Starting phenix.real_space_refine on Thu May 9 04:40:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uux_42600/05_2024/8uux_42600.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uux_42600/05_2024/8uux_42600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uux_42600/05_2024/8uux_42600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uux_42600/05_2024/8uux_42600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uux_42600/05_2024/8uux_42600.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uux_42600/05_2024/8uux_42600.pdb" } resolution = 2.74 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= 0.475 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 Ca 3 9.91 5 S 48 5.16 5 C 7588 2.51 5 N 1938 2.21 5 O 2507 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 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 321": "OD1" <-> "OD2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 447": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 12084 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: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3953 Classifications: {'peptide': 515} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 468} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3869 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: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Time building chain proxies: 6.58, per 1000 atoms: 0.54 Number of scatterers: 12084 At special positions: 0 Unit cell: (118.8, 116.6, 124.3, 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) Ca 3 19.99 S 48 16.00 O 2507 8.00 N 1938 7.00 C 7588 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: 4.48 Conformation dependent library (CDL) restraints added in 2.3 seconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2834 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 22 sheets defined 9.5% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.528A pdb=" N ALA A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 54 through 58 removed outlier: 4.114A 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 140 through 144 removed outlier: 3.747A pdb=" N PHE A 144 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 54 through 58 removed outlier: 4.114A pdb=" N ASN B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.752A 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 282 through 286 removed outlier: 3.563A pdb=" N TRP B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 286' Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.572A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 removed outlier: 3.808A pdb=" N ASN C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing helix 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: 4.087A 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: 3.731A pdb=" N VAL C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 465 removed outlier: 3.579A pdb=" N VAL C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.629A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 202 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 83 removed outlier: 7.176A pdb=" N ILE A 78 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU A 185 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE A 80 " --> pdb=" O CYS A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'A' and resid 447 through 451 removed outlier: 4.795A pdb=" N GLU A 447 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 447 through 451 removed outlier: 4.795A pdb=" N GLU A 447 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE A 497 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SER A 500 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLU A 488 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU A 485 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN A 479 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 487 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 519 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG A 476 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL A 517 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG A 478 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE A 515 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 296 removed outlier: 4.384A pdb=" N ALA A 290 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE A 375 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE A 358 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A 379 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N THR A 354 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N SER A 332 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY A 400 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN A 334 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 398 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU A 336 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 394 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 5.075A 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: 8.278A pdb=" N GLU A 342 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 9.969A 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: 12.741A pdb=" N GLN B 61 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N SER B 207 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY B 65 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.781A pdb=" N CYS B 183 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP B 81 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 181 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 103 removed outlier: 6.166A pdb=" N TYR B 99 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 218 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY B 101 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AB3, first strand: chain 'B' and resid 447 through 451 removed outlier: 4.559A pdb=" N GLU B 447 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B 252 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 447 through 451 removed outlier: 4.559A pdb=" N GLU B 447 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE B 497 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER B 500 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLU B 488 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 485 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN B 479 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE B 487 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 472 " --> pdb=" O TRP B 520 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TRP B 520 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 474 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 268 through 269 removed outlier: 4.496A pdb=" N ARG B 268 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 289 through 298 removed outlier: 4.486A pdb=" N ALA B 290 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE B 375 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE B 358 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER B 332 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY B 400 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN B 334 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B 398 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU B 336 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 394 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN B 340 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG B 392 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLU B 342 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ARG B 390 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 389 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.643A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 78 through 83 removed outlier: 6.578A pdb=" N CYS C 183 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 81 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU C 181 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS C 121 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AC1, first strand: chain 'C' and resid 448 through 451 Processing sheet with id=AC2, first strand: chain 'C' and resid 268 through 269 removed outlier: 4.545A pdb=" N ARG C 268 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 295 through 298 removed outlier: 6.785A pdb=" N PHE C 375 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE C 358 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 337 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER C 332 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY C 400 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN C 334 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE C 398 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU C 336 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 394 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLN C 340 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG C 392 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA C 290 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 427 through 429 removed outlier: 5.139A pdb=" N SER C 500 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU C 488 " --> pdb=" O SER C 500 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU C 485 " --> pdb=" O ASN C 479 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN C 479 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE C 487 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS C 489 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 6.950A 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: 6.629A pdb=" N LEU C 474 " --> pdb=" O VAL C 518 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 828 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: 4.05 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3835 1.34 - 1.46: 2450 1.46 - 1.58: 5740 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 12097 Sorted by residual: bond pdb=" CG GLN B 19 " pdb=" CD GLN B 19 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CB GLN B 19 " pdb=" CG GLN B 19 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CA VAL C 216 " pdb=" C VAL C 216 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.27e-02 6.20e+03 9.45e-01 bond pdb=" CA ASP B 20 " pdb=" C ASP B 20 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.80e-02 3.09e+03 9.35e-01 bond pdb=" N PRO B 31 " pdb=" CA PRO B 31 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 9.05e-01 ... (remaining 12092 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.40: 545 106.40 - 113.29: 6408 113.29 - 120.19: 4129 120.19 - 127.09: 5337 127.09 - 133.98: 169 Bond angle restraints: 16588 Sorted by residual: angle pdb=" C GLN C 469 " pdb=" N SER C 470 " pdb=" CA SER C 470 " ideal model delta sigma weight residual 121.90 115.31 6.59 1.26e+00 6.30e-01 2.74e+01 angle pdb=" C GLN B 469 " pdb=" N SER B 470 " pdb=" CA SER B 470 " ideal model delta sigma weight residual 121.90 115.65 6.25 1.26e+00 6.30e-01 2.46e+01 angle pdb=" C LEU A 481 " pdb=" N THR A 482 " pdb=" CA THR A 482 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C PHE A 461 " pdb=" N ALA A 462 " pdb=" CA ALA A 462 " ideal model delta sigma weight residual 121.54 128.57 -7.03 1.91e+00 2.74e-01 1.36e+01 angle pdb=" N GLY B 195 " pdb=" CA GLY B 195 " pdb=" C GLY B 195 " ideal model delta sigma weight residual 113.18 121.90 -8.72 2.37e+00 1.78e-01 1.35e+01 ... (remaining 16583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 6363 17.64 - 35.28: 623 35.28 - 52.93: 131 52.93 - 70.57: 41 70.57 - 88.21: 15 Dihedral angle restraints: 7173 sinusoidal: 2753 harmonic: 4420 Sorted by residual: dihedral pdb=" CA THR C 363 " pdb=" C THR C 363 " pdb=" N ASN C 364 " pdb=" CA ASN C 364 " ideal model delta harmonic sigma weight residual 180.00 146.48 33.52 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" CA GLY B 195 " pdb=" C GLY B 195 " pdb=" N ASP B 196 " pdb=" CA ASP B 196 " ideal model delta harmonic sigma weight residual 180.00 147.37 32.63 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA ALA C 365 " pdb=" C ALA C 365 " pdb=" N ASP C 366 " pdb=" CA ASP C 366 " ideal model delta harmonic sigma weight residual 180.00 147.41 32.59 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 7170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1119 0.031 - 0.063: 477 0.063 - 0.094: 151 0.094 - 0.125: 130 0.125 - 0.157: 11 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CA ASP B 196 " pdb=" N ASP B 196 " pdb=" C ASP B 196 " pdb=" CB ASP B 196 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA VAL C 414 " pdb=" N VAL C 414 " pdb=" C VAL C 414 " pdb=" CB VAL C 414 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA GLN A 28 " pdb=" N GLN A 28 " pdb=" C GLN A 28 " pdb=" CB GLN A 28 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1885 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 128 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO C 129 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 219 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.49e+00 pdb=" N PRO C 220 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 220 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 220 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 193 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 194 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.027 5.00e-02 4.00e+02 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 344 2.69 - 3.24: 10251 3.24 - 3.79: 17529 3.79 - 4.35: 25488 4.35 - 4.90: 41767 Nonbonded interactions: 95379 Sorted by model distance: nonbonded pdb=" OG1 THR A 434 " pdb=" O HOH A 701 " model vdw 2.133 2.440 nonbonded pdb=" OE1 GLN A 312 " pdb=" O HOH A 702 " model vdw 2.196 2.440 nonbonded pdb=" O HOH A 709 " pdb=" O HOH A 799 " model vdw 2.212 2.440 nonbonded pdb=" O HOH A 703 " pdb=" O HOH A 709 " model vdw 2.214 2.440 nonbonded pdb=" O PRO A 248 " pdb=" O HOH A 701 " model vdw 2.224 2.440 ... (remaining 95374 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 29 through 531 or resid 601)) selection = (chain 'B' and (resid 29 through 531 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: 9.040 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: 0.030 Extract box with map and model: 33.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.780 Find NCS groups from input model: 0.870 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: 0.010 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 : 0.002 0.032 12097 Z= 0.160 Angle : 0.629 8.723 16588 Z= 0.342 Chirality : 0.045 0.157 1888 Planarity : 0.006 0.068 2172 Dihedral : 15.620 88.210 4339 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 0.95 % Allowed : 14.42 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.63 (0.19), residues: 1526 helix: -1.31 (0.57), residues: 56 sheet: -0.11 (0.25), residues: 396 loop : -1.55 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS B 170 PHE 0.014 0.001 PHE C 80 TYR 0.011 0.001 TYR B 227 ARG 0.002 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: A 488 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7740 (mt-10) REVERT: B 197 GLU cc_start: 0.6759 (pm20) cc_final: 0.6334 (pp20) REVERT: C 176 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7409 (mt-10) REVERT: C 507 LEU cc_start: 0.8222 (tp) cc_final: 0.7974 (tp) outliers start: 12 outliers final: 10 residues processed: 165 average time/residue: 1.4396 time to fit residues: 255.5740 Evaluate side-chains 154 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 GLN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12097 Z= 0.337 Angle : 0.766 13.535 16588 Z= 0.396 Chirality : 0.050 0.185 1888 Planarity : 0.007 0.071 2172 Dihedral : 6.538 56.569 1666 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.55 % Favored : 93.38 % Rotamer: Outliers : 3.86 % Allowed : 13.24 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.60 (0.19), residues: 1526 helix: -1.20 (0.59), residues: 51 sheet: -0.14 (0.25), residues: 407 loop : -1.53 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 520 HIS 0.005 0.002 HIS B 170 PHE 0.031 0.003 PHE C 199 TYR 0.022 0.002 TYR B 217 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 156 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 100 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8479 (m) REVERT: A 148 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8707 (ttp) REVERT: A 469 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: A 488 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7889 (mt-10) REVERT: B 19 GLN cc_start: 0.5588 (OUTLIER) cc_final: 0.4922 (mm110) REVERT: B 21 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8098 (pp) REVERT: B 197 GLU cc_start: 0.6865 (pm20) cc_final: 0.6384 (pp20) REVERT: C 155 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: C 176 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7608 (mt-10) REVERT: C 396 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6250 (ttt-90) REVERT: C 407 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: C 447 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6833 (tt0) REVERT: C 469 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: C 507 LEU cc_start: 0.7966 (tp) cc_final: 0.7698 (tp) outliers start: 49 outliers final: 24 residues processed: 186 average time/residue: 1.4938 time to fit residues: 299.5207 Evaluate side-chains 186 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 499 LEU 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: 40.0000 chunk 114 optimal weight: 0.8980 chunk 93 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 137 optimal weight: 50.0000 chunk 47 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 overall best weight: 5.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 340 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12097 Z= 0.332 Angle : 0.766 13.574 16588 Z= 0.396 Chirality : 0.051 0.189 1888 Planarity : 0.007 0.072 2172 Dihedral : 6.612 53.255 1664 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.01 % Favored : 92.86 % Rotamer: Outliers : 4.73 % Allowed : 13.79 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.57 (0.19), residues: 1526 helix: -1.13 (0.62), residues: 51 sheet: -0.06 (0.24), residues: 418 loop : -1.55 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 460 HIS 0.006 0.001 HIS B 170 PHE 0.029 0.002 PHE C 199 TYR 0.023 0.002 TYR C 217 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 154 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 100 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8615 (m) REVERT: A 148 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8687 (ttp) REVERT: A 340 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: A 488 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7951 (mt-10) REVERT: B 19 GLN cc_start: 0.5640 (OUTLIER) cc_final: 0.4760 (mm110) REVERT: B 21 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8108 (pp) REVERT: B 197 GLU cc_start: 0.6788 (pm20) cc_final: 0.6360 (pp20) REVERT: B 514 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8367 (mp) REVERT: C 155 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: C 176 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7887 (mt-10) REVERT: C 396 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6446 (ttt-90) REVERT: C 407 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7277 (tm-30) REVERT: C 447 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6781 (tt0) REVERT: C 469 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7503 (mp10) REVERT: C 507 LEU cc_start: 0.7987 (tp) cc_final: 0.7717 (tp) outliers start: 60 outliers final: 31 residues processed: 196 average time/residue: 1.3702 time to fit residues: 289.7485 Evaluate side-chains 192 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 72 optimal weight: 0.0270 chunk 131 optimal weight: 0.0010 chunk 39 optimal weight: 20.0000 overall best weight: 1.9448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 GLN B 402 GLN C 261 ASN C 340 GLN C 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12097 Z= 0.162 Angle : 0.610 9.159 16588 Z= 0.316 Chirality : 0.045 0.153 1888 Planarity : 0.006 0.064 2172 Dihedral : 6.029 50.324 1664 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 3.07 % Allowed : 15.92 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.31 (0.20), residues: 1526 helix: -0.83 (0.63), residues: 57 sheet: 0.08 (0.24), residues: 421 loop : -1.35 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 170 PHE 0.015 0.001 PHE C 80 TYR 0.014 0.001 TYR A 217 ARG 0.002 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.353 Fit side-chains REVERT: A 100 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8666 (m) REVERT: A 148 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8653 (ttp) REVERT: A 340 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: A 356 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: A 488 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 21 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7899 (pp) REVERT: B 197 GLU cc_start: 0.6820 (pm20) cc_final: 0.6314 (pp20) REVERT: B 514 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8297 (mp) REVERT: C 155 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: C 176 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7704 (mt-10) REVERT: C 340 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: C 396 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6379 (ttt-90) REVERT: C 407 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7295 (tm-30) outliers start: 39 outliers final: 19 residues processed: 177 average time/residue: 1.4367 time to fit residues: 274.0727 Evaluate side-chains 173 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 340 GLN B 402 GLN C 334 GLN C 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 12097 Z= 0.452 Angle : 0.851 16.534 16588 Z= 0.436 Chirality : 0.054 0.215 1888 Planarity : 0.008 0.070 2172 Dihedral : 6.621 49.119 1662 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.21 % Favored : 92.66 % Rotamer: Outliers : 4.65 % Allowed : 15.05 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.57 (0.19), residues: 1526 helix: -1.16 (0.63), residues: 51 sheet: -0.04 (0.24), residues: 406 loop : -1.54 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 102 HIS 0.005 0.002 HIS B 170 PHE 0.036 0.003 PHE C 199 TYR 0.028 0.003 TYR C 217 ARG 0.005 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 149 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: A 100 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8540 (m) REVERT: A 340 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: A 356 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: A 488 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7929 (mt-10) REVERT: B 19 GLN cc_start: 0.5905 (OUTLIER) cc_final: 0.5099 (mm110) REVERT: B 21 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8174 (pp) REVERT: B 514 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8405 (mp) REVERT: C 176 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8033 (mt-10) REVERT: C 396 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6470 (ttt-90) REVERT: C 407 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: C 447 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: C 453 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8356 (mp) REVERT: C 469 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7431 (mp10) REVERT: C 507 LEU cc_start: 0.7989 (tp) cc_final: 0.7709 (tp) outliers start: 59 outliers final: 30 residues processed: 191 average time/residue: 1.4241 time to fit residues: 293.9005 Evaluate side-chains 191 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 29 optimal weight: 30.0000 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 GLN B 402 GLN C 261 ASN C 334 GLN C 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12097 Z= 0.202 Angle : 0.658 9.531 16588 Z= 0.340 Chirality : 0.047 0.167 1888 Planarity : 0.006 0.067 2172 Dihedral : 6.199 46.445 1662 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 3.86 % Allowed : 16.08 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.35 (0.20), residues: 1526 helix: -0.80 (0.66), residues: 51 sheet: 0.11 (0.24), residues: 425 loop : -1.41 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS B 170 PHE 0.021 0.002 PHE C 199 TYR 0.017 0.001 TYR A 217 ARG 0.003 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 146 time to evaluate : 1.328 Fit side-chains REVERT: A 100 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8663 (m) REVERT: A 148 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8733 (ttp) REVERT: A 340 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: A 356 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: A 488 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7846 (mt-10) REVERT: B 21 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7986 (pp) REVERT: B 197 GLU cc_start: 0.6739 (pm20) cc_final: 0.6133 (pp20) REVERT: B 514 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8313 (mp) REVERT: C 176 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7977 (mt-10) REVERT: C 396 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6389 (ttt-90) REVERT: C 407 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: C 447 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: C 453 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8340 (mp) outliers start: 49 outliers final: 27 residues processed: 183 average time/residue: 1.3901 time to fit residues: 274.4612 Evaluate side-chains 182 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 340 GLN B 402 GLN C 340 GLN C 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12097 Z= 0.230 Angle : 0.678 10.599 16588 Z= 0.349 Chirality : 0.047 0.168 1888 Planarity : 0.006 0.067 2172 Dihedral : 6.168 46.271 1662 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.62 % Favored : 93.32 % Rotamer: Outliers : 4.10 % Allowed : 16.00 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1526 helix: -0.76 (0.66), residues: 51 sheet: 0.06 (0.24), residues: 420 loop : -1.36 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.005 0.001 HIS B 170 PHE 0.023 0.002 PHE C 199 TYR 0.017 0.001 TYR B 227 ARG 0.002 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 147 time to evaluate : 1.330 Fit side-chains REVERT: A 100 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8631 (m) REVERT: A 148 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8725 (ttp) REVERT: A 340 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: A 356 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: A 488 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7848 (mt-10) REVERT: B 19 GLN cc_start: 0.5550 (OUTLIER) cc_final: 0.5012 (mm110) REVERT: B 21 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8026 (pp) REVERT: B 197 GLU cc_start: 0.6644 (pm20) cc_final: 0.6055 (pp20) REVERT: B 514 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8317 (mp) REVERT: C 155 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: C 176 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7877 (mt-10) REVERT: C 396 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6334 (ttt-90) REVERT: C 407 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: C 447 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: C 453 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8287 (mp) REVERT: C 469 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7347 (mp10) outliers start: 52 outliers final: 29 residues processed: 182 average time/residue: 1.3975 time to fit residues: 274.5419 Evaluate side-chains 189 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 147 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 40.0000 chunk 44 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 93 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 340 GLN B 402 GLN C 261 ASN C 340 GLN C 479 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12097 Z= 0.352 Angle : 0.781 14.810 16588 Z= 0.400 Chirality : 0.051 0.187 1888 Planarity : 0.007 0.069 2172 Dihedral : 6.471 46.411 1662 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.66 % Rotamer: Outliers : 4.10 % Allowed : 16.15 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.44 (0.20), residues: 1526 helix: -1.02 (0.64), residues: 51 sheet: 0.01 (0.24), residues: 424 loop : -1.46 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 520 HIS 0.006 0.002 HIS B 170 PHE 0.031 0.003 PHE C 199 TYR 0.022 0.002 TYR B 227 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 147 time to evaluate : 1.325 Fit side-chains REVERT: A 100 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8518 (m) REVERT: A 340 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: A 356 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: A 488 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7904 (mt-10) REVERT: B 19 GLN cc_start: 0.5791 (OUTLIER) cc_final: 0.5178 (mm110) REVERT: B 21 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8120 (pp) REVERT: B 197 GLU cc_start: 0.6694 (pm20) cc_final: 0.6222 (pp20) REVERT: B 514 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8384 (mp) REVERT: C 176 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8020 (mt-10) REVERT: C 396 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6419 (ttt-90) REVERT: C 407 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: C 447 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6757 (tt0) REVERT: C 453 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8359 (mp) REVERT: C 469 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7463 (mp10) outliers start: 52 outliers final: 29 residues processed: 183 average time/residue: 1.4120 time to fit residues: 278.2235 Evaluate side-chains 186 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 146 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 499 LEU 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: 6.9990 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 340 GLN B 402 GLN C 340 GLN C 479 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12097 Z= 0.259 Angle : 0.701 10.857 16588 Z= 0.362 Chirality : 0.048 0.172 1888 Planarity : 0.007 0.068 2172 Dihedral : 6.297 46.605 1662 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.55 % Favored : 93.38 % Rotamer: Outliers : 4.18 % Allowed : 16.31 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.38 (0.20), residues: 1526 helix: -0.92 (0.65), residues: 51 sheet: 0.07 (0.24), residues: 418 loop : -1.41 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 169 HIS 0.005 0.001 HIS B 170 PHE 0.025 0.002 PHE C 199 TYR 0.019 0.002 TYR A 217 ARG 0.003 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 145 time to evaluate : 1.345 Fit side-chains REVERT: A 100 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8638 (m) REVERT: A 148 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8700 (ttp) REVERT: A 340 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: A 356 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: A 488 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 19 GLN cc_start: 0.5547 (OUTLIER) cc_final: 0.4998 (mm110) REVERT: B 21 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8000 (pp) REVERT: B 197 GLU cc_start: 0.6787 (pm20) cc_final: 0.6263 (pp20) REVERT: B 514 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8345 (mp) REVERT: C 176 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8037 (mt-10) REVERT: C 396 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6363 (ttt-90) REVERT: C 407 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: C 447 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6796 (tt0) REVERT: C 453 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8352 (mp) REVERT: C 469 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7411 (mp10) REVERT: C 476 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7665 (mtp180) outliers start: 53 outliers final: 34 residues processed: 183 average time/residue: 1.5186 time to fit residues: 301.2030 Evaluate side-chains 193 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 146 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 128 optimal weight: 0.1980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 371 GLN A 455 GLN B 340 GLN B 402 GLN C 261 ASN C 340 GLN C 479 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12097 Z= 0.151 Angle : 0.593 8.946 16588 Z= 0.306 Chirality : 0.045 0.153 1888 Planarity : 0.006 0.067 2172 Dihedral : 5.846 46.278 1662 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 3.07 % Allowed : 17.49 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.19 (0.20), residues: 1526 helix: -0.71 (0.65), residues: 57 sheet: 0.16 (0.24), residues: 416 loop : -1.26 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 520 HIS 0.003 0.001 HIS B 170 PHE 0.013 0.001 PHE C 80 TYR 0.012 0.001 TYR A 217 ARG 0.002 0.000 ARG B 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 148 time to evaluate : 1.265 Fit side-chains REVERT: A 100 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8903 (t) REVERT: A 148 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8712 (ttp) REVERT: A 340 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: A 488 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7830 (mt-10) REVERT: B 21 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7770 (pp) REVERT: B 514 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8290 (mp) REVERT: C 176 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7805 (mt-10) REVERT: C 334 GLN cc_start: 0.7316 (tt0) cc_final: 0.6949 (tt0) REVERT: C 340 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7487 (tp-100) REVERT: C 396 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6283 (ttt-90) REVERT: C 407 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: C 453 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8227 (mp) outliers start: 39 outliers final: 23 residues processed: 179 average time/residue: 1.4524 time to fit residues: 279.6606 Evaluate side-chains 182 residues out of total 1269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 499 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 33 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN B 340 GLN B 402 GLN C 479 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.173342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.151408 restraints weight = 11452.878| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 0.87 r_work: 0.3307 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.3181 rms_B_bonded: 2.66 restraints_weight: 0.1250 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 12097 Z= 0.229 Angle : 0.877 59.195 16588 Z= 0.491 Chirality : 0.050 0.914 1888 Planarity : 0.006 0.066 2172 Dihedral : 5.855 46.250 1662 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 2.60 % Allowed : 17.97 % Favored : 79.43 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.17 (0.20), residues: 1526 helix: -0.68 (0.65), residues: 57 sheet: 0.15 (0.24), residues: 416 loop : -1.25 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 520 HIS 0.003 0.001 HIS B 170 PHE 0.013 0.001 PHE C 80 TYR 0.011 0.001 TYR A 217 ARG 0.002 0.000 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5281.34 seconds wall clock time: 95 minutes 37.16 seconds (5737.16 seconds total)