Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 08:35:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/04_2023/7a4a_11630.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/04_2023/7a4a_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_11630/04_2023/7a4a_11630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/04_2023/7a4a_11630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/04_2023/7a4a_11630.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/04_2023/7a4a_11630.pdb" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-1.21rc1-4938/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 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 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 chiralities: 1 Time building chain proxies: 8.45, per 1000 atoms: 0.43 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: 15.93 Conformation dependent library (CDL) restraints added in 1.9 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: 0.92 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: 8.29 Time building geometry restraints manager: 16.45 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: 7370 14.74 - 29.48: 633 29.48 - 44.22: 136 44.22 - 58.96: 69 58.96 - 73.70: 15 Dihedral angle restraints: 8223 sinusoidal: 3810 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 8220 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: 0.660 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: 0.310 Extract box with map and model: 4.280 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 61.770 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.100 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.380 ------------------------------------------------------------------------------- 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 : 11.654 73.698 3747 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 % 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 *********************** 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 : 1.780 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 outliers start: 35 outliers final: 11 residues processed: 295 average time/residue: 0.4456 time to fit residues: 188.8168 Evaluate side-chains 143 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2225 time to fit residues: 6.5745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.7844 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 10362 Z= 0.347 Angle : 0.710 7.822 14073 Z= 0.382 Chirality : 0.045 0.152 1659 Planarity : 0.005 0.062 1821 Dihedral : 7.107 28.424 1389 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.64 % Favored : 84.36 % Rotamer Outliers : 3.89 % 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: -5.37 (0.17), residues: 1311 helix: -4.21 (0.27), residues: 81 sheet: -2.78 (0.19), residues: 504 loop : -4.22 (0.16), residues: 726 *********************** 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 199 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 1.726 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 outliers start: 46 outliers final: 27 residues processed: 190 average time/residue: 0.3125 time to fit residues: 97.3354 Evaluate side-chains 155 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.719 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 3 residues processed: 27 average time/residue: 0.2184 time to fit residues: 13.1757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 B 99 HIS B 389 ASN C 235 GLN C 389 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.111 10362 Z= 0.347 Angle : 0.693 15.937 14073 Z= 0.367 Chirality : 0.045 0.242 1659 Planarity : 0.005 0.057 1821 Dihedral : 6.720 33.543 1389 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.26 % Favored : 84.74 % Rotamer Outliers : 1.44 % 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: -4.96 (0.18), residues: 1311 helix: -3.99 (0.32), residues: 81 sheet: -2.41 (0.20), residues: 519 loop : -4.03 (0.17), residues: 711 *********************** 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 157 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 1.622 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 outliers start: 17 outliers final: 13 residues processed: 157 average time/residue: 0.3249 time to fit residues: 83.3894 Evaluate side-chains 128 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2226 time to fit residues: 7.3925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 33 optimal weight: 0.0670 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 221 ASN ** 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 389 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 10362 Z= 0.287 Angle : 0.681 15.650 14073 Z= 0.357 Chirality : 0.045 0.219 1659 Planarity : 0.004 0.051 1821 Dihedral : 6.404 30.680 1389 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer Outliers : 1.78 % 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: -4.66 (0.18), residues: 1311 helix: -3.78 (0.36), residues: 81 sheet: -2.32 (0.20), residues: 495 loop : -3.70 (0.17), residues: 735 *********************** 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 161 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.561 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 outliers start: 21 outliers final: 12 residues processed: 158 average time/residue: 0.3492 time to fit residues: 87.5441 Evaluate side-chains 126 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.709 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2246 time to fit residues: 7.0607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 A 431 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 10362 Z= 0.258 Angle : 0.655 14.072 14073 Z= 0.344 Chirality : 0.045 0.206 1659 Planarity : 0.004 0.047 1821 Dihedral : 6.150 28.280 1389 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer Outliers : 1.18 % 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: -4.36 (0.19), residues: 1311 helix: -3.54 (0.40), residues: 81 sheet: -2.06 (0.21), residues: 495 loop : -3.55 (0.18), residues: 735 *********************** 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 148 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.637 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 outliers start: 14 outliers final: 7 residues processed: 146 average time/residue: 0.3436 time to fit residues: 80.0232 Evaluate side-chains 131 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2280 time to fit residues: 4.9868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN ** 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: 0.7863 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 10362 Z= 0.279 Angle : 0.658 13.576 14073 Z= 0.346 Chirality : 0.045 0.195 1659 Planarity : 0.004 0.046 1821 Dihedral : 6.043 25.916 1389 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer Outliers : 1.78 % 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: -4.17 (0.19), residues: 1311 helix: -3.48 (0.40), residues: 81 sheet: -1.82 (0.21), residues: 489 loop : -3.49 (0.18), residues: 741 *********************** 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 147 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.508 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 outliers start: 21 outliers final: 14 residues processed: 140 average time/residue: 0.3142 time to fit residues: 72.3382 Evaluate side-chains 131 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.524 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.2406 time to fit residues: 8.2537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4384 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= 0.254 Angle : 0.643 13.257 14073 Z= 0.338 Chirality : 0.045 0.186 1659 Planarity : 0.003 0.048 1821 Dihedral : 5.914 23.993 1389 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer Outliers : 1.02 % 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: -3.92 (0.20), residues: 1311 helix: -3.37 (0.41), residues: 81 sheet: -1.54 (0.22), residues: 504 loop : -3.44 (0.18), residues: 726 *********************** 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 138 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 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 outliers start: 12 outliers final: 9 residues processed: 133 average time/residue: 0.3344 time to fit residues: 71.7684 Evaluate side-chains 127 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.460 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2370 time to fit residues: 5.6061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** ** 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: 0.7831 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 10362 Z= 0.216 Angle : 0.633 13.394 14073 Z= 0.331 Chirality : 0.045 0.180 1659 Planarity : 0.003 0.045 1821 Dihedral : 5.729 22.287 1389 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer Outliers : 0.85 % 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: -3.65 (0.20), residues: 1311 helix: -3.14 (0.42), residues: 81 sheet: -1.37 (0.22), residues: 495 loop : -3.22 (0.19), residues: 735 *********************** 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 131 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.696 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 outliers start: 10 outliers final: 8 residues processed: 127 average time/residue: 0.3268 time to fit residues: 68.7086 Evaluate side-chains 116 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.761 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2400 time to fit residues: 5.5584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 0.0980 chunk 122 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 10362 Z= 0.206 Angle : 0.622 12.853 14073 Z= 0.323 Chirality : 0.044 0.174 1659 Planarity : 0.003 0.044 1821 Dihedral : 5.518 20.936 1389 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer Outliers : 0.68 % 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: -3.45 (0.20), residues: 1311 helix: -2.83 (0.44), residues: 81 sheet: -1.13 (0.22), residues: 504 loop : -3.22 (0.19), residues: 726 *********************** 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 128 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 1.501 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 outliers start: 8 outliers final: 6 residues processed: 127 average time/residue: 0.3236 time to fit residues: 67.2657 Evaluate side-chains 117 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.627 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2354 time to fit residues: 4.6482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 85 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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** ** 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: 0.7856 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.120 10362 Z= 0.297 Angle : 0.704 27.786 14073 Z= 0.364 Chirality : 0.046 0.463 1659 Planarity : 0.003 0.043 1821 Dihedral : 5.767 24.299 1389 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer Outliers : 0.68 % 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: -3.49 (0.21), residues: 1311 helix: -3.20 (0.37), residues: 99 sheet: -1.15 (0.23), residues: 504 loop : -3.18 (0.19), residues: 708 ********************** 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 124 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.655 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 outliers start: 8 outliers final: 8 residues processed: 120 average time/residue: 0.3195 time to fit residues: 64.4609 Evaluate side-chains 122 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.672 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 8 average time/residue: 0.2512 time to fit residues: 5.5956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 15 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.154131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.110367 restraints weight = 38573.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114465 restraints weight = 18746.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115812 restraints weight = 10919.667| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 10362 Z= 0.210 Angle : 0.661 21.445 14073 Z= 0.344 Chirality : 0.045 0.416 1659 Planarity : 0.003 0.044 1821 Dihedral : 5.587 22.931 1389 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer Outliers : 0.42 % 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: -3.32 (0.21), residues: 1311 helix: -2.90 (0.41), residues: 99 sheet: -1.06 (0.23), residues: 510 loop : -3.09 (0.19), residues: 702 =============================================================================== Job complete usr+sys time: 3764.61 seconds wall clock time: 68 minutes 3.98 seconds (4083.98 seconds total)