Starting phenix.real_space_refine on Sat Feb 17 20:02:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/02_2024/7a4a_11630.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/02_2024/7a4a_11630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/02_2024/7a4a_11630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/02_2024/7a4a_11630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/02_2024/7a4a_11630.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/02_2024/7a4a_11630.pdb" } resolution = 3.76 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 ------------------------------------------------------------------------------- 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 105 5.16 5 C 6294 2.51 5 N 1743 2.21 5 O 2025 1.98 5 H 9618 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 223": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 305": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 223": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 305": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 187": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 223": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 305": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19785 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6581 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 420} Chain: "B" Number of atoms: 6581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6581 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 420} Chain: "C" Number of atoms: 6581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6581 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 420} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.02, per 1000 atoms: 0.46 Number of scatterers: 19785 At special positions: 0 Unit cell: (86.901, 86.901, 134.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 O 2025 8.00 N 1743 7.00 C 6294 6.00 H 9618 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 1 " - pdb=" SG CYS A 41 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 23 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 162 " distance=2.02 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 135 " distance=2.04 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 138 " distance=2.04 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 373 " - pdb=" SG CYS A 404 " distance=2.03 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 41 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 23 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 162 " distance=2.02 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 132 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 138 " distance=2.04 Simple disulfide: pdb=" SG CYS B 246 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 337 " - pdb=" SG CYS B 408 " distance=2.03 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 360 " - pdb=" SG CYS B 382 " distance=2.03 Simple disulfide: pdb=" SG CYS B 373 " - pdb=" SG CYS B 404 " distance=2.03 Simple disulfide: pdb=" SG CYS C 1 " - pdb=" SG CYS C 41 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 23 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 162 " distance=2.02 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 135 " distance=2.04 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 132 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 138 " distance=2.04 Simple disulfide: pdb=" SG CYS C 246 " - pdb=" SG CYS C 257 " distance=2.03 Simple disulfide: pdb=" SG CYS C 264 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 337 " - pdb=" SG CYS C 408 " distance=2.03 Simple disulfide: pdb=" SG CYS C 347 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 360 " - pdb=" SG CYS C 382 " distance=2.03 Simple disulfide: pdb=" SG CYS C 373 " - pdb=" SG CYS C 404 " distance=2.03 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 414 " " NAG B 501 " - " ASN B 414 " " NAG C 501 " - " ASN C 414 " Time building additional restraints: 14.48 Conformation dependent library (CDL) restraints added in 2.1 seconds 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 33 sheets defined 4.8% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 112 through 117 removed outlier: 4.094A pdb=" N SER A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 282 through 289 removed outlier: 3.927A pdb=" N LEU A 289 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 4.094A pdb=" N SER B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.928A pdb=" N LEU B 289 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 removed outlier: 4.095A pdb=" N SER C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.928A pdb=" N LEU C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 removed outlier: 4.028A pdb=" N ILE A 5 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N HIS A 320 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU A 203 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 322 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE A 201 " --> pdb=" O VAL A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 24 removed outlier: 3.645A pdb=" N CYS A 14 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL C 331 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N CYS C 41 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 24 removed outlier: 3.645A pdb=" N CYS A 14 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL C 331 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N CYS C 41 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 300 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 188 removed outlier: 3.568A pdb=" N VAL A 300 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 188 removed outlier: 6.095A pdb=" N CYS A 41 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 331 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N CYS B 14 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR A 330 " --> pdb=" O CYS B 14 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE B 16 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 332 " --> pdb=" O ILE B 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 74 removed outlier: 5.793A pdb=" N ILE A 70 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR A 161 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 72 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 217 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 85 Processing sheet with id=AA8, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA9, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.575A pdb=" N THR A 276 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 433 " --> pdb=" O CYS A 277 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AB2, first strand: chain 'A' and resid 369 through 372 Processing sheet with id=AB3, first strand: chain 'A' and resid 399 through 402 Processing sheet with id=AB4, first strand: chain 'A' and resid 405 through 407 Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 9 removed outlier: 4.028A pdb=" N ILE B 5 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N HIS B 320 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU B 203 " --> pdb=" O HIS B 320 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL B 322 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE B 201 " --> pdb=" O VAL B 322 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 184 through 188 removed outlier: 3.568A pdb=" N VAL B 300 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 184 through 188 removed outlier: 6.095A pdb=" N CYS B 41 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 331 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N CYS C 14 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR B 330 " --> pdb=" O CYS C 14 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE C 16 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS B 332 " --> pdb=" O ILE C 16 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 74 removed outlier: 5.793A pdb=" N ILE B 70 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYR B 161 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 72 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 217 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 77 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 244 through 245 Processing sheet with id=AC2, first strand: chain 'B' and resid 265 through 267 removed outlier: 3.575A pdb=" N THR B 276 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 433 " --> pdb=" O CYS B 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AC4, first strand: chain 'B' and resid 369 through 372 Processing sheet with id=AC5, first strand: chain 'B' and resid 399 through 402 Processing sheet with id=AC6, first strand: chain 'B' and resid 405 through 407 Processing sheet with id=AC7, first strand: chain 'C' and resid 5 through 9 removed outlier: 4.027A pdb=" N ILE C 5 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N HIS C 320 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU C 203 " --> pdb=" O HIS C 320 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL C 322 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE C 201 " --> pdb=" O VAL C 322 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 69 through 74 removed outlier: 5.793A pdb=" N ILE C 70 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR C 161 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE C 72 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 217 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 77 through 85 Processing sheet with id=AD1, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AD2, first strand: chain 'C' and resid 265 through 267 removed outlier: 3.574A pdb=" N THR C 276 " --> pdb=" O THR C 265 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 433 " --> pdb=" O CYS C 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AD4, first strand: chain 'C' and resid 369 through 372 Processing sheet with id=AD5, first strand: chain 'C' and resid 399 through 402 Processing sheet with id=AD6, first strand: chain 'C' and resid 405 through 407 366 hydrogen bonds defined for protein. 861 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: 7.72 Time building geometry restraints manager: 15.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9618 1.03 - 1.23: 170 1.23 - 1.43: 4112 1.43 - 1.63: 5960 1.63 - 1.82: 120 Bond restraints: 19980 Sorted by residual: bond pdb=" CA ASN A 67 " pdb=" CB ASN A 67 " ideal model delta sigma weight residual 1.527 1.496 0.031 1.75e-02 3.27e+03 3.15e+00 bond pdb=" CA ASN B 67 " pdb=" CB ASN B 67 " ideal model delta sigma weight residual 1.527 1.496 0.031 1.75e-02 3.27e+03 3.13e+00 bond pdb=" CA ASN C 67 " pdb=" CB ASN C 67 " ideal model delta sigma weight residual 1.527 1.496 0.030 1.75e-02 3.27e+03 3.00e+00 bond pdb=" CB ILE B 207 " pdb=" CG2 ILE B 207 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.90e+00 bond pdb=" CB ILE C 207 " pdb=" CG2 ILE C 207 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 ... (remaining 19975 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.70: 399 106.70 - 113.56: 23868 113.56 - 120.42: 5720 120.42 - 127.28: 5899 127.28 - 134.15: 102 Bond angle restraints: 35988 Sorted by residual: angle pdb=" N LEU A 270 " pdb=" CA LEU A 270 " pdb=" CB LEU A 270 " ideal model delta sigma weight residual 114.17 110.47 3.70 1.14e+00 7.69e-01 1.05e+01 angle pdb=" N LEU C 270 " pdb=" CA LEU C 270 " pdb=" CB LEU C 270 " ideal model delta sigma weight residual 114.17 110.50 3.67 1.14e+00 7.69e-01 1.04e+01 angle pdb=" N LEU B 270 " pdb=" CA LEU B 270 " pdb=" CB LEU B 270 " ideal model delta sigma weight residual 114.17 110.50 3.67 1.14e+00 7.69e-01 1.04e+01 angle pdb=" C TRP B 196 " pdb=" N ASN B 197 " pdb=" CA ASN B 197 " ideal model delta sigma weight residual 122.17 117.39 4.78 1.54e+00 4.22e-01 9.64e+00 angle pdb=" C TRP A 196 " pdb=" N ASN A 197 " pdb=" CA ASN A 197 " ideal model delta sigma weight residual 122.17 117.39 4.78 1.54e+00 4.22e-01 9.62e+00 ... (remaining 35983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 8684 14.74 - 29.48: 723 29.48 - 44.22: 184 44.22 - 58.96: 111 58.96 - 73.70: 15 Dihedral angle restraints: 9717 sinusoidal: 5304 harmonic: 4413 Sorted by residual: dihedral pdb=" CA GLU C 71 " pdb=" C GLU C 71 " pdb=" N PHE C 72 " pdb=" CA PHE C 72 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLU B 71 " pdb=" C GLU B 71 " pdb=" N PHE B 72 " pdb=" CA PHE B 72 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLU A 71 " pdb=" C GLU A 71 " pdb=" N PHE A 72 " pdb=" CA PHE A 72 " ideal model delta harmonic sigma weight residual 180.00 -152.12 -27.88 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 9714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 889 0.030 - 0.059: 506 0.059 - 0.089: 187 0.089 - 0.119: 56 0.119 - 0.149: 21 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA PRO A 190 " pdb=" N PRO A 190 " pdb=" C PRO A 190 " pdb=" CB PRO A 190 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA PRO C 190 " pdb=" N PRO C 190 " pdb=" C PRO C 190 " pdb=" CB PRO C 190 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA PRO B 190 " pdb=" N PRO B 190 " pdb=" C PRO B 190 " pdb=" CB PRO B 190 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 1656 not shown) Planarity restraints: 3081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 211 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO A 212 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 211 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO B 212 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 211 " 0.048 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO C 212 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.039 5.00e-02 4.00e+02 ... (remaining 3078 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1021 2.17 - 2.78: 39337 2.78 - 3.38: 49624 3.38 - 3.99: 67698 3.99 - 4.60: 104566 Nonbonded interactions: 262246 Sorted by model distance: nonbonded pdb=" O LYS A 332 " pdb=" H ILE B 16 " model vdw 1.558 1.850 nonbonded pdb=" O LYS B 332 " pdb=" H ILE C 16 " model vdw 1.573 1.850 nonbonded pdb=" HH TYR C 120 " pdb=" O PHE C 259 " model vdw 1.593 1.850 nonbonded pdb=" HH TYR B 120 " pdb=" O PHE B 259 " model vdw 1.603 1.850 nonbonded pdb=" HH TYR A 120 " pdb=" O PHE A 259 " model vdw 1.610 1.850 ... (remaining 262241 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 group one per residue 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: 0.990 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: 0.290 Extract box with map and model: 3.570 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 62.480 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.007 0.055 10362 Z= 0.497 Angle : 0.710 6.857 14073 Z= 0.401 Chirality : 0.043 0.149 1659 Planarity : 0.006 0.073 1821 Dihedral : 11.730 73.698 3810 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.81 % Favored : 87.19 % Rotamer: Outliers : 2.96 % Allowed : 7.19 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -6.00 (0.16), residues: 1311 helix: -4.78 (0.19), residues: 81 sheet: -3.30 (0.17), residues: 543 loop : -4.57 (0.16), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 196 HIS 0.004 0.001 HIS C 88 PHE 0.023 0.001 PHE B 72 TYR 0.008 0.001 TYR C 148 ARG 0.008 0.001 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 263 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.6805 (tp30) cc_final: 0.6570 (mt-10) REVERT: A 211 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9028 (pp) REVERT: B 211 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8891 (pp) REVERT: B 308 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: C 211 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8971 (pp) outliers start: 35 outliers final: 11 residues processed: 295 average time/residue: 0.4473 time to fit residues: 189.3230 Evaluate side-chains 147 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 94 HIS A 285 HIS A 318 GLN A 389 ASN B 37 GLN B 94 HIS B 99 HIS B 285 HIS B 318 GLN B 389 ASN C 37 GLN C 94 HIS C 285 HIS C 318 GLN C 389 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 10362 Z= 0.332 Angle : 0.717 8.051 14073 Z= 0.384 Chirality : 0.046 0.164 1659 Planarity : 0.005 0.063 1821 Dihedral : 8.293 48.834 1476 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.48 % Favored : 84.52 % Rotamer: Outliers : 4.31 % Allowed : 15.40 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -5.35 (0.17), residues: 1311 helix: -4.18 (0.28), residues: 81 sheet: -2.75 (0.19), residues: 504 loop : -4.23 (0.16), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 196 HIS 0.004 0.001 HIS C 145 PHE 0.026 0.002 PHE B 72 TYR 0.010 0.001 TYR A 161 ARG 0.004 0.000 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 152 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 PHE cc_start: 0.7535 (m-10) cc_final: 0.6950 (m-80) REVERT: A 214 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8939 (mp) REVERT: A 221 ASN cc_start: 0.7990 (t0) cc_final: 0.7713 (t0) REVERT: B 214 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8592 (mp) outliers start: 51 outliers final: 32 residues processed: 193 average time/residue: 0.3010 time to fit residues: 95.4676 Evaluate side-chains 160 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN A 431 GLN B 99 HIS B 389 ASN C 99 HIS C 235 GLN C 389 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 10362 Z= 0.340 Angle : 0.690 15.683 14073 Z= 0.364 Chirality : 0.045 0.236 1659 Planarity : 0.005 0.058 1821 Dihedral : 7.639 49.283 1472 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % Rotamer: Outliers : 3.81 % Allowed : 16.50 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -4.83 (0.18), residues: 1311 helix: -3.71 (0.39), residues: 63 sheet: -2.37 (0.20), residues: 519 loop : -3.94 (0.17), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 196 HIS 0.004 0.001 HIS C 378 PHE 0.022 0.002 PHE A 72 TYR 0.011 0.001 TYR A 161 ARG 0.004 0.001 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 THR cc_start: 0.9080 (m) cc_final: 0.8858 (p) REVERT: A 211 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9049 (pp) REVERT: A 221 ASN cc_start: 0.8008 (t0) cc_final: 0.7748 (t0) REVERT: B 181 THR cc_start: 0.9069 (m) cc_final: 0.8849 (p) REVERT: C 181 THR cc_start: 0.9029 (m) cc_final: 0.8758 (p) outliers start: 45 outliers final: 37 residues processed: 179 average time/residue: 0.3374 time to fit residues: 99.6696 Evaluate side-chains 159 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN C 99 HIS C 389 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 10362 Z= 0.255 Angle : 0.664 14.636 14073 Z= 0.349 Chirality : 0.045 0.219 1659 Planarity : 0.004 0.052 1821 Dihedral : 7.387 49.237 1472 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 3.64 % Allowed : 17.94 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.53 (0.19), residues: 1311 helix: -3.37 (0.47), residues: 63 sheet: -2.27 (0.20), residues: 492 loop : -3.64 (0.17), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 196 HIS 0.011 0.001 HIS B 99 PHE 0.019 0.001 PHE C 72 TYR 0.007 0.001 TYR A 161 ARG 0.003 0.000 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8143 (mm110) REVERT: A 211 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.9007 (pp) REVERT: A 221 ASN cc_start: 0.8011 (t0) cc_final: 0.7724 (t0) REVERT: A 412 ILE cc_start: 0.9158 (pt) cc_final: 0.8873 (mt) REVERT: B 38 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7952 (mm110) REVERT: B 42 LEU cc_start: 0.9108 (mt) cc_final: 0.8847 (mp) REVERT: B 181 THR cc_start: 0.9063 (m) cc_final: 0.8773 (p) REVERT: C 181 THR cc_start: 0.9018 (m) cc_final: 0.8748 (p) outliers start: 43 outliers final: 32 residues processed: 180 average time/residue: 0.3532 time to fit residues: 101.5496 Evaluate side-chains 152 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN A 431 GLN B 99 HIS ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN C 99 HIS C 389 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 10362 Z= 0.278 Angle : 0.657 14.072 14073 Z= 0.345 Chirality : 0.045 0.206 1659 Planarity : 0.004 0.051 1821 Dihedral : 7.226 49.622 1472 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 3.98 % Allowed : 18.36 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -4.44 (0.19), residues: 1311 helix: -3.60 (0.40), residues: 81 sheet: -2.04 (0.21), residues: 492 loop : -3.65 (0.17), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 196 HIS 0.007 0.001 HIS C 100 PHE 0.019 0.001 PHE C 72 TYR 0.012 0.001 TYR A 148 ARG 0.003 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9011 (pp) REVERT: A 221 ASN cc_start: 0.8025 (t0) cc_final: 0.7713 (t0) REVERT: A 412 ILE cc_start: 0.9164 (pt) cc_final: 0.8873 (mt) REVERT: B 42 LEU cc_start: 0.9103 (mt) cc_final: 0.8859 (mp) REVERT: B 181 THR cc_start: 0.9100 (m) cc_final: 0.8827 (p) REVERT: B 267 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8565 (p) REVERT: C 181 THR cc_start: 0.9038 (m) cc_final: 0.8798 (p) outliers start: 47 outliers final: 38 residues processed: 173 average time/residue: 0.3196 time to fit residues: 91.7855 Evaluate side-chains 163 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10362 Z= 0.259 Angle : 0.639 13.690 14073 Z= 0.336 Chirality : 0.045 0.197 1659 Planarity : 0.004 0.049 1821 Dihedral : 7.140 49.509 1472 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.66 % Favored : 87.34 % Rotamer: Outliers : 3.98 % Allowed : 18.61 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -4.24 (0.19), residues: 1311 helix: -3.59 (0.41), residues: 81 sheet: -1.81 (0.21), residues: 489 loop : -3.58 (0.17), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 196 HIS 0.008 0.001 HIS B 99 PHE 0.019 0.001 PHE C 144 TYR 0.008 0.001 TYR C 161 ARG 0.004 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9001 (pp) REVERT: A 221 ASN cc_start: 0.8045 (t0) cc_final: 0.7738 (t0) REVERT: A 412 ILE cc_start: 0.9144 (pt) cc_final: 0.8872 (mt) REVERT: B 38 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7954 (mm110) REVERT: B 181 THR cc_start: 0.9119 (m) cc_final: 0.8858 (p) REVERT: C 181 THR cc_start: 0.9067 (m) cc_final: 0.8841 (p) outliers start: 47 outliers final: 40 residues processed: 169 average time/residue: 0.3075 time to fit residues: 85.2667 Evaluate side-chains 163 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN C 99 HIS ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10362 Z= 0.261 Angle : 0.634 13.407 14073 Z= 0.333 Chirality : 0.044 0.190 1659 Planarity : 0.004 0.049 1821 Dihedral : 7.057 49.687 1472 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.51 % Favored : 87.49 % Rotamer: Outliers : 4.57 % Allowed : 18.44 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.89 (0.20), residues: 1311 helix: -3.11 (0.50), residues: 63 sheet: -1.59 (0.21), residues: 516 loop : -3.41 (0.18), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 196 HIS 0.008 0.001 HIS A 99 PHE 0.015 0.001 PHE C 72 TYR 0.013 0.001 TYR A 148 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 124 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9016 (pp) REVERT: A 221 ASN cc_start: 0.8052 (t0) cc_final: 0.7744 (t0) REVERT: A 412 ILE cc_start: 0.9115 (pt) cc_final: 0.8875 (mt) REVERT: B 38 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7981 (mm110) REVERT: B 181 THR cc_start: 0.9141 (m) cc_final: 0.8913 (p) REVERT: B 412 ILE cc_start: 0.9118 (pt) cc_final: 0.8789 (mt) REVERT: C 181 THR cc_start: 0.9122 (m) cc_final: 0.8901 (p) outliers start: 54 outliers final: 45 residues processed: 167 average time/residue: 0.3234 time to fit residues: 90.2994 Evaluate side-chains 163 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 116 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10362 Z= 0.221 Angle : 0.626 13.285 14073 Z= 0.328 Chirality : 0.044 0.185 1659 Planarity : 0.004 0.048 1821 Dihedral : 6.957 50.151 1472 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 4.06 % Allowed : 19.29 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.69 (0.20), residues: 1311 helix: -3.01 (0.51), residues: 63 sheet: -1.39 (0.22), residues: 501 loop : -3.30 (0.18), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 196 HIS 0.005 0.001 HIS A 99 PHE 0.014 0.001 PHE C 72 TYR 0.006 0.001 TYR C 433 ARG 0.003 0.000 ARG C 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 123 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8920 (pp) REVERT: A 221 ASN cc_start: 0.7996 (t0) cc_final: 0.7706 (t0) REVERT: A 412 ILE cc_start: 0.9088 (pt) cc_final: 0.8866 (mt) REVERT: B 181 THR cc_start: 0.9147 (m) cc_final: 0.8903 (p) outliers start: 48 outliers final: 38 residues processed: 161 average time/residue: 0.3012 time to fit residues: 80.0568 Evaluate side-chains 151 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 112 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 10362 Z= 0.218 Angle : 0.702 32.747 14073 Z= 0.360 Chirality : 0.047 0.451 1659 Planarity : 0.004 0.048 1821 Dihedral : 6.890 54.753 1472 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.72 % Allowed : 19.80 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.50 (0.20), residues: 1311 helix: -2.88 (0.51), residues: 63 sheet: -1.23 (0.22), residues: 501 loop : -3.20 (0.19), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 196 HIS 0.006 0.001 HIS A 99 PHE 0.014 0.001 PHE B 144 TYR 0.015 0.001 TYR A 148 ARG 0.002 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 122 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: -0.1474 (OUTLIER) cc_final: -0.1690 (m) REVERT: A 211 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8949 (pp) REVERT: A 221 ASN cc_start: 0.7994 (t0) cc_final: 0.7691 (t0) REVERT: A 244 LEU cc_start: 0.8694 (mt) cc_final: 0.8473 (mt) REVERT: B 181 THR cc_start: 0.9150 (m) cc_final: 0.8928 (p) REVERT: B 412 ILE cc_start: 0.9108 (pt) cc_final: 0.8796 (mt) outliers start: 44 outliers final: 40 residues processed: 154 average time/residue: 0.2969 time to fit residues: 77.3930 Evaluate side-chains 159 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10362 Z= 0.239 Angle : 0.692 29.858 14073 Z= 0.358 Chirality : 0.046 0.397 1659 Planarity : 0.004 0.048 1821 Dihedral : 6.896 52.963 1472 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 3.72 % Allowed : 20.39 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.46 (0.21), residues: 1311 helix: -2.74 (0.52), residues: 63 sheet: -1.30 (0.22), residues: 543 loop : -3.18 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 196 HIS 0.005 0.001 HIS A 99 PHE 0.019 0.001 PHE A 25 TYR 0.008 0.001 TYR C 161 ARG 0.003 0.000 ARG A 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 125 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 THR cc_start: -0.1600 (OUTLIER) cc_final: -0.1810 (m) REVERT: A 211 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.9005 (pp) REVERT: A 221 ASN cc_start: 0.7996 (t0) cc_final: 0.7708 (t0) REVERT: A 293 GLN cc_start: 0.8327 (tp40) cc_final: 0.8096 (tp40) REVERT: A 412 ILE cc_start: 0.8843 (mt) cc_final: 0.8518 (tt) REVERT: B 181 THR cc_start: 0.9156 (m) cc_final: 0.8940 (p) outliers start: 44 outliers final: 39 residues processed: 158 average time/residue: 0.3117 time to fit residues: 81.8188 Evaluate side-chains 161 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 120 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108899 restraints weight = 38731.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111640 restraints weight = 22320.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113359 restraints weight = 13382.271| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10362 Z= 0.236 Angle : 0.678 27.605 14073 Z= 0.353 Chirality : 0.045 0.347 1659 Planarity : 0.004 0.048 1821 Dihedral : 6.868 52.887 1472 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 3.72 % Allowed : 20.39 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.51 (0.21), residues: 1311 helix: -2.99 (0.45), residues: 81 sheet: -1.20 (0.23), residues: 513 loop : -3.23 (0.19), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 196 HIS 0.003 0.001 HIS C 77 PHE 0.015 0.001 PHE A 72 TYR 0.014 0.001 TYR A 148 ARG 0.003 0.000 ARG A 381 =============================================================================== Job complete usr+sys time: 4086.69 seconds wall clock time: 73 minutes 33.17 seconds (4413.17 seconds total)