Starting phenix.real_space_refine on Sat Dec 9 17:11:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ku9_0776/12_2023/6ku9_0776.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ku9_0776/12_2023/6ku9_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_0776/12_2023/6ku9_0776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ku9_0776/12_2023/6ku9_0776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ku9_0776/12_2023/6ku9_0776.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ku9_0776/12_2023/6ku9_0776.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6.44, per 1000 atoms: 0.55 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: 4.03 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: 1.62 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: 4.23 Time building geometry restraints manager: 4.46 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: 0.570 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: 3.440 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 34.500 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.970 ------------------------------------------------------------------------------- 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 : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 13 residues processed: 254 average time/residue: 1.2437 time to fit residues: 341.3682 Evaluate side-chains 165 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 1.2996 time to fit residues: 3.3195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 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: 0.5718 ------------------------------------------------------------------------------- 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: 0.8378 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12102 Z= 0.157 Angle : 0.555 6.566 16488 Z= 0.290 Chirality : 0.045 0.215 1761 Planarity : 0.005 0.040 2142 Dihedral : 4.911 20.521 1578 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 3.16 % Allowed : 12.19 % Favored : 84.65 % 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: -1.59 (0.20), residues: 1437 helix: -1.78 (0.45), residues: 93 sheet: 0.37 (0.21), residues: 528 loop : -2.06 (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 0.014 0.001 TYR B 561 ARG 0.008 0.000 ARG C 388 *********************** 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 204 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 16 residues processed: 190 average time/residue: 1.2566 time to fit residues: 258.8669 Evaluate side-chains 164 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 1.0922 time to fit residues: 5.3969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 0.0020 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 0.0770 overall best weight: 0.8950 ------------------------------------------------------------------------------- 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 A 133 GLN ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12102 Z= 0.192 Angle : 0.557 6.466 16488 Z= 0.289 Chirality : 0.045 0.164 1761 Planarity : 0.004 0.038 2142 Dihedral : 4.687 17.979 1578 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 3.24 % Allowed : 12.65 % Favored : 84.10 % 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: -1.31 (0.20), residues: 1437 helix: -1.19 (0.45), residues: 111 sheet: 0.47 (0.20), residues: 528 loop : -1.85 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 461 HIS 0.005 0.001 HIS B 102 PHE 0.010 0.001 PHE C 161 TYR 0.019 0.001 TYR C 607 ARG 0.008 0.000 ARG C 388 *********************** 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 190 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 148 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 29 residues processed: 175 average time/residue: 1.2406 time to fit residues: 235.8494 Evaluate side-chains 173 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.377 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 0.9214 time to fit residues: 10.0653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 0.0870 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 0.0970 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 133 GLN A 196 ASN A 369 ASN A 484 HIS B 102 HIS B 369 ASN C 190 ASN C 369 ASN C 484 HIS C 502 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12102 Z= 0.141 Angle : 0.517 7.117 16488 Z= 0.266 Chirality : 0.044 0.170 1761 Planarity : 0.004 0.037 2142 Dihedral : 4.384 17.090 1578 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.70 % Allowed : 14.51 % Favored : 82.79 % 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: -1.04 (0.20), residues: 1437 helix: -0.50 (0.49), residues: 111 sheet: 0.60 (0.21), residues: 528 loop : -1.70 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 461 HIS 0.007 0.001 HIS C 102 PHE 0.035 0.001 PHE A 101 TYR 0.021 0.001 TYR C 607 ARG 0.008 0.000 ARG C 388 *********************** 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 181 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.362 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 23 residues processed: 169 average time/residue: 1.2634 time to fit residues: 231.0135 Evaluate side-chains 162 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.5692 time to fit residues: 3.7159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 102 HIS A 369 ASN A 416 ASN B 107 HIS B 369 ASN B 410 ASN C 75 ASN C 369 ASN C 416 ASN C 502 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12102 Z= 0.384 Angle : 0.646 7.804 16488 Z= 0.334 Chirality : 0.049 0.175 1761 Planarity : 0.005 0.044 2142 Dihedral : 4.983 18.569 1578 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.09 % Allowed : 14.58 % Favored : 82.33 % 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: -1.10 (0.20), residues: 1437 helix: -0.67 (0.48), residues: 111 sheet: 0.38 (0.19), residues: 576 loop : -1.69 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 461 HIS 0.014 0.001 HIS C 102 PHE 0.016 0.002 PHE A 606 TYR 0.023 0.002 TYR C 607 ARG 0.009 0.001 ARG C 388 *********************** 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 175 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 135 time to evaluate : 1.374 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 26 residues processed: 165 average time/residue: 1.2260 time to fit residues: 219.6484 Evaluate side-chains 159 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 4 average time/residue: 0.7783 time to fit residues: 5.1841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.5980 chunk 125 optimal weight: 10.0000 chunk 27 optimal weight: 0.0170 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 133 GLN B 196 ASN B 369 ASN C 502 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12102 Z= 0.161 Angle : 0.536 7.611 16488 Z= 0.275 Chirality : 0.044 0.157 1761 Planarity : 0.004 0.037 2142 Dihedral : 4.515 18.240 1578 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.93 % Allowed : 15.51 % Favored : 81.56 % 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: -0.21 (0.51), residues: 111 sheet: 0.50 (0.20), residues: 543 loop : -1.47 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 474 HIS 0.006 0.001 HIS C 102 PHE 0.030 0.001 PHE A 101 TYR 0.018 0.001 TYR C 607 ARG 0.009 0.000 ARG C 388 *********************** 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 174 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.475 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 29 residues processed: 163 average time/residue: 1.3462 time to fit residues: 238.4646 Evaluate side-chains 165 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.546 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 7 average time/residue: 0.8262 time to fit residues: 8.4390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0870 chunk 79 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 133 GLN B 369 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2463 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= 0.194 Angle : 0.550 7.100 16488 Z= 0.281 Chirality : 0.045 0.154 1761 Planarity : 0.004 0.038 2142 Dihedral : 4.492 17.066 1578 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.24 % Allowed : 16.13 % Favored : 81.64 % 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: -0.77 (0.21), residues: 1437 helix: -0.08 (0.51), residues: 111 sheet: 0.54 (0.20), residues: 543 loop : -1.40 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 474 HIS 0.006 0.001 HIS C 102 PHE 0.030 0.001 PHE A 101 TYR 0.018 0.001 TYR A 607 ARG 0.009 0.000 ARG C 388 *********************** 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 167 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.471 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 27 residues processed: 163 average time/residue: 1.3058 time to fit residues: 231.0350 Evaluate side-chains 164 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 25 residues processed: 2 average time/residue: 1.5985 time to fit residues: 5.2135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 0.0770 chunk 12 optimal weight: 0.0060 chunk 109 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 overall best weight: 0.5154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 133 GLN B 80 HIS B 369 ASN C 369 ASN C 502 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12102 Z= 0.148 Angle : 0.535 9.213 16488 Z= 0.271 Chirality : 0.044 0.149 1761 Planarity : 0.004 0.038 2142 Dihedral : 4.303 17.270 1578 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.78 % Allowed : 16.36 % Favored : 80.86 % 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: 0.17 (0.52), residues: 111 sheet: 0.72 (0.21), residues: 525 loop : -1.41 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 474 HIS 0.005 0.001 HIS C 102 PHE 0.029 0.001 PHE A 101 TYR 0.018 0.001 TYR C 607 ARG 0.010 0.000 ARG C 388 *********************** 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 174 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.532 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 29 residues processed: 166 average time/residue: 1.3008 time to fit residues: 233.7965 Evaluate side-chains 163 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 5 average time/residue: 0.4946 time to fit residues: 4.7922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS B 369 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN C 502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12102 Z= 0.221 Angle : 0.570 10.728 16488 Z= 0.289 Chirality : 0.045 0.155 1761 Planarity : 0.004 0.038 2142 Dihedral : 4.458 17.758 1578 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.55 % Allowed : 16.67 % Favored : 80.79 % 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: -0.66 (0.21), residues: 1437 helix: 0.03 (0.51), residues: 111 sheet: 0.49 (0.20), residues: 570 loop : -1.27 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 461 HIS 0.006 0.001 HIS A 102 PHE 0.029 0.001 PHE A 101 TYR 0.018 0.001 TYR A 607 ARG 0.009 0.000 ARG C 388 *********************** 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 169 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.439 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 28 residues processed: 163 average time/residue: 1.2117 time to fit residues: 214.9910 Evaluate side-chains 160 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 26 residues processed: 2 average time/residue: 0.8645 time to fit residues: 3.8065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS B 246 HIS B 369 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12102 Z= 0.275 Angle : 0.609 12.014 16488 Z= 0.310 Chirality : 0.047 0.160 1761 Planarity : 0.004 0.039 2142 Dihedral : 4.703 19.909 1578 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.31 % Allowed : 17.21 % Favored : 80.48 % 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: -0.75 (0.21), residues: 1437 helix: -0.11 (0.50), residues: 111 sheet: 0.68 (0.20), residues: 528 loop : -1.44 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 461 HIS 0.007 0.001 HIS A 102 PHE 0.028 0.001 PHE A 101 TYR 0.022 0.001 TYR A 607 ARG 0.009 0.000 ARG C 388 ********************** 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 160 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.496 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 27 residues processed: 159 average time/residue: 1.2735 time to fit residues: 220.7482 Evaluate side-chains 154 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 1.9131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS B 369 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.091478 restraints weight = 13402.587| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.27 r_work: 0.2824 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12102 Z= 0.248 Angle : 0.588 11.313 16488 Z= 0.299 Chirality : 0.046 0.157 1761 Planarity : 0.004 0.040 2142 Dihedral : 4.635 18.912 1578 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.55 % Allowed : 17.05 % Favored : 80.40 % 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: -0.71 (0.21), residues: 1437 helix: -0.04 (0.51), residues: 111 sheet: 0.54 (0.20), residues: 555 loop : -1.35 (0.21), residues: 771 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 0.028 0.001 PHE A 101 TYR 0.017 0.001 TYR B 561 ARG 0.010 0.000 ARG C 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4451.40 seconds wall clock time: 79 minutes 58.38 seconds (4798.38 seconds total)