Starting phenix.real_space_refine on Mon Aug 5 01:58:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uv3_42604/08_2024/8uv3_42604.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uv3_42604/08_2024/8uv3_42604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uv3_42604/08_2024/8uv3_42604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uv3_42604/08_2024/8uv3_42604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uv3_42604/08_2024/8uv3_42604.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uv3_42604/08_2024/8uv3_42604.cif" } resolution = 2.72 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= 0.006 sd= 0.484 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 Mg 3 5.21 5 S 48 5.16 5 C 7599 2.51 5 N 1941 2.21 5 O 2478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 20": "OD1" <-> "OD2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C ASP 366": "OD1" <-> "OD2" Residue "C ASP 388": "OD1" <-> "OD2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C ARG 396": "NH1" <-> "NH2" Residue "C ASP 443": "OD1" <-> "OD2" Residue "C TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12069 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3949 Classifications: {'peptide': 514} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 468} Chain: "B" Number of atoms: 3967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3967 Classifications: {'peptide': 517} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 470} Chain: "C" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3874 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 458} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Time building chain proxies: 9.58, per 1000 atoms: 0.79 Number of scatterers: 12069 At special positions: 0 Unit cell: (119.9, 117.7, 122.1, 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 48 16.00 Mg 3 11.99 O 2478 8.00 N 1941 7.00 C 7599 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: 4.53 Conformation dependent library (CDL) restraints added in 2.1 seconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2840 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 21 sheets defined 8.5% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 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 Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.993A pdb=" N THR A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 144 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.772A pdb=" N ALA B 45 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 removed outlier: 4.054A pdb=" N ASN B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.588A 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 140 through 144 removed outlier: 3.567A pdb=" N PHE B 144 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.669A pdb=" N VAL B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 52 through 58 removed outlier: 4.025A pdb=" N ASN C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 88 removed outlier: 3.571A 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: 4.060A pdb=" N THR C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.544A pdb=" N TRP C 285 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 282 through 286' Processing helix chain 'C' and resid 454 through 465 removed outlier: 3.636A pdb=" N VAL C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER C 459 " --> pdb=" O GLN C 455 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 461 " --> pdb=" O PHE C 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.604A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ARG A 204 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA A 113 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU A 206 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL A 111 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LYS A 208 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLN A 109 " --> pdb=" O LYS A 208 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 210 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU A 107 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A 212 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.604A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ARG A 204 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA A 113 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU A 206 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL A 111 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LYS A 208 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLN A 109 " --> pdb=" O LYS A 208 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 210 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU A 107 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A 212 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 83 removed outlier: 6.836A pdb=" N CYS A 183 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP A 81 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A 181 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS A 121 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA A 119 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 451 removed outlier: 5.408A pdb=" N ILE A 497 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER A 500 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLU A 488 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 477 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU A 488 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 475 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS A 490 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 473 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 478 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 508 removed outlier: 5.408A pdb=" N ILE A 497 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER A 500 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLU A 488 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 477 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU A 488 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 475 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LYS A 490 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 473 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 472 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 519 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 296 removed outlier: 4.716A pdb=" N ALA A 290 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE A 375 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE A 358 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR A 379 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N THR A 354 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER A 332 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLY A 400 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN A 334 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 398 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU A 336 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 394 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN A 340 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG A 392 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 389 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 69 removed outlier: 6.530A pdb=" N LEU B 205 " --> pdb=" O CYS B 62 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N LEU B 64 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N GLY B 203 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N GLU B 66 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N VAL B 201 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.763A pdb=" N ILE B 78 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 185 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 80 " --> pdb=" O CYS B 183 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS B 121 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA B 119 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 103 removed outlier: 6.263A pdb=" N TYR B 99 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B 218 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLY B 101 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 448 through 451 Processing sheet with id=AB2, first strand: chain 'B' and resid 268 through 269 removed outlier: 4.368A pdb=" N ARG B 268 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 289 through 297 removed outlier: 4.629A pdb=" N ALA B 290 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE B 375 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE B 358 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN B 334 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLY B 400 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLU B 336 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 398 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU B 338 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ARG B 396 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N GLN B 340 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N VAL B 394 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N GLU B 342 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 13.222A pdb=" N ARG B 392 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 389 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 427 through 429 removed outlier: 5.371A pdb=" N SER B 500 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLU B 488 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 485 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN B 479 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 487 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA B 472 " --> pdb=" O TRP B 520 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TRP B 520 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 6.554A 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: 6.133A pdb=" N LEU C 205 " --> pdb=" O CYS C 62 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N LEU C 64 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N GLY C 203 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N GLU C 66 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N VAL C 201 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.293A 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: 6.133A pdb=" N LEU C 205 " --> pdb=" O CYS C 62 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N LEU C 64 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N GLY C 203 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N GLU C 66 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N VAL C 201 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.293A 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: 6.550A pdb=" N CYS C 183 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP C 81 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU C 181 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS C 121 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA C 119 " --> pdb=" O PRO C 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 448 through 451 Processing sheet with id=AB9, first strand: chain 'C' and resid 268 through 269 removed outlier: 4.426A pdb=" N ARG C 268 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 289 through 297 removed outlier: 4.333A pdb=" N ALA C 290 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 377 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 337 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER C 332 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY C 400 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN C 334 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE C 398 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLU C 336 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 394 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN C 340 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG C 392 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLU C 342 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ARG C 390 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 289 " --> pdb=" O ALA C 393 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 427 through 429 Processing sheet with id=AC3, first strand: chain 'C' and resid 485 through 492 removed outlier: 6.939A pdb=" N TYR C 477 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU C 488 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 475 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS C 490 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU C 473 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA C 472 " --> pdb=" O TRP C 520 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP C 520 " --> pdb=" O ALA C 472 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU C 474 " --> pdb=" O VAL C 518 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 783 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: 3.86 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2148 1.32 - 1.44: 3071 1.44 - 1.57: 6823 1.57 - 1.69: 2 1.69 - 1.81: 72 Bond restraints: 12116 Sorted by residual: bond pdb=" CB ASN A 115 " pdb=" CG ASN A 115 " ideal model delta sigma weight residual 1.516 1.424 0.092 2.50e-02 1.60e+03 1.35e+01 bond pdb=" C ASN B 192 " pdb=" N SER B 193 " ideal model delta sigma weight residual 1.335 1.246 0.088 3.04e-02 1.08e+03 8.47e+00 bond pdb=" CB VAL C 103 " pdb=" CG1 VAL C 103 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.53e+00 bond pdb=" C TYR A 130 " pdb=" N PHE A 131 " ideal model delta sigma weight residual 1.331 1.289 0.042 1.63e-02 3.76e+03 6.60e+00 bond pdb=" CB THR C 219 " pdb=" CG2 THR C 219 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.88e+00 ... (remaining 12111 not shown) Histogram of bond angle deviations from ideal: 94.13 - 102.19: 29 102.19 - 110.26: 2924 110.26 - 118.32: 6396 118.32 - 126.39: 7029 126.39 - 134.45: 236 Bond angle restraints: 16614 Sorted by residual: angle pdb=" N ALA B 25 " pdb=" CA ALA B 25 " pdb=" C ALA B 25 " ideal model delta sigma weight residual 112.97 105.19 7.78 1.06e+00 8.90e-01 5.39e+01 angle pdb=" N VAL B 22 " pdb=" CA VAL B 22 " pdb=" C VAL B 22 " ideal model delta sigma weight residual 108.63 113.50 -4.87 8.60e-01 1.35e+00 3.20e+01 angle pdb=" N LEU B 21 " pdb=" CA LEU B 21 " pdb=" C LEU B 21 " ideal model delta sigma weight residual 108.24 115.32 -7.08 1.32e+00 5.74e-01 2.88e+01 angle pdb=" CA VAL A 216 " pdb=" C VAL A 216 " pdb=" N TYR A 217 " ideal model delta sigma weight residual 117.37 121.32 -3.95 7.40e-01 1.83e+00 2.85e+01 angle pdb=" C PHE A 215 " pdb=" N VAL A 216 " pdb=" CA VAL A 216 " ideal model delta sigma weight residual 122.97 117.77 5.20 9.80e-01 1.04e+00 2.82e+01 ... (remaining 16609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6426 17.73 - 35.47: 627 35.47 - 53.20: 104 53.20 - 70.93: 14 70.93 - 88.67: 16 Dihedral angle restraints: 7187 sinusoidal: 2759 harmonic: 4428 Sorted by residual: dihedral pdb=" CA VAL B 26 " pdb=" C VAL B 26 " pdb=" N GLU B 27 " pdb=" CA GLU B 27 " ideal model delta harmonic sigma weight residual 180.00 -135.36 -44.64 0 5.00e+00 4.00e-02 7.97e+01 dihedral pdb=" CA GLU B 27 " pdb=" C GLU B 27 " pdb=" N GLN B 28 " pdb=" CA GLN B 28 " ideal model delta harmonic sigma weight residual 180.00 136.50 43.50 0 5.00e+00 4.00e-02 7.57e+01 dihedral pdb=" CA PRO A 194 " pdb=" C PRO A 194 " pdb=" N GLY A 195 " pdb=" CA GLY A 195 " ideal model delta harmonic sigma weight residual 180.00 140.73 39.27 0 5.00e+00 4.00e-02 6.17e+01 ... (remaining 7184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1408 0.068 - 0.136: 417 0.136 - 0.204: 53 0.204 - 0.272: 9 0.272 - 0.340: 4 Chirality restraints: 1891 Sorted by residual: chirality pdb=" CB VAL C 151 " pdb=" CA VAL C 151 " pdb=" CG1 VAL C 151 " pdb=" CG2 VAL C 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA PHE C 199 " pdb=" N PHE C 199 " pdb=" C PHE C 199 " pdb=" CB PHE C 199 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB THR B 219 " pdb=" CA THR B 219 " pdb=" OG1 THR B 219 " pdb=" CG2 THR B 219 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1888 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 199 " 0.039 2.00e-02 2.50e+03 2.71e-02 1.29e+01 pdb=" CG PHE C 199 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE C 199 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 199 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 199 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE C 199 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 199 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 128 " -0.056 5.00e-02 4.00e+02 8.46e-02 1.15e+01 pdb=" N PRO C 129 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 89 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO B 90 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.039 5.00e-02 4.00e+02 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 122 2.46 - 3.07: 7043 3.07 - 3.68: 17009 3.68 - 4.29: 26650 4.29 - 4.90: 44152 Nonbonded interactions: 94976 Sorted by model distance: nonbonded pdb="MG MG A 601 " pdb=" O HOH A 755 " model vdw 1.851 2.170 nonbonded pdb="MG MG C 601 " pdb=" O HOH C 742 " model vdw 1.877 2.170 nonbonded pdb="MG MG B 601 " pdb=" O HOH B 706 " model vdw 1.904 2.170 nonbonded pdb=" OE1 GLN C 438 " pdb="MG MG C 601 " model vdw 1.941 2.170 nonbonded pdb=" OE1 GLN A 469 " pdb=" O HOH A 701 " model vdw 1.990 3.040 ... (remaining 94971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 530 or resid 601)) selection = (chain 'B' and (resid 28 through 530 or resid 601)) selection = chain 'C' } 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: 9.780 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 36.080 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:13.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.010 0.092 12116 Z= 0.658 Angle : 1.059 15.640 16614 Z= 0.571 Chirality : 0.064 0.340 1891 Planarity : 0.009 0.085 2176 Dihedral : 14.694 88.666 4347 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.98 % Favored : 91.82 % Rotamer: Outliers : 0.39 % Allowed : 6.06 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.17), residues: 1528 helix: -4.59 (0.31), residues: 55 sheet: -1.23 (0.24), residues: 398 loop : -3.03 (0.14), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP B 102 HIS 0.008 0.002 HIS B 94 PHE 0.056 0.004 PHE C 199 TYR 0.040 0.003 TYR C 217 ARG 0.010 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 GLU cc_start: 0.5430 (pm20) cc_final: 0.5030 (mp0) REVERT: A 255 ASP cc_start: 0.7645 (t0) cc_final: 0.7427 (t0) REVERT: A 281 ILE cc_start: 0.8422 (mt) cc_final: 0.8202 (mm) REVERT: A 407 GLU cc_start: 0.5554 (mm-30) cc_final: 0.4629 (tt0) REVERT: A 486 LEU cc_start: 0.8095 (mt) cc_final: 0.7839 (mt) REVERT: B 21 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7750 (pp) REVERT: B 455 GLN cc_start: 0.7491 (tp-100) cc_final: 0.7207 (mm-40) REVERT: C 148 MET cc_start: 0.8376 (ttm) cc_final: 0.8091 (ttm) REVERT: C 235 ILE cc_start: 0.7968 (mt) cc_final: 0.7668 (mm) REVERT: C 238 ARG cc_start: 0.7401 (ptp-170) cc_final: 0.7117 (ptp90) REVERT: C 356 GLU cc_start: 0.5364 (mm-30) cc_final: 0.5114 (mm-30) REVERT: C 392 ARG cc_start: 0.7602 (ttt-90) cc_final: 0.7365 (ttp-170) REVERT: C 478 ARG cc_start: 0.7291 (ttm170) cc_final: 0.6938 (ttm170) REVERT: C 488 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6879 (pt0) outliers start: 5 outliers final: 5 residues processed: 156 average time/residue: 1.3871 time to fit residues: 233.3224 Evaluate side-chains 142 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 50.0000 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 46 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 40.0000 chunk 138 optimal weight: 10.0000 overall best weight: 0.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 261 ASN A 526 GLN B 73 ASN B 105 ASN B 140 GLN B 170 HIS B 261 ASN B 266 ASN B 270 HIS B 340 GLN B 455 GLN B 493 ASN C 61 GLN C 105 ASN C 270 HIS C 334 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12116 Z= 0.155 Angle : 0.617 7.510 16614 Z= 0.326 Chirality : 0.045 0.147 1891 Planarity : 0.006 0.059 2176 Dihedral : 6.130 42.656 1665 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.42 % Allowed : 9.52 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.63 (0.19), residues: 1528 helix: -3.19 (0.50), residues: 56 sheet: -0.78 (0.24), residues: 417 loop : -2.22 (0.16), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 460 HIS 0.003 0.001 HIS A 270 PHE 0.019 0.001 PHE B 355 TYR 0.013 0.001 TYR A 250 ARG 0.003 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 255 ASP cc_start: 0.7431 (t0) cc_final: 0.7178 (t70) REVERT: A 274 THR cc_start: 0.8604 (t) cc_final: 0.8374 (t) REVERT: A 281 ILE cc_start: 0.8452 (mt) cc_final: 0.8238 (mm) REVERT: A 337 ILE cc_start: 0.6741 (pt) cc_final: 0.6364 (pp) REVERT: A 407 GLU cc_start: 0.5305 (mm-30) cc_final: 0.4526 (tt0) REVERT: A 486 LEU cc_start: 0.8310 (mt) cc_final: 0.8033 (mt) REVERT: A 488 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6791 (mt-10) REVERT: A 516 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: B 21 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7423 (pp) REVERT: B 22 VAL cc_start: 0.7309 (m) cc_final: 0.7098 (m) REVERT: B 315 SER cc_start: 0.7757 (t) cc_final: 0.7512 (m) REVERT: B 322 ARG cc_start: 0.7246 (mtm-85) cc_final: 0.6661 (mtm-85) REVERT: C 148 MET cc_start: 0.8271 (ttm) cc_final: 0.8036 (ttm) REVERT: C 229 MET cc_start: 0.8457 (tpt) cc_final: 0.7588 (tpt) REVERT: C 235 ILE cc_start: 0.8073 (mt) cc_final: 0.7833 (mm) REVERT: C 238 ARG cc_start: 0.7345 (ptp-170) cc_final: 0.7099 (ptp90) REVERT: C 356 GLU cc_start: 0.5508 (mm-30) cc_final: 0.5164 (mm-30) REVERT: C 405 ILE cc_start: 0.8250 (mp) cc_final: 0.8012 (pt) REVERT: C 437 ARG cc_start: 0.5726 (mtm180) cc_final: 0.5518 (mtm-85) REVERT: C 478 ARG cc_start: 0.7709 (ttm170) cc_final: 0.7316 (ttp-110) REVERT: C 488 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7053 (pt0) REVERT: C 512 ASP cc_start: 0.7853 (p0) cc_final: 0.7546 (p0) outliers start: 18 outliers final: 7 residues processed: 155 average time/residue: 1.3886 time to fit residues: 232.0299 Evaluate side-chains 140 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 407 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 30.0000 chunk 42 optimal weight: 0.4980 chunk 114 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 30.0000 chunk 138 optimal weight: 7.9990 chunk 149 optimal weight: 40.0000 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 47 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 173 GLN A 236 GLN C 49 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12116 Z= 0.153 Angle : 0.608 7.338 16614 Z= 0.314 Chirality : 0.045 0.156 1891 Planarity : 0.006 0.055 2176 Dihedral : 5.708 41.289 1660 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.34 % Allowed : 11.88 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.08 (0.19), residues: 1528 helix: -2.33 (0.58), residues: 57 sheet: -0.50 (0.24), residues: 423 loop : -1.82 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 520 HIS 0.003 0.001 HIS A 270 PHE 0.019 0.001 PHE C 199 TYR 0.011 0.001 TYR A 217 ARG 0.004 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 175 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7493 (mt0) REVERT: A 176 GLU cc_start: 0.7787 (pm20) cc_final: 0.7464 (pm20) REVERT: A 281 ILE cc_start: 0.8463 (mt) cc_final: 0.8251 (mm) REVERT: A 337 ILE cc_start: 0.6644 (pt) cc_final: 0.6275 (pp) REVERT: A 407 GLU cc_start: 0.5417 (mm-30) cc_final: 0.4563 (tt0) REVERT: A 486 LEU cc_start: 0.8252 (mt) cc_final: 0.7988 (mt) REVERT: B 21 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7758 (pp) REVERT: B 315 SER cc_start: 0.7696 (t) cc_final: 0.7385 (m) REVERT: B 322 ARG cc_start: 0.7194 (mtm-85) cc_final: 0.6627 (mtm-85) REVERT: C 148 MET cc_start: 0.8353 (ttm) cc_final: 0.8074 (ttm) REVERT: C 229 MET cc_start: 0.8483 (tpt) cc_final: 0.7745 (tpt) REVERT: C 235 ILE cc_start: 0.8091 (mt) cc_final: 0.7863 (mm) REVERT: C 238 ARG cc_start: 0.7257 (ptp-170) cc_final: 0.7002 (ptp90) REVERT: C 356 GLU cc_start: 0.5553 (mm-30) cc_final: 0.5236 (mm-30) REVERT: C 392 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.5418 (ttt-90) REVERT: C 428 VAL cc_start: 0.8267 (t) cc_final: 0.8027 (m) REVERT: C 478 ARG cc_start: 0.7662 (ttm170) cc_final: 0.7146 (ttp-110) REVERT: C 488 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6973 (pt0) REVERT: C 512 ASP cc_start: 0.7819 (p0) cc_final: 0.7493 (p0) REVERT: C 516 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7445 (mt-10) outliers start: 17 outliers final: 8 residues processed: 146 average time/residue: 1.4481 time to fit residues: 227.6607 Evaluate side-chains 137 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 407 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 146 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12116 Z= 0.290 Angle : 0.727 11.590 16614 Z= 0.376 Chirality : 0.050 0.186 1891 Planarity : 0.007 0.062 2176 Dihedral : 6.205 46.212 1660 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.75 % Allowed : 11.96 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.05 (0.19), residues: 1528 helix: -2.20 (0.59), residues: 57 sheet: -0.46 (0.24), residues: 418 loop : -1.80 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 169 HIS 0.004 0.001 HIS C 170 PHE 0.036 0.002 PHE C 199 TYR 0.023 0.002 TYR A 217 ARG 0.004 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7905 (pm20) cc_final: 0.7057 (pm20) REVERT: A 224 ARG cc_start: 0.7919 (mtp-110) cc_final: 0.7641 (mtp180) REVERT: A 238 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6569 (ptt180) REVERT: A 281 ILE cc_start: 0.8419 (mt) cc_final: 0.8208 (mm) REVERT: A 337 ILE cc_start: 0.6637 (pt) cc_final: 0.6265 (pp) REVERT: A 356 GLU cc_start: 0.5694 (mm-30) cc_final: 0.5463 (mm-30) REVERT: A 407 GLU cc_start: 0.5551 (mm-30) cc_final: 0.4677 (tt0) REVERT: A 478 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.7358 (ttm-80) REVERT: A 486 LEU cc_start: 0.8316 (mt) cc_final: 0.8042 (mt) REVERT: A 514 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8290 (mm) REVERT: B 21 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7851 (pp) REVERT: B 322 ARG cc_start: 0.7172 (mtm-85) cc_final: 0.6607 (mtm-85) REVERT: C 148 MET cc_start: 0.8428 (ttm) cc_final: 0.8133 (ttm) REVERT: C 235 ILE cc_start: 0.8067 (mt) cc_final: 0.7840 (mm) REVERT: C 238 ARG cc_start: 0.7288 (ptp-170) cc_final: 0.7040 (ptp90) REVERT: C 356 GLU cc_start: 0.5445 (mm-30) cc_final: 0.5092 (mm-30) REVERT: C 392 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.5415 (ttt-90) REVERT: C 428 VAL cc_start: 0.8284 (t) cc_final: 0.7958 (m) REVERT: C 488 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6891 (pt0) REVERT: C 512 ASP cc_start: 0.7748 (p0) cc_final: 0.7415 (p0) REVERT: C 516 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7479 (mt-10) outliers start: 35 outliers final: 12 residues processed: 152 average time/residue: 1.3358 time to fit residues: 219.6554 Evaluate side-chains 140 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 407 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 125 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 131 optimal weight: 0.0980 chunk 37 optimal weight: 7.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12116 Z= 0.253 Angle : 0.693 10.090 16614 Z= 0.360 Chirality : 0.048 0.170 1891 Planarity : 0.007 0.065 2176 Dihedral : 6.121 45.578 1660 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.52 % Allowed : 12.43 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.92 (0.20), residues: 1528 helix: -1.96 (0.61), residues: 56 sheet: -0.41 (0.24), residues: 425 loop : -1.71 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 169 HIS 0.004 0.001 HIS C 170 PHE 0.031 0.002 PHE C 199 TYR 0.021 0.002 TYR A 217 ARG 0.004 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7983 (pm20) cc_final: 0.7323 (pm20) REVERT: A 238 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6455 (ptt180) REVERT: A 274 THR cc_start: 0.8634 (t) cc_final: 0.8402 (t) REVERT: A 281 ILE cc_start: 0.8419 (mt) cc_final: 0.8213 (mm) REVERT: A 337 ILE cc_start: 0.6644 (pt) cc_final: 0.6274 (pp) REVERT: A 407 GLU cc_start: 0.5500 (mm-30) cc_final: 0.4623 (tt0) REVERT: A 478 ARG cc_start: 0.7678 (mtm-85) cc_final: 0.7381 (ttm-80) REVERT: A 486 LEU cc_start: 0.8339 (mt) cc_final: 0.8063 (mt) REVERT: B 21 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7831 (pp) REVERT: B 253 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6915 (pt) REVERT: B 322 ARG cc_start: 0.7165 (mtm-85) cc_final: 0.6625 (mtm-85) REVERT: B 432 PHE cc_start: 0.7503 (m-80) cc_final: 0.7118 (m-80) REVERT: C 148 MET cc_start: 0.8446 (ttm) cc_final: 0.8148 (ttm) REVERT: C 235 ILE cc_start: 0.8049 (mt) cc_final: 0.7837 (mm) REVERT: C 238 ARG cc_start: 0.7295 (ptp-170) cc_final: 0.7050 (ptp90) REVERT: C 356 GLU cc_start: 0.5453 (mm-30) cc_final: 0.5076 (mm-30) REVERT: C 392 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.5492 (ttt-90) REVERT: C 405 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7915 (pt) REVERT: C 428 VAL cc_start: 0.8263 (t) cc_final: 0.8045 (m) REVERT: C 433 ARG cc_start: 0.7493 (ttm170) cc_final: 0.7259 (ttm170) REVERT: C 488 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6894 (pt0) REVERT: C 512 ASP cc_start: 0.7728 (p0) cc_final: 0.7393 (p0) outliers start: 32 outliers final: 16 residues processed: 151 average time/residue: 1.4066 time to fit residues: 229.5640 Evaluate side-chains 145 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 86 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 0.2980 chunk 122 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12116 Z= 0.162 Angle : 0.604 7.526 16614 Z= 0.312 Chirality : 0.046 0.141 1891 Planarity : 0.006 0.058 2176 Dihedral : 5.670 42.672 1660 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.57 % Allowed : 13.61 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.71 (0.20), residues: 1528 helix: -1.61 (0.63), residues: 56 sheet: -0.30 (0.24), residues: 421 loop : -1.55 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 270 PHE 0.016 0.001 PHE C 199 TYR 0.015 0.001 TYR A 217 ARG 0.003 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.318 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7899 (pm20) cc_final: 0.6857 (pt0) REVERT: A 238 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6426 (ptt180) REVERT: A 281 ILE cc_start: 0.8417 (mt) cc_final: 0.8202 (mm) REVERT: A 337 ILE cc_start: 0.6627 (pt) cc_final: 0.6264 (pp) REVERT: A 364 ASN cc_start: 0.4258 (OUTLIER) cc_final: 0.3628 (m-40) REVERT: A 407 GLU cc_start: 0.5466 (mm-30) cc_final: 0.4616 (tt0) REVERT: A 478 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.7326 (ttm-80) REVERT: A 486 LEU cc_start: 0.8274 (mt) cc_final: 0.8006 (mt) REVERT: B 21 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7746 (pp) REVERT: B 253 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6728 (pt) REVERT: B 315 SER cc_start: 0.7742 (t) cc_final: 0.7393 (m) REVERT: B 322 ARG cc_start: 0.7161 (mtm-85) cc_final: 0.6585 (mtm-85) REVERT: B 432 PHE cc_start: 0.7439 (m-80) cc_final: 0.7078 (m-80) REVERT: C 148 MET cc_start: 0.8357 (ttm) cc_final: 0.8074 (ttm) REVERT: C 238 ARG cc_start: 0.7275 (ptp-170) cc_final: 0.7035 (ptp90) REVERT: C 356 GLU cc_start: 0.5439 (mm-30) cc_final: 0.5147 (mm-30) REVERT: C 428 VAL cc_start: 0.8255 (t) cc_final: 0.8046 (m) REVERT: C 488 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7040 (pt0) REVERT: C 512 ASP cc_start: 0.7747 (p0) cc_final: 0.7434 (p0) outliers start: 20 outliers final: 9 residues processed: 146 average time/residue: 1.5631 time to fit residues: 246.6880 Evaluate side-chains 139 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 407 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.0170 chunk 16 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN C 334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12116 Z= 0.251 Angle : 0.683 9.882 16614 Z= 0.352 Chirality : 0.048 0.164 1891 Planarity : 0.006 0.062 2176 Dihedral : 5.956 45.390 1660 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.52 % Allowed : 13.22 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.72 (0.20), residues: 1528 helix: -1.71 (0.63), residues: 56 sheet: -0.28 (0.24), residues: 415 loop : -1.56 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 520 HIS 0.003 0.001 HIS C 170 PHE 0.030 0.002 PHE C 199 TYR 0.021 0.002 TYR A 217 ARG 0.003 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7985 (pm20) cc_final: 0.6957 (pt0) REVERT: A 238 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6448 (ptt180) REVERT: A 281 ILE cc_start: 0.8421 (mt) cc_final: 0.8213 (mm) REVERT: A 337 ILE cc_start: 0.6715 (pt) cc_final: 0.6353 (pp) REVERT: A 364 ASN cc_start: 0.4267 (OUTLIER) cc_final: 0.3649 (m-40) REVERT: A 478 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7374 (ttm-80) REVERT: A 486 LEU cc_start: 0.8334 (mt) cc_final: 0.8055 (mt) REVERT: B 21 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7826 (pp) REVERT: B 322 ARG cc_start: 0.7160 (mtm-85) cc_final: 0.6593 (mtm-85) REVERT: B 432 PHE cc_start: 0.7504 (m-80) cc_final: 0.7102 (m-80) REVERT: C 148 MET cc_start: 0.8444 (ttm) cc_final: 0.8151 (ttm) REVERT: C 238 ARG cc_start: 0.7285 (ptp-170) cc_final: 0.7049 (ptp90) REVERT: C 356 GLU cc_start: 0.5507 (mm-30) cc_final: 0.5113 (mm-30) REVERT: C 392 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.5498 (ttt-90) REVERT: C 405 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7930 (pt) REVERT: C 428 VAL cc_start: 0.8388 (t) cc_final: 0.8144 (m) REVERT: C 433 ARG cc_start: 0.7737 (ttm170) cc_final: 0.7485 (ttm170) REVERT: C 488 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7044 (pt0) REVERT: C 512 ASP cc_start: 0.7735 (p0) cc_final: 0.7410 (p0) outliers start: 32 outliers final: 15 residues processed: 146 average time/residue: 1.4245 time to fit residues: 225.1982 Evaluate side-chains 143 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 50.0000 chunk 44 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12116 Z= 0.232 Angle : 0.666 8.778 16614 Z= 0.344 Chirality : 0.048 0.158 1891 Planarity : 0.006 0.063 2176 Dihedral : 5.925 45.143 1660 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.44 % Allowed : 13.45 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.68 (0.20), residues: 1528 helix: -1.60 (0.63), residues: 56 sheet: -0.29 (0.24), residues: 416 loop : -1.52 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.004 0.001 HIS A 270 PHE 0.029 0.002 PHE C 199 TYR 0.020 0.002 TYR A 217 ARG 0.003 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7964 (pm20) cc_final: 0.6983 (pt0) REVERT: A 238 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6431 (ptt180) REVERT: A 274 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8349 (t) REVERT: A 281 ILE cc_start: 0.8424 (mt) cc_final: 0.8214 (mm) REVERT: A 337 ILE cc_start: 0.6689 (pt) cc_final: 0.6329 (pp) REVERT: A 364 ASN cc_start: 0.4272 (OUTLIER) cc_final: 0.3637 (m-40) REVERT: A 478 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7405 (ttm-80) REVERT: A 486 LEU cc_start: 0.8330 (mt) cc_final: 0.8041 (mt) REVERT: B 21 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7782 (pp) REVERT: B 315 SER cc_start: 0.7772 (t) cc_final: 0.7284 (m) REVERT: B 322 ARG cc_start: 0.7173 (mtm-85) cc_final: 0.6618 (mtm-85) REVERT: B 432 PHE cc_start: 0.7496 (m-80) cc_final: 0.7099 (m-80) REVERT: C 148 MET cc_start: 0.8431 (ttm) cc_final: 0.8141 (ttm) REVERT: C 238 ARG cc_start: 0.7279 (ptp-170) cc_final: 0.7051 (ptp90) REVERT: C 356 GLU cc_start: 0.5504 (mm-30) cc_final: 0.5136 (mm-30) REVERT: C 392 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.5540 (ttt-90) REVERT: C 405 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7904 (pt) REVERT: C 428 VAL cc_start: 0.8257 (t) cc_final: 0.8049 (m) REVERT: C 433 ARG cc_start: 0.7750 (ttm170) cc_final: 0.7490 (ttm170) REVERT: C 488 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7050 (pt0) REVERT: C 512 ASP cc_start: 0.7655 (p0) cc_final: 0.7331 (p0) outliers start: 31 outliers final: 18 residues processed: 146 average time/residue: 1.3704 time to fit residues: 216.1952 Evaluate side-chains 145 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 30.0000 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 144 optimal weight: 30.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.003 0.031 12116 Z= 0.190 Angle : 0.633 7.934 16614 Z= 0.326 Chirality : 0.046 0.145 1891 Planarity : 0.006 0.061 2176 Dihedral : 5.762 44.333 1660 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.12 % Allowed : 14.08 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.61 (0.20), residues: 1528 helix: -1.46 (0.64), residues: 56 sheet: -0.26 (0.24), residues: 417 loop : -1.46 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS A 270 PHE 0.023 0.002 PHE C 199 TYR 0.020 0.001 TYR A 217 ARG 0.003 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7031 (pt0) REVERT: A 238 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6415 (ptt180) REVERT: A 274 THR cc_start: 0.8547 (t) cc_final: 0.8299 (t) REVERT: A 281 ILE cc_start: 0.8420 (mt) cc_final: 0.8202 (mm) REVERT: A 337 ILE cc_start: 0.6656 (pt) cc_final: 0.6310 (pp) REVERT: A 364 ASN cc_start: 0.4277 (OUTLIER) cc_final: 0.3620 (m-40) REVERT: A 407 GLU cc_start: 0.5617 (mm-30) cc_final: 0.4689 (tt0) REVERT: A 478 ARG cc_start: 0.7646 (ttm-80) cc_final: 0.7370 (ttm-80) REVERT: A 486 LEU cc_start: 0.8311 (mt) cc_final: 0.8026 (mt) REVERT: B 21 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7767 (pp) REVERT: B 322 ARG cc_start: 0.7176 (mtm-85) cc_final: 0.6637 (mtm-85) REVERT: B 373 ARG cc_start: 0.6197 (mtp-110) cc_final: 0.5809 (mtm110) REVERT: B 432 PHE cc_start: 0.7471 (m-80) cc_final: 0.7102 (m-80) REVERT: C 148 MET cc_start: 0.8339 (ttm) cc_final: 0.8049 (ttm) REVERT: C 238 ARG cc_start: 0.7284 (ptp-170) cc_final: 0.7052 (ptp90) REVERT: C 356 GLU cc_start: 0.5599 (mm-30) cc_final: 0.5262 (mm-30) REVERT: C 392 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.5509 (ttt-90) REVERT: C 405 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7834 (pt) REVERT: C 433 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7495 (ttm170) REVERT: C 488 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7155 (pt0) REVERT: C 512 ASP cc_start: 0.7657 (p0) cc_final: 0.7337 (p0) outliers start: 27 outliers final: 15 residues processed: 145 average time/residue: 1.3631 time to fit residues: 213.1973 Evaluate side-chains 145 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 139 optimal weight: 30.0000 chunk 120 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN B 140 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12116 Z= 0.289 Angle : 0.725 11.565 16614 Z= 0.373 Chirality : 0.049 0.181 1891 Planarity : 0.007 0.064 2176 Dihedral : 6.108 46.598 1660 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.81 % Allowed : 14.40 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.72 (0.20), residues: 1528 helix: -1.71 (0.63), residues: 56 sheet: -0.29 (0.24), residues: 410 loop : -1.55 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 520 HIS 0.004 0.001 HIS A 270 PHE 0.034 0.002 PHE C 199 TYR 0.023 0.002 TYR C 217 ARG 0.003 0.000 ARG C 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7061 (pt0) REVERT: A 238 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6409 (ptt180) REVERT: A 274 THR cc_start: 0.8533 (t) cc_final: 0.8296 (t) REVERT: A 281 ILE cc_start: 0.8424 (mt) cc_final: 0.8213 (mm) REVERT: A 337 ILE cc_start: 0.6678 (pt) cc_final: 0.6328 (pp) REVERT: A 364 ASN cc_start: 0.4293 (OUTLIER) cc_final: 0.3624 (m-40) REVERT: A 407 GLU cc_start: 0.5701 (mm-30) cc_final: 0.4760 (tt0) REVERT: A 478 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7423 (ttm-80) REVERT: A 486 LEU cc_start: 0.8341 (mt) cc_final: 0.8031 (mt) REVERT: A 514 ILE cc_start: 0.8458 (mt) cc_final: 0.8254 (mm) REVERT: B 21 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7724 (pp) REVERT: B 432 PHE cc_start: 0.7521 (m-80) cc_final: 0.7158 (m-80) REVERT: C 148 MET cc_start: 0.8450 (ttm) cc_final: 0.8165 (ttm) REVERT: C 238 ARG cc_start: 0.7275 (ptp-170) cc_final: 0.7048 (ptp90) REVERT: C 356 GLU cc_start: 0.5287 (mm-30) cc_final: 0.4952 (mm-30) REVERT: C 392 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.5536 (ttt-90) REVERT: C 405 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7921 (pt) REVERT: C 433 ARG cc_start: 0.7759 (ttm170) cc_final: 0.7474 (ttm170) REVERT: C 488 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7142 (pt0) REVERT: C 512 ASP cc_start: 0.7658 (p0) cc_final: 0.7331 (p0) outliers start: 23 outliers final: 16 residues processed: 142 average time/residue: 1.4564 time to fit residues: 223.1723 Evaluate side-chains 144 residues out of total 1271 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 50.0000 chunk 111 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN C 334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.209018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.193351 restraints weight = 11060.469| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 0.67 r_work: 0.3867 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 1.59 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12116 Z= 0.216 Angle : 0.658 8.488 16614 Z= 0.338 Chirality : 0.047 0.153 1891 Planarity : 0.006 0.062 2176 Dihedral : 5.883 45.038 1660 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.97 % Allowed : 14.08 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.20), residues: 1528 helix: -1.57 (0.64), residues: 56 sheet: -0.27 (0.24), residues: 427 loop : -1.47 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 520 HIS 0.004 0.001 HIS A 270 PHE 0.027 0.002 PHE C 199 TYR 0.021 0.001 TYR A 217 ARG 0.003 0.000 ARG A 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4590.71 seconds wall clock time: 84 minutes 17.97 seconds (5057.97 seconds total)