 " pdb=" OP4 LLP A 257 " pdb=" P LLP A 257 " ideal model delta sinusoidal sigma weight residual 208.96 94.84 114.12 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" CG LLP D 257 " pdb=" CD LLP D 257 " pdb=" CE LLP D 257 " pdb=" NZ LLP D 257 " ideal model delta sinusoidal sigma weight residual 119.81 -144.85 -95.34 1 3.00e+01 1.11e-03 1.17e+01 dihedral pdb=" CB GLU C 133 " pdb=" CG GLU C 133 " pdb=" CD GLU C 133 " pdb=" OE1 GLU C 133 " ideal model delta sinusoidal sigma weight residual 0.00 89.19 -89.19 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1603 0.032 - 0.064: 440 0.064 - 0.096: 139 0.096 - 0.128: 61 0.128 - 0.160: 4 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA ILE D 199 " pdb=" N ILE D 199 " pdb=" C ILE D 199 " pdb=" CB ILE D 199 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA PRO D 134 " pdb=" N PRO D 134 " pdb=" C PRO D 134 " pdb=" CB PRO D 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA PRO C 134 " pdb=" N PRO C 134 " pdb=" C PRO C 134 " pdb=" CB PRO C 134 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2244 not shown) Planarity restraints: 2621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP D 257 " 0.162 2.00e-02 2.50e+03 2.80e-01 7.83e+02 pdb=" NZ LLP D 257 " -0.380 2.00e-02 2.50e+03 pdb=" C4 LLP D 257 " -0.134 2.00e-02 2.50e+03 pdb=" C4' LLP D 257 " 0.353 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 257 " -0.159 2.00e-02 2.50e+03 2.77e-01 7.67e+02 pdb=" NZ LLP A 257 " 0.374 2.00e-02 2.50e+03 pdb=" C4 LLP A 257 " 0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 257 " -0.351 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP C 257 " -0.152 2.00e-02 2.50e+03 2.47e-01 6.12e+02 pdb=" NZ LLP C 257 " 0.329 2.00e-02 2.50e+03 pdb=" C4 LLP C 257 " 0.133 2.00e-02 2.50e+03 pdb=" C4' LLP C 257 " -0.310 2.00e-02 2.50e+03 ... (remaining 2618 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1841 2.75 - 3.29: 14339 3.29 - 3.83: 24135 3.83 - 4.36: 27644 4.36 - 4.90: 47861 Nonbonded interactions: 115820 Sorted by model distance: nonbonded pdb=" OG1 THR C 155 " pdb=" O LYS C 158 " model vdw 2.214 2.440 nonbonded pdb=" OG SER B 354 " pdb=" OD1 ASN B 356 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR C 327 " pdb=" O PRO C 406 " model vdw 2.261 2.440 nonbonded pdb=" OD2 ASP B 438 " pdb=" OH TYR B 457 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR C 77 " pdb=" O ASN C 293 " model vdw 2.266 2.440 ... (remaining 115815 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' and resid 16 through 482) selection = (chain 'C' and resid 16 through 482) selection = (chain 'D' and (resid 16 through 278 or (resid 279 and (name N or name CA or nam \ e C or name O or name CB )) or resid 280 through 482)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.530 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: 0.010 Extract box with map and model: 13.360 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 41.340 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.006 0.186 14943 Z= 0.449 Angle : 0.546 10.767 20257 Z= 0.300 Chirality : 0.036 0.160 2247 Planarity : 0.010 0.280 2621 Dihedral : 11.702 114.122 5561 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.17), residues: 1855 helix: -0.37 (0.16), residues: 884 sheet: -1.45 (0.35), residues: 192 loop : -2.76 (0.18), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 111 HIS 0.002 0.000 HIS D 135 PHE 0.010 0.001 PHE A 418 TYR 0.005 0.000 TYR D 457 ARG 0.002 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7599 (ptm) cc_final: 0.7075 (ttp) REVERT: A 191 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.8016 (ttp80) REVERT: A 287 ASN cc_start: 0.7847 (t0) cc_final: 0.7569 (t0) REVERT: C 142 ASP cc_start: 0.8375 (t0) cc_final: 0.8149 (t0) REVERT: C 229 MET cc_start: 0.7628 (ptm) cc_final: 0.7419 (ptm) REVERT: D 447 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8236 (tm-30) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2628 time to fit residues: 61.6394 Evaluate side-chains 94 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 88 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 44 GLN B 109 GLN C 148 HIS ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 HIS C 385 ASN D 70 ASN D 221 ASN D 328 GLN ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14943 Z= 0.204 Angle : 0.506 6.333 20257 Z= 0.251 Chirality : 0.038 0.138 2247 Planarity : 0.003 0.040 2621 Dihedral : 8.095 103.262 2171 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.17 % Allowed : 7.83 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 1855 helix: 1.02 (0.18), residues: 871 sheet: -1.07 (0.36), residues: 197 loop : -2.08 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 111 HIS 0.004 0.001 HIS A 148 PHE 0.016 0.001 PHE D 268 TYR 0.011 0.001 TYR A 269 ARG 0.008 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8330 (mtm-85) cc_final: 0.8116 (mtm-85) outliers start: 18 outliers final: 14 residues processed: 102 average time/residue: 0.2475 time to fit residues: 39.6195 Evaluate side-chains 91 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 169 optimal weight: 0.6980 chunk 182 optimal weight: 20.0000 chunk 150 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN C 334 ASN ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14943 Z= 0.182 Angle : 0.479 8.942 20257 Z= 0.237 Chirality : 0.037 0.133 2247 Planarity : 0.003 0.043 2621 Dihedral : 7.852 98.444 2171 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.24 % Allowed : 10.44 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.20), residues: 1855 helix: 1.44 (0.18), residues: 883 sheet: -0.92 (0.37), residues: 198 loop : -1.77 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 15 HIS 0.003 0.001 HIS D 249 PHE 0.016 0.001 PHE D 268 TYR 0.013 0.001 TYR A 183 ARG 0.008 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8654 (mtm-85) cc_final: 0.8258 (mtm110) outliers start: 19 outliers final: 15 residues processed: 95 average time/residue: 0.2423 time to fit residues: 36.7643 Evaluate side-chains 96 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS A 330 GLN A 334 ASN ** C 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14943 Z= 0.436 Angle : 0.681 11.211 20257 Z= 0.346 Chirality : 0.043 0.175 2247 Planarity : 0.005 0.042 2621 Dihedral : 8.541 91.470 2171 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.15 % Allowed : 12.92 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1855 helix: 1.18 (0.18), residues: 877 sheet: -0.99 (0.38), residues: 181 loop : -1.70 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 111 HIS 0.007 0.002 HIS B 249 PHE 0.020 0.002 PHE D 268 TYR 0.016 0.002 TYR A 183 ARG 0.009 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 74 time to evaluate : 1.657 Fit side-chains REVERT: A 226 MET cc_start: 0.8298 (tmm) cc_final: 0.7967 (ttt) REVERT: A 358 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8329 (pp) outliers start: 33 outliers final: 23 residues processed: 98 average time/residue: 0.2159 time to fit residues: 34.9636 Evaluate side-chains 95 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 409 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS A 306 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14943 Z= 0.135 Angle : 0.482 7.211 20257 Z= 0.241 Chirality : 0.037 0.133 2247 Planarity : 0.003 0.048 2621 Dihedral : 7.839 88.986 2171 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.50 % Allowed : 14.03 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1855 helix: 1.71 (0.18), residues: 874 sheet: -0.97 (0.37), residues: 201 loop : -1.42 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 15 HIS 0.004 0.001 HIS A 231 PHE 0.010 0.001 PHE D 268 TYR 0.010 0.001 TYR C 73 ARG 0.005 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 1.814 Fit side-chains revert: symmetry clash REVERT: A 226 MET cc_start: 0.8072 (tmm) cc_final: 0.7844 (ttt) REVERT: A 358 LEU cc_start: 0.8482 (pp) cc_final: 0.8247 (pp) outliers start: 23 outliers final: 16 residues processed: 104 average time/residue: 0.2277 time to fit residues: 38.7196 Evaluate side-chains 94 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 405 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS B 148 HIS ** C 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 HIS ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14943 Z= 0.400 Angle : 0.636 7.946 20257 Z= 0.322 Chirality : 0.041 0.144 2247 Planarity : 0.004 0.047 2621 Dihedral : 8.332 87.770 2171 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.48 % Allowed : 13.97 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1855 helix: 1.46 (0.18), residues: 872 sheet: -0.86 (0.39), residues: 180 loop : -1.53 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 15 HIS 0.007 0.001 HIS A 231 PHE 0.018 0.002 PHE D 268 TYR 0.013 0.002 TYR D 172 ARG 0.005 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 74 time to evaluate : 1.606 Fit side-chains REVERT: A 226 MET cc_start: 0.8233 (tmm) cc_final: 0.7904 (ttt) REVERT: A 358 LEU cc_start: 0.8578 (pp) cc_final: 0.8346 (pp) REVERT: C 231 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7304 (t-90) outliers start: 38 outliers final: 27 residues processed: 103 average time/residue: 0.2158 time to fit residues: 36.3444 Evaluate side-chains 100 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 405 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.4980 chunk 100 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14943 Z= 0.146 Angle : 0.496 7.324 20257 Z= 0.247 Chirality : 0.038 0.135 2247 Planarity : 0.003 0.049 2621 Dihedral : 7.893 86.109 2171 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.57 % Allowed : 14.56 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1855 helix: 1.77 (0.18), residues: 879 sheet: -0.94 (0.37), residues: 202 loop : -1.34 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 15 HIS 0.005 0.001 HIS A 231 PHE 0.010 0.001 PHE D 268 TYR 0.009 0.001 TYR D 172 ARG 0.004 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 1.860 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.7243 (mtt) cc_final: 0.6934 (mtm) REVERT: A 226 MET cc_start: 0.8043 (tmm) cc_final: 0.7839 (ttt) REVERT: C 231 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7308 (t-90) outliers start: 24 outliers final: 22 residues processed: 97 average time/residue: 0.2255 time to fit residues: 35.8463 Evaluate side-chains 103 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 405 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 122 optimal weight: 0.0770 chunk 88 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14943 Z= 0.186 Angle : 0.505 8.230 20257 Z= 0.251 Chirality : 0.038 0.136 2247 Planarity : 0.003 0.048 2621 Dihedral : 7.870 87.080 2171 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.96 % Allowed : 14.82 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1855 helix: 1.85 (0.18), residues: 879 sheet: -0.88 (0.37), residues: 201 loop : -1.29 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 15 HIS 0.004 0.001 HIS A 231 PHE 0.012 0.001 PHE D 268 TYR 0.010 0.001 TYR D 172 ARG 0.004 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 1.666 Fit side-chains REVERT: A 226 MET cc_start: 0.8038 (tmm) cc_final: 0.7754 (ttt) REVERT: C 142 ASP cc_start: 0.7967 (t0) cc_final: 0.7742 (t0) REVERT: C 231 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7340 (t-90) outliers start: 30 outliers final: 28 residues processed: 101 average time/residue: 0.2199 time to fit residues: 36.4843 Evaluate side-chains 105 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 76 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 405 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 166 optimal weight: 0.0770 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14943 Z= 0.204 Angle : 0.516 8.610 20257 Z= 0.256 Chirality : 0.038 0.140 2247 Planarity : 0.003 0.048 2621 Dihedral : 7.868 89.245 2171 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.28 % Allowed : 14.62 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1855 helix: 1.85 (0.18), residues: 880 sheet: -0.90 (0.37), residues: 202 loop : -1.22 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 15 HIS 0.003 0.001 HIS D 249 PHE 0.012 0.001 PHE D 268 TYR 0.010 0.001 TYR D 172 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 78 time to evaluate : 1.871 Fit side-chains REVERT: A 226 MET cc_start: 0.8038 (tmm) cc_final: 0.7759 (ttt) REVERT: C 142 ASP cc_start: 0.8049 (t0) cc_final: 0.7814 (t0) REVERT: C 231 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7343 (t-90) outliers start: 35 outliers final: 30 residues processed: 106 average time/residue: 0.2497 time to fit residues: 43.2973 Evaluate side-chains 109 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 78 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 405 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 0.0980 chunk 185 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS D 148 HIS ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14943 Z= 0.158 Angle : 0.502 11.223 20257 Z= 0.247 Chirality : 0.037 0.136 2247 Planarity : 0.003 0.048 2621 Dihedral : 7.713 85.181 2171 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.09 % Allowed : 14.95 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1855 helix: 1.93 (0.18), residues: 881 sheet: -0.86 (0.37), residues: 202 loop : -1.15 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 15 HIS 0.002 0.001 HIS D 231 PHE 0.010 0.001 PHE D 268 TYR 0.009 0.001 TYR D 172 ARG 0.003 0.000 ARG A 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 1.754 Fit side-chains revert: symmetry clash REVERT: C 142 ASP cc_start: 0.8002 (t0) cc_final: 0.7757 (t0) REVERT: C 231 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7357 (t-90) outliers start: 32 outliers final: 29 residues processed: 107 average time/residue: 0.2173 time to fit residues: 38.3425 Evaluate side-chains 110 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 80 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 262 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 405 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 5.9990 chunk 157 optimal weight: 0.0370 chunk 45 optimal weight: 0.0770 chunk 136 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS D 148 HIS ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.080846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.061677 restraints weight = 62066.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.063584 restraints weight = 34705.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.064824 restraints weight = 24323.839| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14943 Z= 0.116 Angle : 0.480 10.825 20257 Z= 0.234 Chirality : 0.037 0.136 2247 Planarity : 0.003 0.048 2621 Dihedral : 7.493 83.828 2171 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.44 % Allowed : 15.67 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1855 helix: 2.10 (0.18), residues: 874 sheet: -0.79 (0.37), residues: 199 loop : -1.05 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 111 HIS 0.003 0.000 HIS A 231 PHE 0.008 0.001 PHE A 418 TYR 0.008 0.001 TYR C 172 ARG 0.003 0.000 ARG A 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2591.66 seconds wall clock time: 48 minutes 42.76 seconds (2922.76 seconds total)