Starting phenix.real_space_refine on Fri Jan 19 13:45:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6l_10103/01_2024/6s6l_10103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6l_10103/01_2024/6s6l_10103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6l_10103/01_2024/6s6l_10103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6l_10103/01_2024/6s6l_10103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6l_10103/01_2024/6s6l_10103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6l_10103/01_2024/6s6l_10103.pdb" } resolution = 3.1 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= 0.003 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 7476 2.51 5 N 1905 2.21 5 O 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 11587 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3838 Classifications: {'peptide': 500} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 455} Chain breaks: 2 Chain: "B" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3886 Classifications: {'peptide': 508} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 43, 'TRANS': 461} Chain breaks: 1 Chain: "C" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3863 Classifications: {'peptide': 502} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 457} Time building chain proxies: 6.54, per 1000 atoms: 0.56 Number of scatterers: 11587 At special positions: 0 Unit cell: (97.98, 110.76, 116.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2158 8.00 N 1905 7.00 C 7476 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: 4.00 Conformation dependent library (CDL) restraints added in 2.1 seconds 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2792 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 19 sheets defined 10.2% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 54 through 58 removed outlier: 4.128A pdb=" N ASN A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 88 removed outlier: 3.584A pdb=" N LEU A 88 " --> pdb=" O GLY A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.798A pdb=" N THR A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 144 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 removed outlier: 3.870A pdb=" N CYS A 240 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.634A pdb=" N VAL A 286 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 removed outlier: 3.692A pdb=" N VAL A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.066A pdb=" N ALA B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.910A pdb=" N ASN B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.839A pdb=" N LEU B 88 " --> pdb=" O GLY B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 137 through 142 removed outlier: 4.575A pdb=" N THR B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 removed outlier: 3.846A pdb=" N CYS B 240 " --> pdb=" O PRO B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.736A pdb=" N VAL B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.593A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 58 removed outlier: 3.764A pdb=" N ASN C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 88 removed outlier: 3.865A pdb=" N LEU C 88 " --> pdb=" O GLY C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 85 through 88' Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 137 through 142 removed outlier: 4.049A pdb=" N THR C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 465 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.692A pdb=" N SER A 202 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASN A 105 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASP A 212 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A 103 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASN A 214 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLY A 101 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 216 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR A 99 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.275A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 202 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASN A 105 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASP A 212 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A 103 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASN A 214 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLY A 101 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 216 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR A 99 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 83 removed outlier: 6.835A pdb=" N ILE A 78 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU A 185 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 80 " --> pdb=" O CYS A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 451 removed outlier: 3.515A pdb=" N LEU A 507 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 451 removed outlier: 5.169A pdb=" N ILE A 497 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER A 500 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLU A 488 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU A 485 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 479 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 487 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 519 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG A 476 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A 517 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG A 478 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N PHE A 515 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 269 removed outlier: 4.324A pdb=" N ARG A 268 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 298 removed outlier: 4.724A pdb=" N ALA A 290 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 17.065A pdb=" N ARG A 373 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 12.507A pdb=" N GLY A 360 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE A 375 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE A 358 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLY A 333 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER A 332 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY A 400 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN A 334 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A 398 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU A 336 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 394 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLN A 340 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG A 392 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N GLU A 342 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N ARG A 390 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 60 through 69 removed outlier: 4.218A pdb=" N CYS B 62 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 205 " --> pdb=" O CYS B 62 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N LEU B 64 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N GLY B 203 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N GLU B 66 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N VAL B 201 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.672A pdb=" N CYS B 183 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP B 81 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 181 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS B 121 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ALA B 119 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 171 Processing sheet with id=AB2, first strand: chain 'B' and resid 251 through 253 removed outlier: 3.992A pdb=" N GLU B 447 " --> pdb=" O MET B 436 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 289 through 298 removed outlier: 6.837A pdb=" N PHE B 375 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE B 358 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN B 334 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLY B 400 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU B 336 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE B 398 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N GLU B 338 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ARG B 396 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLN B 340 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N VAL B 394 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N GLU B 342 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 12.228A pdb=" N ARG B 392 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 427 through 429 removed outlier: 4.005A pdb=" N TYR B 496 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER B 500 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N GLU B 488 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 487 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 477 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA B 472 " --> pdb=" O TRP B 520 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRP B 520 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU B 474 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.482A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLY C 101 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.482A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLY C 101 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 78 through 83 removed outlier: 6.567A pdb=" N CYS C 183 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP C 81 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU C 181 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LYS C 121 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 447 through 451 removed outlier: 4.139A pdb=" N GLU C 447 " --> pdb=" O MET C 436 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU C 252 " --> pdb=" O PHE C 509 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 447 through 451 removed outlier: 4.139A pdb=" N GLU C 447 " --> pdb=" O MET C 436 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE C 497 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR C 496 " --> pdb=" O TYR C 492 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N SER C 500 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLU C 488 " --> pdb=" O SER C 500 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU C 485 " --> pdb=" O ASN C 479 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 479 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA C 472 " --> pdb=" O TRP C 520 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TRP C 520 " --> pdb=" O ALA C 472 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C 474 " --> pdb=" O VAL C 518 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 289 through 298 removed outlier: 4.392A pdb=" N ALA C 290 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE C 375 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE C 358 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER C 332 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY C 400 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN C 334 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE C 398 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU C 336 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLN C 340 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG C 392 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLU C 342 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N ARG C 390 " --> pdb=" O GLU C 342 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 939 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: 3.68 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1943 1.31 - 1.44: 3204 1.44 - 1.57: 6688 1.57 - 1.70: 0 1.70 - 1.83: 72 Bond restraints: 11907 Sorted by residual: bond pdb=" CB VAL B 60 " pdb=" CG2 VAL B 60 " ideal model delta sigma weight residual 1.521 1.367 0.154 3.30e-02 9.18e+02 2.19e+01 bond pdb=" CA CYS A 183 " pdb=" CB CYS A 183 " ideal model delta sigma weight residual 1.534 1.439 0.096 2.47e-02 1.64e+03 1.50e+01 bond pdb=" C ASN B 192 " pdb=" N SER B 193 " ideal model delta sigma weight residual 1.335 1.233 0.101 3.04e-02 1.08e+03 1.11e+01 bond pdb=" CB THR C 219 " pdb=" CG2 THR C 219 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.78e+00 bond pdb=" CB VAL B 103 " pdb=" CG1 VAL B 103 " ideal model delta sigma weight residual 1.521 1.421 0.100 3.30e-02 9.18e+02 9.24e+00 ... (remaining 11902 not shown) Histogram of bond angle deviations from ideal: 93.95 - 103.10: 150 103.10 - 112.25: 6042 112.25 - 121.41: 6806 121.41 - 130.56: 3280 130.56 - 139.71: 49 Bond angle restraints: 16327 Sorted by residual: angle pdb=" CA LEU B 112 " pdb=" CB LEU B 112 " pdb=" CG LEU B 112 " ideal model delta sigma weight residual 116.30 135.44 -19.14 3.50e+00 8.16e-02 2.99e+01 angle pdb=" C TYR A 186 " pdb=" N THR A 187 " pdb=" CA THR A 187 " ideal model delta sigma weight residual 121.59 139.71 -18.12 3.54e+00 7.98e-02 2.62e+01 angle pdb=" N PRO B 132 " pdb=" CA PRO B 132 " pdb=" C PRO B 132 " ideal model delta sigma weight residual 112.47 122.46 -9.99 2.06e+00 2.36e-01 2.35e+01 angle pdb=" CA VAL B 22 " pdb=" C VAL B 22 " pdb=" N PRO B 23 " ideal model delta sigma weight residual 117.00 121.16 -4.16 9.50e-01 1.11e+00 1.91e+01 angle pdb=" C VAL B 216 " pdb=" N TYR B 217 " pdb=" CA TYR B 217 " ideal model delta sigma weight residual 121.86 115.08 6.78 1.58e+00 4.01e-01 1.84e+01 ... (remaining 16322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.00: 6617 14.00 - 28.00: 360 28.00 - 42.01: 63 42.01 - 56.01: 9 56.01 - 70.01: 3 Dihedral angle restraints: 7052 sinusoidal: 2701 harmonic: 4351 Sorted by residual: dihedral pdb=" CA PRO B 194 " pdb=" C PRO B 194 " pdb=" N GLY B 195 " pdb=" CA GLY B 195 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA VAL C 103 " pdb=" C VAL C 103 " pdb=" N GLY C 104 " pdb=" CA GLY C 104 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA LEU A 64 " pdb=" C LEU A 64 " pdb=" N GLY A 65 " pdb=" CA GLY A 65 " ideal model delta harmonic sigma weight residual 180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 7049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1533 0.089 - 0.178: 289 0.178 - 0.267: 34 0.267 - 0.356: 5 0.356 - 0.445: 1 Chirality restraints: 1862 Sorted by residual: chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA PRO B 132 " pdb=" N PRO B 132 " pdb=" C PRO B 132 " pdb=" CB PRO B 132 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CG LEU A 206 " pdb=" CB LEU A 206 " pdb=" CD1 LEU A 206 " pdb=" CD2 LEU A 206 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1859 not shown) Planarity restraints: 2135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 61 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" CD GLN B 61 " 0.049 2.00e-02 2.50e+03 pdb=" OE1 GLN B 61 " -0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN B 61 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 219 " -0.014 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C THR B 219 " 0.047 2.00e-02 2.50e+03 pdb=" O THR B 219 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO B 220 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 52 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO B 53 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 53 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 53 " -0.037 5.00e-02 4.00e+02 ... (remaining 2132 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2813 2.79 - 3.32: 9528 3.32 - 3.85: 20007 3.85 - 4.37: 23381 4.37 - 4.90: 40613 Nonbonded interactions: 96342 Sorted by model distance: nonbonded pdb=" OD2 ASP A 52 " pdb=" OH TYR B 99 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" O CYS C 143 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR A 241 " pdb=" OG SER B 282 " model vdw 2.283 2.440 nonbonded pdb=" OG SER A 282 " pdb=" OG1 THR B 241 " model vdw 2.317 2.440 nonbonded pdb=" OG1 THR B 363 " pdb=" OE1 GLU B 407 " model vdw 2.317 2.440 ... (remaining 96337 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 221 or resid 229 through 531)) selection = (chain 'B' and (resid 30 through 191 or resid 199 through 531)) selection = (chain 'C' and (resid 30 through 191 or resid 199 through 221 or resid 229 throu \ gh 531)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.170 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: 25.420 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 32.350 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 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 : 0.014 0.154 11907 Z= 0.917 Angle : 1.122 19.136 16327 Z= 0.582 Chirality : 0.069 0.445 1862 Planarity : 0.010 0.066 2135 Dihedral : 9.314 70.011 4260 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.16 % Allowed : 1.52 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.07 % 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: -2.85 (0.18), residues: 1498 helix: -2.94 (0.38), residues: 58 sheet: -1.44 (0.23), residues: 427 loop : -2.14 (0.17), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP A 102 HIS 0.015 0.004 HIS B 94 PHE 0.032 0.005 PHE A 80 TYR 0.030 0.004 TYR A 186 ARG 0.019 0.002 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 MET cc_start: 0.8881 (ptt) cc_final: 0.8163 (ptp) outliers start: 2 outliers final: 2 residues processed: 126 average time/residue: 0.3495 time to fit residues: 58.2575 Evaluate side-chains 94 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 103 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 40.0000 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 40.0000 chunk 76 optimal weight: 50.0000 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 45 optimal weight: 30.0000 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 105 ASN A 170 HIS A 214 ASN A 334 GLN A 479 ASN B 105 ASN B 170 HIS B 265 GLN B 334 GLN C 105 ASN C 170 HIS C 173 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11907 Z= 0.256 Angle : 0.634 11.594 16327 Z= 0.317 Chirality : 0.047 0.167 1862 Planarity : 0.007 0.059 2135 Dihedral : 5.841 56.982 1628 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.40 % Allowed : 4.88 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.07 % 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: -2.04 (0.19), residues: 1498 helix: -1.23 (0.54), residues: 62 sheet: -1.04 (0.24), residues: 415 loop : -1.56 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 264 HIS 0.003 0.001 HIS C 170 PHE 0.023 0.002 PHE C 289 TYR 0.018 0.002 TYR A 496 ARG 0.008 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 436 MET cc_start: 0.3512 (mtm) cc_final: 0.2782 (mtm) REVERT: C 98 MET cc_start: 0.8867 (ptt) cc_final: 0.8243 (ptp) REVERT: C 469 GLN cc_start: 0.6665 (mt0) cc_final: 0.6441 (mm-40) outliers start: 5 outliers final: 1 residues processed: 104 average time/residue: 0.3154 time to fit residues: 44.4379 Evaluate side-chains 88 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 40.0000 chunk 42 optimal weight: 50.0000 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 50.0000 chunk 37 optimal weight: 50.0000 chunk 136 optimal weight: 30.0000 chunk 147 optimal weight: 50.0000 chunk 121 optimal weight: 50.0000 chunk 135 optimal weight: 30.0000 chunk 46 optimal weight: 30.0000 chunk 109 optimal weight: 0.9980 overall best weight: 18.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 73 ASN C 49 ASN C 50 GLN C 340 GLN ** C 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.133 11907 Z= 1.075 Angle : 1.021 14.232 16327 Z= 0.504 Chirality : 0.067 0.359 1862 Planarity : 0.009 0.090 2135 Dihedral : 6.524 59.109 1626 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.52 % Allowed : 7.21 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.07 % 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: -1.94 (0.20), residues: 1498 helix: -1.04 (0.57), residues: 56 sheet: -1.01 (0.24), residues: 410 loop : -1.48 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP B 264 HIS 0.012 0.003 HIS A 170 PHE 0.029 0.003 PHE A 117 TYR 0.030 0.003 TYR C 217 ARG 0.011 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 179 MET cc_start: 0.8343 (ttm) cc_final: 0.8066 (tpp) REVERT: B 436 MET cc_start: 0.3740 (mtm) cc_final: 0.3059 (mtm) outliers start: 19 outliers final: 9 residues processed: 111 average time/residue: 0.3270 time to fit residues: 48.6534 Evaluate side-chains 94 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 288 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 40.0000 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 30.0000 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 39 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11907 Z= 0.346 Angle : 0.661 11.711 16327 Z= 0.327 Chirality : 0.048 0.325 1862 Planarity : 0.007 0.057 2135 Dihedral : 5.778 55.459 1626 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.36 % Allowed : 7.69 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.07 % 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: -1.54 (0.20), residues: 1498 helix: -0.57 (0.59), residues: 57 sheet: -0.81 (0.24), residues: 410 loop : -1.18 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 264 HIS 0.004 0.001 HIS A 94 PHE 0.019 0.002 PHE C 80 TYR 0.018 0.002 TYR A 496 ARG 0.004 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6567 (mp10) REVERT: A 488 GLU cc_start: 0.6245 (mt-10) cc_final: 0.5971 (tt0) REVERT: C 98 MET cc_start: 0.8612 (ptt) cc_final: 0.8175 (ptp) REVERT: C 469 GLN cc_start: 0.6767 (mt0) cc_final: 0.6532 (mm-40) outliers start: 17 outliers final: 10 residues processed: 105 average time/residue: 0.3044 time to fit residues: 43.8086 Evaluate side-chains 93 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 288 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 40.0000 chunk 130 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 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 73 ASN C 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11907 Z= 0.248 Angle : 0.605 11.376 16327 Z= 0.298 Chirality : 0.046 0.195 1862 Planarity : 0.006 0.060 2135 Dihedral : 5.399 55.528 1626 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.76 % Allowed : 8.25 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.07 % 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: -1.32 (0.20), residues: 1498 helix: -0.13 (0.61), residues: 57 sheet: -0.77 (0.25), residues: 398 loop : -0.98 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 264 HIS 0.003 0.001 HIS A 94 PHE 0.018 0.002 PHE B 375 TYR 0.020 0.001 TYR C 501 ARG 0.008 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 175 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6468 (mp10) REVERT: A 488 GLU cc_start: 0.6370 (mt-10) cc_final: 0.6063 (tt0) REVERT: C 469 GLN cc_start: 0.6763 (mt0) cc_final: 0.6513 (mm-40) outliers start: 22 outliers final: 12 residues processed: 107 average time/residue: 0.2985 time to fit residues: 44.3088 Evaluate side-chains 94 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 413 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 10.0000 chunk 130 optimal weight: 50.0000 chunk 28 optimal weight: 50.0000 chunk 85 optimal weight: 40.0000 chunk 35 optimal weight: 6.9990 chunk 145 optimal weight: 40.0000 chunk 120 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 50.0000 chunk 139 optimal weight: 40.0000 overall best weight: 5.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11907 Z= 0.373 Angle : 0.656 11.736 16327 Z= 0.323 Chirality : 0.048 0.346 1862 Planarity : 0.006 0.063 2135 Dihedral : 5.489 56.616 1626 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.92 % Allowed : 8.97 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.07 % 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: -1.26 (0.21), residues: 1498 helix: -0.01 (0.61), residues: 57 sheet: -0.76 (0.25), residues: 398 loop : -0.93 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 264 HIS 0.004 0.001 HIS A 94 PHE 0.017 0.002 PHE A 117 TYR 0.018 0.002 TYR C 501 ARG 0.006 0.000 ARG C 433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: A 175 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6443 (mp10) REVERT: A 488 GLU cc_start: 0.6312 (mt-10) cc_final: 0.6035 (tt0) REVERT: C 469 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6085 (mt0) outliers start: 24 outliers final: 17 residues processed: 100 average time/residue: 0.2905 time to fit residues: 40.6302 Evaluate side-chains 99 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 469 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 122 optimal weight: 30.0000 chunk 81 optimal weight: 10.0000 chunk 144 optimal weight: 40.0000 chunk 90 optimal weight: 50.0000 chunk 88 optimal weight: 0.0570 chunk 66 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11907 Z= 0.287 Angle : 0.606 11.543 16327 Z= 0.299 Chirality : 0.046 0.294 1862 Planarity : 0.006 0.063 2135 Dihedral : 5.297 56.213 1626 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.00 % Allowed : 9.21 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.07 % 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: -1.15 (0.21), residues: 1498 helix: 0.24 (0.63), residues: 57 sheet: -0.64 (0.25), residues: 380 loop : -0.89 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP B 264 HIS 0.003 0.001 HIS A 94 PHE 0.016 0.002 PHE C 117 TYR 0.017 0.001 TYR C 501 ARG 0.003 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7158 (tm-30) REVERT: A 175 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6417 (mp10) REVERT: A 488 GLU cc_start: 0.6328 (mt-10) cc_final: 0.6058 (tt0) REVERT: C 469 GLN cc_start: 0.6758 (OUTLIER) cc_final: 0.6132 (mt0) outliers start: 25 outliers final: 19 residues processed: 101 average time/residue: 0.2957 time to fit residues: 41.3220 Evaluate side-chains 104 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 469 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 50.0000 chunk 43 optimal weight: 20.0000 chunk 28 optimal weight: 50.0000 chunk 91 optimal weight: 50.0000 chunk 98 optimal weight: 0.0980 chunk 71 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 50.0000 chunk 126 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11907 Z= 0.241 Angle : 0.587 11.416 16327 Z= 0.288 Chirality : 0.045 0.223 1862 Planarity : 0.006 0.063 2135 Dihedral : 5.172 56.134 1626 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.08 % Allowed : 8.97 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.07 % 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: -1.11 (0.21), residues: 1498 helix: -0.08 (0.60), residues: 63 sheet: -0.63 (0.25), residues: 388 loop : -0.83 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 264 HIS 0.003 0.001 HIS A 94 PHE 0.017 0.002 PHE C 375 TYR 0.017 0.001 TYR C 501 ARG 0.003 0.000 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 175 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6396 (mp10) REVERT: A 488 GLU cc_start: 0.6306 (mt-10) cc_final: 0.6027 (tt0) REVERT: C 469 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6136 (mt0) outliers start: 26 outliers final: 19 residues processed: 102 average time/residue: 0.2948 time to fit residues: 41.8368 Evaluate side-chains 103 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 469 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 8.9990 chunk 138 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 50.0000 chunk 121 optimal weight: 50.0000 chunk 127 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 chunk 142 optimal weight: 30.0000 chunk 86 optimal weight: 0.0970 overall best weight: 7.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11907 Z= 0.457 Angle : 0.684 11.738 16327 Z= 0.336 Chirality : 0.050 0.472 1862 Planarity : 0.006 0.063 2135 Dihedral : 5.484 57.078 1626 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.92 % Allowed : 9.61 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.07 % 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: -1.07 (0.21), residues: 1498 helix: 0.31 (0.62), residues: 57 sheet: -0.65 (0.25), residues: 394 loop : -0.79 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 264 HIS 0.004 0.001 HIS B 94 PHE 0.020 0.002 PHE A 117 TYR 0.019 0.002 TYR C 501 ARG 0.004 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 175 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6466 (mp10) REVERT: A 488 GLU cc_start: 0.6381 (mt-10) cc_final: 0.6047 (tt0) REVERT: C 98 MET cc_start: 0.8577 (ptt) cc_final: 0.8338 (ptp) REVERT: C 469 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.6013 (mt0) outliers start: 24 outliers final: 17 residues processed: 98 average time/residue: 0.2895 time to fit residues: 39.5422 Evaluate side-chains 100 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 469 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11907 Z= 0.286 Angle : 0.607 11.595 16327 Z= 0.298 Chirality : 0.047 0.414 1862 Planarity : 0.006 0.066 2135 Dihedral : 5.242 56.319 1626 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.68 % Allowed : 9.77 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.07 % 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: -0.98 (0.21), residues: 1498 helix: 0.57 (0.63), residues: 57 sheet: -0.60 (0.25), residues: 402 loop : -0.73 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 264 HIS 0.003 0.001 HIS A 94 PHE 0.016 0.002 PHE C 117 TYR 0.016 0.001 TYR C 501 ARG 0.003 0.000 ARG A 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7161 (tm-30) REVERT: A 175 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6445 (mp10) REVERT: A 488 GLU cc_start: 0.6289 (mt-10) cc_final: 0.6068 (tt0) REVERT: C 469 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6127 (mt0) outliers start: 21 outliers final: 19 residues processed: 96 average time/residue: 0.2982 time to fit residues: 39.6746 Evaluate side-chains 101 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 469 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 30.0000 chunk 104 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 86 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.214493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.202618 restraints weight = 14978.858| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 0.64 r_work: 0.4068 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 1.26 restraints_weight: 0.2500 r_work: 0.3984 rms_B_bonded: 1.87 restraints_weight: 0.1250 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11907 Z= 0.382 Angle : 0.657 11.707 16327 Z= 0.322 Chirality : 0.049 0.427 1862 Planarity : 0.006 0.067 2135 Dihedral : 5.374 56.794 1626 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.76 % Allowed : 9.85 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.07 % 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: -0.96 (0.21), residues: 1498 helix: 0.51 (0.63), residues: 57 sheet: -0.58 (0.25), residues: 392 loop : -0.73 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 264 HIS 0.004 0.001 HIS A 94 PHE 0.018 0.002 PHE A 117 TYR 0.017 0.002 TYR C 501 ARG 0.004 0.000 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2512.54 seconds wall clock time: 46 minutes 34.49 seconds (2794.49 seconds total)