Starting phenix.real_space_refine on Sat Jul 20 19:02:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ku9_0776/07_2024/6ku9_0776.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ku9_0776/07_2024/6ku9_0776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ku9_0776/07_2024/6ku9_0776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ku9_0776/07_2024/6ku9_0776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ku9_0776/07_2024/6ku9_0776.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ku9_0776/07_2024/6ku9_0776.cif" } resolution = 2.67 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 7548 2.51 5 N 2022 2.21 5 O 2124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 103": "OD1" <-> "OD2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 510": "OD1" <-> "OD2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ASP 305": "OD1" <-> "OD2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 366": "OD1" <-> "OD2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 510": "OD1" <-> "OD2" Residue "B GLU 591": "OE1" <-> "OE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 103": "OD1" <-> "OD2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 366": "OD1" <-> "OD2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C ARG 380": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 510": "OD1" <-> "OD2" Residue "C GLU 591": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11739 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "B" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Chain: "C" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3913 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 450} Chain breaks: 3 Time building chain proxies: 7.11, per 1000 atoms: 0.61 Number of scatterers: 11739 At special positions: 0 Unit cell: (97.099, 92.735, 108.009, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2124 8.00 N 2022 7.00 C 7548 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: 3.51 Conformation dependent library (CDL) restraints added in 2.2 seconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 30 sheets defined 10.5% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.815A pdb=" N LYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 474 through 477 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.816A pdb=" N LYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 Processing helix chain 'B' and resid 474 through 477 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.815A pdb=" N LYS C 213 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 Processing helix chain 'C' and resid 474 through 477 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 560 through 566 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU A 407 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU A 110 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN A 409 " --> pdb=" O HIS A 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS A 108 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU A 411 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY A 106 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR A 413 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET A 104 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 415 " --> pdb=" O HIS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU A 407 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU A 110 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN A 409 " --> pdb=" O HIS A 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS A 108 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU A 411 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY A 106 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR A 413 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET A 104 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN A 415 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 101 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 345 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 93 removed outlier: 3.983A pdb=" N ASP A 201 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 195 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 158 removed outlier: 6.252A pdb=" N SER A 387 " --> pdb=" O CYS A 519 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER A 521 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG A 389 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER A 523 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE A 391 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 176 through 179 Processing sheet with id=AA7, first strand: chain 'A' and resid 234 through 241 removed outlier: 5.438A pdb=" N ASN A 309 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG A 307 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 23.103A pdb=" N ARG A 308 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 18.677A pdb=" N CYS B 314 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 12.478A pdb=" N VAL A 310 " --> pdb=" O TYR B 312 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N TYR B 312 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR A 312 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG B 307 " --> pdb=" O PRO B 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASN B 309 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 234 through 241 removed outlier: 5.438A pdb=" N ASN A 309 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG A 307 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR C 312 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N TYR A 312 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 12.488A pdb=" N VAL C 310 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 18.685A pdb=" N CYS A 314 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 23.112A pdb=" N ARG C 308 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG C 307 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASN C 309 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 234 through 241 removed outlier: 5.437A pdb=" N ASN B 309 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG B 307 " --> pdb=" O PRO B 240 " (cutoff:3.500A) removed outlier: 23.097A pdb=" N ARG B 308 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 18.671A pdb=" N CYS C 314 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 12.473A pdb=" N VAL B 310 " --> pdb=" O TYR C 312 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N TYR C 312 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 312 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG C 307 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASN C 309 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AB2, first strand: chain 'A' and resid 439 through 446 removed outlier: 4.197A pdb=" N TYR A 465 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 451 through 455 removed outlier: 3.852A pdb=" N ASN A 539 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 528 through 534 Processing sheet with id=AB5, first strand: chain 'B' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU B 407 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU B 110 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN B 409 " --> pdb=" O HIS B 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS B 108 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU B 411 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY B 106 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR B 413 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET B 104 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN B 415 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU B 407 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU B 110 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN B 409 " --> pdb=" O HIS B 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS B 108 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU B 411 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY B 106 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR B 413 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET B 104 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN B 415 " --> pdb=" O HIS B 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 101 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 345 " --> pdb=" O PHE B 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 89 through 93 removed outlier: 3.984A pdb=" N ASP B 201 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL B 195 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER B 199 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'B' and resid 153 through 158 removed outlier: 6.252A pdb=" N SER B 387 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N SER B 521 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG B 389 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER B 523 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE B 391 " --> pdb=" O SER B 523 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 176 through 179 Processing sheet with id=AC2, first strand: chain 'B' and resid 245 through 246 Processing sheet with id=AC3, first strand: chain 'B' and resid 439 through 446 removed outlier: 4.197A pdb=" N TYR B 465 " --> pdb=" O SER B 628 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 451 through 455 removed outlier: 3.852A pdb=" N ASN B 539 " --> pdb=" O ASP B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU C 407 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU C 110 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN C 409 " --> pdb=" O HIS C 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS C 108 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU C 411 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY C 106 " --> pdb=" O GLU C 411 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR C 413 " --> pdb=" O MET C 104 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET C 104 " --> pdb=" O TYR C 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN C 415 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 72 through 77 removed outlier: 6.920A pdb=" N LEU C 407 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU C 110 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN C 409 " --> pdb=" O HIS C 108 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS C 108 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU C 411 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY C 106 " --> pdb=" O GLU C 411 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR C 413 " --> pdb=" O MET C 104 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET C 104 " --> pdb=" O TYR C 413 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN C 415 " --> pdb=" O HIS C 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE C 101 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE C 345 " --> pdb=" O PHE C 101 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 89 through 93 removed outlier: 3.983A pdb=" N ASP C 201 " --> pdb=" O PHE C 193 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL C 195 " --> pdb=" O SER C 199 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER C 199 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AC9, first strand: chain 'C' and resid 153 through 158 removed outlier: 6.251A pdb=" N SER C 387 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER C 521 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG C 389 " --> pdb=" O SER C 521 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER C 523 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 391 " --> pdb=" O SER C 523 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 176 through 179 Processing sheet with id=AD2, first strand: chain 'C' and resid 439 through 446 removed outlier: 4.198A pdb=" N TYR C 465 " --> pdb=" O SER C 628 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 451 through 455 removed outlier: 3.851A pdb=" N ASN C 539 " --> pdb=" O ASP C 611 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1107 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: 3.85 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3749 1.34 - 1.46: 2705 1.46 - 1.58: 5579 1.58 - 1.70: 0 1.70 - 1.81: 69 Bond restraints: 12102 Sorted by residual: bond pdb=" CB GLU B 453 " pdb=" CG GLU B 453 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.32e+00 bond pdb=" CB GLU A 453 " pdb=" CG GLU A 453 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.29e+00 bond pdb=" CB GLU C 453 " pdb=" CG GLU C 453 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.25e+00 bond pdb=" C GLY A 129 " pdb=" O GLY A 129 " ideal model delta sigma weight residual 1.236 1.222 0.015 1.09e-02 8.42e+03 1.77e+00 bond pdb=" N CYS C 243 " pdb=" CA CYS C 243 " ideal model delta sigma weight residual 1.462 1.478 -0.017 1.31e-02 5.83e+03 1.63e+00 ... (remaining 12097 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.76: 540 106.76 - 113.60: 6422 113.60 - 120.43: 4518 120.43 - 127.26: 4800 127.26 - 134.10: 208 Bond angle restraints: 16488 Sorted by residual: angle pdb=" N GLY C 129 " pdb=" CA GLY C 129 " pdb=" C GLY C 129 " ideal model delta sigma weight residual 112.13 118.99 -6.86 1.34e+00 5.57e-01 2.62e+01 angle pdb=" CA GLU B 453 " pdb=" CB GLU B 453 " pdb=" CG GLU B 453 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA GLU C 453 " pdb=" CB GLU C 453 " pdb=" CG GLU C 453 " ideal model delta sigma weight residual 114.10 123.79 -9.69 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA GLU A 453 " pdb=" CB GLU A 453 " pdb=" CG GLU A 453 " ideal model delta sigma weight residual 114.10 123.76 -9.66 2.00e+00 2.50e-01 2.33e+01 angle pdb=" N GLY A 129 " pdb=" CA GLY A 129 " pdb=" C GLY A 129 " ideal model delta sigma weight residual 112.13 118.12 -5.99 1.34e+00 5.57e-01 2.00e+01 ... (remaining 16483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 6283 15.95 - 31.90: 575 31.90 - 47.85: 161 47.85 - 63.80: 60 63.80 - 79.75: 10 Dihedral angle restraints: 7089 sinusoidal: 2856 harmonic: 4233 Sorted by residual: dihedral pdb=" CA ASN A 449 " pdb=" C ASN A 449 " pdb=" N HIS A 450 " pdb=" CA HIS A 450 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ASN C 449 " pdb=" C ASN C 449 " pdb=" N HIS C 450 " pdb=" CA HIS C 450 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ASN B 449 " pdb=" C ASN B 449 " pdb=" N HIS B 450 " pdb=" CA HIS B 450 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 7086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1350 0.058 - 0.116: 305 0.116 - 0.174: 91 0.174 - 0.232: 7 0.232 - 0.290: 8 Chirality restraints: 1761 Sorted by residual: chirality pdb=" CA PHE C 508 " pdb=" N PHE C 508 " pdb=" C PHE C 508 " pdb=" CB PHE C 508 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE C 350 " pdb=" CA ILE C 350 " pdb=" CG1 ILE C 350 " pdb=" CG2 ILE C 350 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA HIS C 102 " pdb=" N HIS C 102 " pdb=" C HIS C 102 " pdb=" CB HIS C 102 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1758 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 450 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C HIS B 450 " 0.056 2.00e-02 2.50e+03 pdb=" O HIS B 450 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS B 451 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 450 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C HIS A 450 " 0.056 2.00e-02 2.50e+03 pdb=" O HIS A 450 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS A 451 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 450 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C HIS C 450 " -0.056 2.00e-02 2.50e+03 pdb=" O HIS C 450 " 0.021 2.00e-02 2.50e+03 pdb=" N HIS C 451 " 0.019 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2415 2.79 - 3.31: 9314 3.31 - 3.84: 19286 3.84 - 4.37: 23653 4.37 - 4.90: 40420 Nonbonded interactions: 95088 Sorted by model distance: nonbonded pdb=" O SER A 555 " pdb=" OG SER A 559 " model vdw 2.258 2.440 nonbonded pdb=" O SER C 555 " pdb=" OG SER C 559 " model vdw 2.258 2.440 nonbonded pdb=" O SER B 555 " pdb=" OG SER B 559 " model vdw 2.259 2.440 nonbonded pdb=" O PHE A 508 " pdb=" N ASP A 510 " model vdw 2.282 2.520 nonbonded pdb=" OE2 GLU C 185 " pdb=" OH TYR C 224 " model vdw 2.313 2.440 ... (remaining 95083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.760 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.380 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 : 0.005 0.059 12102 Z= 0.347 Angle : 0.895 11.152 16488 Z= 0.502 Chirality : 0.056 0.290 1761 Planarity : 0.008 0.064 2142 Dihedral : 14.504 79.753 4371 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.54 % Favored : 93.11 % Rotamer: Outliers : 5.48 % Allowed : 6.10 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.19), residues: 1437 helix: -3.17 (0.36), residues: 93 sheet: -0.20 (0.19), residues: 567 loop : -2.53 (0.18), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 396 HIS 0.005 0.001 HIS A 102 PHE 0.016 0.002 PHE B 193 TYR 0.012 0.002 TYR C 561 ARG 0.009 0.001 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 202 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8208 (m) REVERT: A 388 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7940 (mtp-110) REVERT: A 394 LYS cc_start: 0.8628 (tppp) cc_final: 0.8375 (tptt) REVERT: A 455 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7535 (mt) REVERT: A 510 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7153 (t0) REVERT: B 354 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6340 (pm20) REVERT: B 387 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8610 (p) REVERT: B 388 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7830 (mtp-110) REVERT: B 538 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8290 (ttpp) REVERT: B 575 ASP cc_start: 0.7981 (m-30) cc_final: 0.7771 (m-30) REVERT: C 80 HIS cc_start: 0.8103 (t-170) cc_final: 0.7539 (t-90) REVERT: C 313 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8934 (t) REVERT: C 354 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6298 (pm20) REVERT: C 387 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8780 (p) REVERT: C 388 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7648 (mtp85) REVERT: C 455 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7619 (mt) REVERT: C 581 MET cc_start: 0.9184 (ttt) cc_final: 0.8766 (ttt) REVERT: C 593 GLN cc_start: 0.6338 (OUTLIER) cc_final: 0.5880 (tt0) REVERT: C 622 ASP cc_start: 0.7342 (m-30) cc_final: 0.6968 (m-30) outliers start: 71 outliers final: 13 residues processed: 254 average time/residue: 1.2944 time to fit residues: 354.8166 Evaluate side-chains 174 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 593 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 130 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 102 HIS A 171 ASN A 483 GLN B 102 HIS B 171 ASN B 369 ASN B 483 GLN C 102 HIS C 171 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12102 Z= 0.169 Angle : 0.549 6.479 16488 Z= 0.287 Chirality : 0.045 0.214 1761 Planarity : 0.005 0.043 2142 Dihedral : 6.838 67.374 1621 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 3.16 % Allowed : 11.50 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.20), residues: 1437 helix: -1.72 (0.46), residues: 93 sheet: 0.39 (0.20), residues: 528 loop : -2.04 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 474 HIS 0.006 0.001 HIS A 80 PHE 0.029 0.001 PHE B 101 TYR 0.013 0.001 TYR B 561 ARG 0.005 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7448 (mt0) REVERT: A 360 LYS cc_start: 0.8638 (tptm) cc_final: 0.8412 (tppt) REVERT: A 388 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7882 (mtp-110) REVERT: A 455 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7568 (mp) REVERT: A 508 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6652 (p90) REVERT: A 510 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7408 (t0) REVERT: B 354 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6290 (pm20) REVERT: B 538 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8257 (ttpp) REVERT: B 575 ASP cc_start: 0.7949 (m-30) cc_final: 0.7739 (m-30) REVERT: C 354 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6319 (pm20) REVERT: C 388 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7581 (mtp85) REVERT: C 455 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7651 (mp) REVERT: C 463 ILE cc_start: 0.8648 (mt) cc_final: 0.8394 (mm) REVERT: C 502 HIS cc_start: 0.7788 (m-70) cc_final: 0.6418 (t-90) REVERT: C 581 MET cc_start: 0.9166 (ttt) cc_final: 0.8791 (ttt) REVERT: C 622 ASP cc_start: 0.7386 (m-30) cc_final: 0.7118 (m-30) outliers start: 41 outliers final: 15 residues processed: 189 average time/residue: 1.2990 time to fit residues: 266.2379 Evaluate side-chains 166 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 0.0020 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 0.0270 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 0.0030 overall best weight: 0.9058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 107 HIS B 75 ASN B 196 ASN B 369 ASN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN B 502 HIS C 80 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12102 Z= 0.191 Angle : 0.550 6.585 16488 Z= 0.286 Chirality : 0.045 0.163 1761 Planarity : 0.004 0.039 2142 Dihedral : 5.857 46.347 1603 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 2.93 % Allowed : 12.27 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1437 helix: -1.13 (0.46), residues: 111 sheet: 0.53 (0.20), residues: 528 loop : -1.82 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 461 HIS 0.008 0.001 HIS C 80 PHE 0.010 0.001 PHE C 161 TYR 0.016 0.001 TYR B 561 ARG 0.003 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7403 (mt0) REVERT: A 360 LYS cc_start: 0.8625 (tptm) cc_final: 0.8414 (tppt) REVERT: A 388 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7851 (mtp-110) REVERT: A 451 HIS cc_start: 0.7127 (p-80) cc_final: 0.6719 (p-80) REVERT: A 502 HIS cc_start: 0.7966 (m-70) cc_final: 0.6537 (t70) REVERT: A 508 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6626 (p90) REVERT: A 510 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7462 (t0) REVERT: B 206 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: B 388 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7738 (mtp-110) REVERT: B 453 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7509 (tt0) REVERT: B 538 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8274 (ttpp) REVERT: B 575 ASP cc_start: 0.7867 (m-30) cc_final: 0.7609 (m-30) REVERT: C 80 HIS cc_start: 0.7708 (t-90) cc_final: 0.7498 (t-90) REVERT: C 202 GLU cc_start: 0.7523 (tt0) cc_final: 0.7288 (tm-30) REVERT: C 388 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7532 (mtp85) REVERT: C 463 ILE cc_start: 0.8632 (mt) cc_final: 0.8359 (mm) REVERT: C 581 MET cc_start: 0.9074 (ttt) cc_final: 0.8697 (ttt) REVERT: C 622 ASP cc_start: 0.7397 (m-30) cc_final: 0.7128 (m-30) outliers start: 38 outliers final: 27 residues processed: 173 average time/residue: 1.2110 time to fit residues: 227.9301 Evaluate side-chains 172 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 196 ASN B 102 HIS B 107 HIS B 196 ASN B 369 ASN B 502 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12102 Z= 0.223 Angle : 0.558 6.503 16488 Z= 0.289 Chirality : 0.045 0.187 1761 Planarity : 0.004 0.041 2142 Dihedral : 5.481 45.984 1592 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.47 % Allowed : 13.04 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1437 helix: -0.69 (0.49), residues: 111 sheet: 0.48 (0.20), residues: 576 loop : -1.73 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 474 HIS 0.007 0.001 HIS A 102 PHE 0.035 0.001 PHE A 101 TYR 0.018 0.001 TYR B 561 ARG 0.003 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 144 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 PHE cc_start: 0.8490 (p90) cc_final: 0.8207 (p90) REVERT: A 133 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7393 (mt0) REVERT: A 360 LYS cc_start: 0.8643 (tptm) cc_final: 0.8437 (tppt) REVERT: A 388 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7814 (mtp-110) REVERT: A 502 HIS cc_start: 0.7969 (m-70) cc_final: 0.6523 (t70) REVERT: A 508 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6434 (p90) REVERT: B 133 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7411 (mt0) REVERT: B 206 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7094 (m-30) REVERT: B 242 LEU cc_start: 0.7555 (mt) cc_final: 0.7196 (mt) REVERT: B 388 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7756 (mtp-110) REVERT: B 538 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8294 (ttpp) REVERT: B 607 TYR cc_start: 0.7606 (m-10) cc_final: 0.7342 (m-10) REVERT: C 202 GLU cc_start: 0.7571 (tt0) cc_final: 0.7322 (tm-30) REVERT: C 242 LEU cc_start: 0.7502 (mt) cc_final: 0.6905 (mt) REVERT: C 388 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7538 (mtp85) REVERT: C 463 ILE cc_start: 0.8629 (mt) cc_final: 0.8341 (mm) REVERT: C 581 MET cc_start: 0.9028 (ttt) cc_final: 0.8702 (ttt) REVERT: C 607 TYR cc_start: 0.7518 (m-80) cc_final: 0.6612 (m-10) REVERT: C 622 ASP cc_start: 0.7420 (m-30) cc_final: 0.7166 (m-30) outliers start: 45 outliers final: 27 residues processed: 175 average time/residue: 1.2976 time to fit residues: 245.4659 Evaluate side-chains 168 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.1980 chunk 79 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 80 HIS A 416 ASN B 196 ASN B 369 ASN B 410 ASN B 502 HIS C 80 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12102 Z= 0.256 Angle : 0.574 6.527 16488 Z= 0.298 Chirality : 0.046 0.193 1761 Planarity : 0.004 0.041 2142 Dihedral : 5.030 42.883 1584 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.09 % Allowed : 13.81 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.21), residues: 1437 helix: -0.53 (0.49), residues: 111 sheet: 0.49 (0.19), residues: 576 loop : -1.64 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.007 0.001 HIS B 102 PHE 0.034 0.001 PHE C 101 TYR 0.018 0.001 TYR B 561 ARG 0.002 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 136 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 133 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7432 (mt0) REVERT: A 388 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7832 (mtp-110) REVERT: A 451 HIS cc_start: 0.7124 (p-80) cc_final: 0.6602 (p-80) REVERT: A 502 HIS cc_start: 0.7982 (m-70) cc_final: 0.6524 (t70) REVERT: A 508 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6757 (p90) REVERT: A 607 TYR cc_start: 0.7502 (m-80) cc_final: 0.7236 (m-80) REVERT: B 133 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: B 206 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: B 388 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7768 (mtp-110) REVERT: B 538 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8285 (ttpp) REVERT: C 388 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7537 (mtp85) REVERT: C 453 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7117 (tm-30) REVERT: C 463 ILE cc_start: 0.8623 (mt) cc_final: 0.8324 (mm) REVERT: C 581 MET cc_start: 0.9003 (ttt) cc_final: 0.8669 (ttt) REVERT: C 622 ASP cc_start: 0.7373 (m-30) cc_final: 0.7117 (m-30) outliers start: 40 outliers final: 26 residues processed: 160 average time/residue: 1.2625 time to fit residues: 218.9924 Evaluate side-chains 166 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 27 optimal weight: 0.1980 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 115 optimal weight: 0.0470 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 416 ASN A 484 HIS B 196 ASN B 369 ASN B 502 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12102 Z= 0.154 Angle : 0.518 6.170 16488 Z= 0.268 Chirality : 0.044 0.175 1761 Planarity : 0.004 0.037 2142 Dihedral : 4.678 46.386 1584 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.85 % Allowed : 14.97 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1437 helix: -0.15 (0.51), residues: 111 sheet: 0.72 (0.21), residues: 528 loop : -1.51 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 474 HIS 0.006 0.001 HIS A 102 PHE 0.036 0.001 PHE C 101 TYR 0.022 0.001 TYR C 607 ARG 0.001 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7431 (mt0) REVERT: A 360 LYS cc_start: 0.8638 (tptm) cc_final: 0.8415 (tppp) REVERT: A 388 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7842 (mtp-110) REVERT: A 451 HIS cc_start: 0.7069 (p-80) cc_final: 0.6676 (p-80) REVERT: A 463 ILE cc_start: 0.8665 (mt) cc_final: 0.8292 (mm) REVERT: A 502 HIS cc_start: 0.7947 (m-70) cc_final: 0.6510 (t70) REVERT: B 133 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7466 (mt0) REVERT: B 206 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7038 (m-30) REVERT: B 388 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7753 (mtp-110) REVERT: B 538 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8221 (ttpp) REVERT: C 102 HIS cc_start: 0.6391 (OUTLIER) cc_final: 0.5994 (t-90) REVERT: C 202 GLU cc_start: 0.7491 (tt0) cc_final: 0.7270 (tm-30) REVERT: C 242 LEU cc_start: 0.7885 (mt) cc_final: 0.7296 (mt) REVERT: C 388 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7518 (mtp85) REVERT: C 447 ASN cc_start: 0.8241 (p0) cc_final: 0.7705 (p0) REVERT: C 451 HIS cc_start: 0.6987 (p-80) cc_final: 0.6600 (p-80) REVERT: C 453 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7357 (tm-30) REVERT: C 463 ILE cc_start: 0.8570 (mt) cc_final: 0.8324 (mm) REVERT: C 581 MET cc_start: 0.9057 (ttt) cc_final: 0.8671 (ttt) REVERT: C 622 ASP cc_start: 0.7384 (m-30) cc_final: 0.7132 (m-30) outliers start: 37 outliers final: 21 residues processed: 165 average time/residue: 1.2821 time to fit residues: 229.3207 Evaluate side-chains 161 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 620 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0980 chunk 79 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 0.0970 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 102 HIS B 196 ASN B 369 ASN B 502 HIS C 80 HIS C 484 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12102 Z= 0.178 Angle : 0.535 6.491 16488 Z= 0.274 Chirality : 0.045 0.185 1761 Planarity : 0.004 0.037 2142 Dihedral : 4.568 44.271 1582 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.47 % Allowed : 15.51 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1437 helix: -0.01 (0.52), residues: 111 sheet: 0.78 (0.21), residues: 528 loop : -1.47 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.007 0.001 HIS C 80 PHE 0.036 0.001 PHE C 101 TYR 0.015 0.001 TYR B 561 ARG 0.001 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 388 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7856 (mtp-110) REVERT: A 451 HIS cc_start: 0.6927 (p-80) cc_final: 0.6617 (p-80) REVERT: A 463 ILE cc_start: 0.8664 (mt) cc_final: 0.8311 (mm) REVERT: B 133 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7462 (mt0) REVERT: B 206 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7029 (m-30) REVERT: B 388 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7757 (mtp-110) REVERT: B 538 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8222 (ttpp) REVERT: B 575 ASP cc_start: 0.7826 (m-30) cc_final: 0.7589 (m-30) REVERT: C 202 GLU cc_start: 0.7520 (tt0) cc_final: 0.7291 (tm-30) REVERT: C 242 LEU cc_start: 0.7993 (mt) cc_final: 0.7358 (mt) REVERT: C 388 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7515 (mtp85) REVERT: C 447 ASN cc_start: 0.8134 (p0) cc_final: 0.7641 (p0) REVERT: C 451 HIS cc_start: 0.6980 (p-80) cc_final: 0.6656 (p-80) REVERT: C 463 ILE cc_start: 0.8561 (mt) cc_final: 0.8314 (mm) REVERT: C 502 HIS cc_start: 0.7683 (m170) cc_final: 0.6418 (t-90) REVERT: C 581 MET cc_start: 0.9055 (ttt) cc_final: 0.8675 (ttt) REVERT: C 622 ASP cc_start: 0.7391 (m-30) cc_final: 0.7139 (m-30) outliers start: 32 outliers final: 26 residues processed: 161 average time/residue: 1.2419 time to fit residues: 217.2782 Evaluate side-chains 169 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 620 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS B 80 HIS B 196 ASN B 246 HIS B 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12102 Z= 0.331 Angle : 0.622 8.404 16488 Z= 0.321 Chirality : 0.048 0.204 1761 Planarity : 0.004 0.042 2142 Dihedral : 4.961 43.322 1580 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.78 % Allowed : 15.90 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1437 helix: -0.38 (0.49), residues: 111 sheet: 0.55 (0.20), residues: 576 loop : -1.54 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.010 0.001 HIS A 102 PHE 0.036 0.002 PHE C 101 TYR 0.020 0.002 TYR B 561 ARG 0.004 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7937 (m-80) cc_final: 0.7603 (m-80) REVERT: A 388 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7837 (mtp-110) REVERT: A 451 HIS cc_start: 0.7232 (p-80) cc_final: 0.6659 (p-80) REVERT: B 133 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7445 (mt0) REVERT: B 206 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7153 (m-30) REVERT: B 388 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7717 (mtp-110) REVERT: B 502 HIS cc_start: 0.7663 (m170) cc_final: 0.6348 (t-90) REVERT: B 538 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8280 (ttpp) REVERT: B 575 ASP cc_start: 0.7859 (m-30) cc_final: 0.7631 (m-30) REVERT: B 622 ASP cc_start: 0.7457 (m-30) cc_final: 0.7185 (m-30) REVERT: C 388 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7520 (mtp85) REVERT: C 447 ASN cc_start: 0.8246 (p0) cc_final: 0.7742 (p0) REVERT: C 463 ILE cc_start: 0.8594 (mt) cc_final: 0.8294 (mm) REVERT: C 581 MET cc_start: 0.8972 (ttt) cc_final: 0.8666 (ttt) REVERT: C 607 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.7047 (m-80) REVERT: C 622 ASP cc_start: 0.7452 (m-30) cc_final: 0.7205 (m-30) outliers start: 36 outliers final: 28 residues processed: 159 average time/residue: 1.2315 time to fit residues: 212.5626 Evaluate side-chains 162 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 607 TYR Chi-restraints excluded: chain C residue 620 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS B 196 ASN B 369 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12102 Z= 0.182 Angle : 0.552 9.535 16488 Z= 0.281 Chirality : 0.045 0.184 1761 Planarity : 0.004 0.039 2142 Dihedral : 4.478 18.706 1578 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.24 % Allowed : 16.67 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1437 helix: -0.01 (0.51), residues: 111 sheet: 0.64 (0.21), residues: 555 loop : -1.35 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.006 0.001 HIS A 102 PHE 0.038 0.001 PHE C 101 TYR 0.016 0.001 TYR C 607 ARG 0.002 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.326 Fit side-chains REVERT: A 388 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7860 (mtp-110) REVERT: A 451 HIS cc_start: 0.7088 (p-80) cc_final: 0.6553 (p-80) REVERT: B 133 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7418 (mt0) REVERT: B 206 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7064 (m-30) REVERT: B 388 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7762 (mtp-110) REVERT: B 502 HIS cc_start: 0.7677 (m170) cc_final: 0.6174 (t-90) REVERT: B 538 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8233 (ttpp) REVERT: B 575 ASP cc_start: 0.7822 (m-30) cc_final: 0.7573 (m-30) REVERT: C 202 GLU cc_start: 0.7540 (tt0) cc_final: 0.7288 (tm-30) REVERT: C 388 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7516 (mtp85) REVERT: C 463 ILE cc_start: 0.8555 (mt) cc_final: 0.8287 (mm) REVERT: C 581 MET cc_start: 0.9029 (ttt) cc_final: 0.8637 (ttt) REVERT: C 607 TYR cc_start: 0.7455 (m-10) cc_final: 0.7216 (m-80) REVERT: C 622 ASP cc_start: 0.7407 (m-30) cc_final: 0.7150 (m-30) outliers start: 29 outliers final: 26 residues processed: 153 average time/residue: 1.2789 time to fit residues: 212.0780 Evaluate side-chains 159 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 620 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 80 HIS A 416 ASN B 196 ASN B 369 ASN B 502 HIS C 75 ASN C 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 12102 Z= 0.444 Angle : 0.677 9.202 16488 Z= 0.349 Chirality : 0.051 0.214 1761 Planarity : 0.005 0.046 2142 Dihedral : 5.074 21.427 1578 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.70 % Allowed : 16.20 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1437 helix: -0.49 (0.49), residues: 111 sheet: 0.51 (0.20), residues: 576 loop : -1.52 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 474 HIS 0.011 0.001 HIS A 102 PHE 0.038 0.002 PHE C 101 TYR 0.022 0.002 TYR B 561 ARG 0.006 0.001 ARG C 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7796 (m-80) cc_final: 0.7473 (m-80) REVERT: A 388 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7837 (mtp-110) REVERT: A 451 HIS cc_start: 0.7280 (p-80) cc_final: 0.6546 (p-80) REVERT: B 133 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7429 (mt0) REVERT: B 206 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7230 (m-30) REVERT: B 388 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7737 (mtp-110) REVERT: B 502 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.6348 (t-90) REVERT: B 538 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8311 (ttpp) REVERT: B 575 ASP cc_start: 0.7863 (m-30) cc_final: 0.7634 (m-30) REVERT: B 622 ASP cc_start: 0.7473 (m-30) cc_final: 0.7141 (m-30) REVERT: C 388 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7516 (mtp85) REVERT: C 447 ASN cc_start: 0.8261 (p0) cc_final: 0.7792 (p0) REVERT: C 622 ASP cc_start: 0.7489 (m-30) cc_final: 0.7209 (m-30) outliers start: 35 outliers final: 30 residues processed: 158 average time/residue: 1.2784 time to fit residues: 218.7453 Evaluate side-chains 158 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 519 CYS Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 519 CYS Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 620 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS B 196 ASN B 369 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.093396 restraints weight = 13490.501| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.26 r_work: 0.2758 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12102 Z= 0.168 Angle : 0.548 9.240 16488 Z= 0.280 Chirality : 0.045 0.177 1761 Planarity : 0.004 0.041 2142 Dihedral : 4.556 19.101 1578 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.39 % Allowed : 16.59 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1437 helix: 0.04 (0.52), residues: 111 sheet: 0.76 (0.21), residues: 528 loop : -1.42 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 474 HIS 0.006 0.001 HIS B 503 PHE 0.040 0.001 PHE C 101 TYR 0.014 0.001 TYR C 607 ARG 0.001 0.000 ARG C 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4523.39 seconds wall clock time: 80 minutes 32.59 seconds (4832.59 seconds total)