Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:28:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/12_2022/7a4a_11630.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/12_2022/7a4a_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_11630/12_2022/7a4a_11630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/12_2022/7a4a_11630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/12_2022/7a4a_11630.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4a_11630/12_2022/7a4a_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 Convert atoms to be neutral 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-4807/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: 9.28, per 1000 atoms: 0.47 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: 12.58 Conformation dependent library (CDL) restraints added in 1.8 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: 0.67 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: 6.32 Time building geometry restraints manager: 13.39 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: 7388 14.74 - 29.48: 633 29.48 - 44.22: 136 44.22 - 58.96: 69 58.96 - 73.70: 15 Dihedral angle restraints: 8241 sinusoidal: 3828 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 8238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 895 0.030 - 0.059: 503 0.059 - 0.089: 187 0.089 - 0.119: 53 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 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. 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: 0.880 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: 4.270 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.170 Process input model: 56.910 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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= 0.494 Angle : 0.705 6.857 14073 Z= 0.400 Chirality : 0.043 0.149 1659 Planarity : 0.006 0.073 1821 Dihedral : 11.639 73.698 3765 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.43 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 : 1.578 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: 0.3941 time to fit residues: 168.7248 Evaluate side-chains 143 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1686 time to fit residues: 5.2641 ------------------------------------------------------------------------------- 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 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 10362 Z= 0.321 Angle : 0.710 7.708 14073 Z= 0.381 Chirality : 0.045 0.153 1659 Planarity : 0.005 0.062 1821 Dihedral : 7.137 27.734 1407 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.87 % Favored : 84.13 % Rotamer Outliers : 4.06 % 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: -5.38 (0.17), residues: 1311 helix: -4.20 (0.27), residues: 81 sheet: -2.79 (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 200 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 152 time to evaluate : 1.673 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: 48 outliers final: 27 residues processed: 190 average time/residue: 0.2944 time to fit residues: 91.4834 Evaluate side-chains 156 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.662 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: 0.2233 time to fit residues: 13.3974 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.6980 chunk 40 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 389 ASN C 235 GLN C 389 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.110 10362 Z= 0.317 Angle : 0.684 15.799 14073 Z= 0.362 Chirality : 0.045 0.239 1659 Planarity : 0.004 0.054 1821 Dihedral : 6.649 33.364 1407 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.80 % Favored : 85.20 % Rotamer Outliers : 1.35 % 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: -4.76 (0.18), residues: 1311 helix: -3.59 (0.40), residues: 63 sheet: -2.36 (0.20), residues: 519 loop : -3.86 (0.17), residues: 729 *********************** 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 155 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.649 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: 16 outliers final: 12 residues processed: 155 average time/residue: 0.3151 time to fit residues: 80.8113 Evaluate side-chains 127 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2120 time to fit residues: 6.8154 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 78 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN 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: 0.7899 moved from start: 0.3536 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= 0.330 Angle : 0.697 16.583 14073 Z= 0.367 Chirality : 0.046 0.217 1659 Planarity : 0.004 0.053 1821 Dihedral : 6.516 31.633 1407 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer Outliers : 2.12 % 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: -4.69 (0.18), residues: 1311 helix: -3.82 (0.36), residues: 81 sheet: -2.25 (0.20), residues: 519 loop : -3.82 (0.17), residues: 711 *********************** 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 154 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.570 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 outliers start: 25 outliers final: 14 residues processed: 149 average time/residue: 0.3094 time to fit residues: 76.6879 Evaluate side-chains 125 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.636 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2375 time to fit residues: 8.1044 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7862 moved from start: 0.3919 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= 0.251 Angle : 0.652 14.738 14073 Z= 0.342 Chirality : 0.045 0.205 1659 Planarity : 0.004 0.049 1821 Dihedral : 6.113 28.185 1407 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer Outliers : 1.52 % 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: -4.34 (0.19), residues: 1311 helix: -3.59 (0.39), residues: 81 sheet: -2.01 (0.21), residues: 492 loop : -3.56 (0.18), residues: 738 *********************** 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 156 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.559 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: 18 outliers final: 10 residues processed: 150 average time/residue: 0.3599 time to fit residues: 84.2279 Evaluate side-chains 130 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2249 time to fit residues: 6.0634 ------------------------------------------------------------------------------- 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: 0.8980 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4179 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= 0.264 Angle : 0.652 13.914 14073 Z= 0.342 Chirality : 0.045 0.196 1659 Planarity : 0.003 0.046 1821 Dihedral : 6.021 26.462 1407 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.46 (0.40), residues: 81 sheet: -1.83 (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 144 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.572 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 outliers start: 17 outliers final: 11 residues processed: 141 average time/residue: 0.3116 time to fit residues: 72.0684 Evaluate side-chains 132 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.616 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2205 time to fit residues: 6.7123 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 10362 Z= 0.220 Angle : 0.632 13.848 14073 Z= 0.330 Chirality : 0.044 0.188 1659 Planarity : 0.003 0.045 1821 Dihedral : 5.817 24.233 1407 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % 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: -3.91 (0.20), residues: 1311 helix: -3.33 (0.42), residues: 81 sheet: -1.57 (0.21), residues: 519 loop : -3.42 (0.18), residues: 711 *********************** 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 : 1.444 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: 12 outliers final: 6 residues processed: 136 average time/residue: 0.3110 time to fit residues: 69.4186 Evaluate side-chains 122 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.642 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2194 time to fit residues: 4.4903 ------------------------------------------------------------------------------- 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: 0.6980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 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** 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: 0.7886 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 10362 Z= 0.281 Angle : 0.653 13.508 14073 Z= 0.344 Chirality : 0.045 0.182 1659 Planarity : 0.003 0.046 1821 Dihedral : 5.883 23.680 1407 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % 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: -3.80 (0.20), residues: 1311 helix: -3.46 (0.39), residues: 81 sheet: -1.43 (0.22), residues: 504 loop : -3.36 (0.18), residues: 726 *********************** 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 132 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.610 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: 14 outliers final: 9 residues processed: 127 average time/residue: 0.3037 time to fit residues: 63.9718 Evaluate side-chains 124 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.696 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2479 time to fit residues: 6.2159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0068 > 50: distance: 142 - 159: 9.805 distance: 159 - 160: 23.570 distance: 159 - 165: 16.973 distance: 160 - 161: 18.918 distance: 160 - 163: 11.687 distance: 160 - 166: 15.143 distance: 161 - 162: 23.137 distance: 161 - 173: 24.734 distance: 163 - 164: 16.129 distance: 164 - 165: 30.788 distance: 164 - 169: 24.072 distance: 164 - 170: 3.543 distance: 165 - 171: 20.763 distance: 165 - 172: 27.993 distance: 173 - 174: 12.481 distance: 173 - 181: 24.801 distance: 174 - 175: 17.314 distance: 174 - 177: 28.627 distance: 174 - 182: 13.355 distance: 175 - 176: 23.863 distance: 175 - 192: 30.945 distance: 177 - 178: 18.920 distance: 177 - 183: 17.740 distance: 177 - 184: 14.053 distance: 178 - 179: 26.650 distance: 178 - 180: 11.863 distance: 178 - 185: 21.687 distance: 179 - 186: 8.903 distance: 179 - 188: 5.850 distance: 180 - 189: 16.645 distance: 180 - 190: 8.263 distance: 180 - 191: 11.782 distance: 192 - 193: 13.256 distance: 192 - 198: 24.363 distance: 193 - 194: 16.873 distance: 193 - 196: 23.016 distance: 193 - 199: 20.069 distance: 194 - 195: 3.728 distance: 194 - 206: 40.463 distance: 196 - 197: 16.569 distance: 196 - 200: 22.575 distance: 196 - 201: 15.685 distance: 197 - 198: 15.436 distance: 197 - 202: 21.198 distance: 197 - 203: 12.004 distance: 198 - 204: 15.316 distance: 198 - 205: 9.984 distance: 206 - 207: 36.031 distance: 206 - 215: 17.027 distance: 206 - 326: 23.494 distance: 207 - 208: 8.250 distance: 207 - 210: 22.046 distance: 207 - 216: 18.311 distance: 208 - 209: 12.676 distance: 208 - 223: 9.294 distance: 210 - 211: 7.122 distance: 210 - 217: 26.533 distance: 210 - 218: 34.393 distance: 211 - 212: 12.687 distance: 211 - 219: 19.739 distance: 211 - 220: 6.878 distance: 212 - 213: 8.846 distance: 212 - 214: 10.522 distance: 214 - 221: 4.751 distance: 214 - 222: 7.423 distance: 223 - 224: 7.554 distance: 223 - 230: 10.664 distance: 224 - 225: 18.578 distance: 224 - 227: 29.455 distance: 224 - 231: 20.699 distance: 225 - 226: 10.618 distance: 225 - 237: 14.141 distance: 227 - 228: 17.085 distance: 227 - 229: 14.072 distance: 227 - 232: 13.524 distance: 228 - 233: 9.888 distance: 229 - 234: 13.453 distance: 229 - 235: 4.092 distance: 229 - 236: 10.575 distance: 237 - 238: 19.299 distance: 237 - 243: 7.138 distance: 238 - 239: 9.232 distance: 238 - 241: 11.415 distance: 238 - 244: 18.802 distance: 239 - 240: 38.281 distance: 239 - 248: 15.476 distance: 241 - 242: 13.358 distance: 241 - 245: 19.397 distance: 241 - 246: 7.909 distance: 242 - 247: 31.582 distance: 248 - 249: 18.996 distance: 248 - 257: 17.128 distance: 249 - 250: 10.285 distance: 249 - 252: 11.556 distance: 249 - 258: 4.123 distance: 250 - 251: 12.318 distance: 250 - 270: 13.967 distance: 252 - 253: 6.573 distance: 252 - 259: 11.655 distance: 252 - 260: 10.647 distance: 253 - 254: 17.760 distance: 253 - 261: 15.116 distance: 253 - 262: 6.015 distance: 254 - 255: 11.906 distance: 254 - 263: 8.874 distance: 254 - 264: 10.210 distance: 255 - 256: 11.698 distance: 255 - 265: 9.077 distance: 255 - 266: 8.834 distance: 256 - 267: 6.520 distance: 256 - 268: 5.705 distance: 256 - 269: 11.699 distance: 270 - 271: 18.546 distance: 270 - 278: 12.723 distance: 271 - 272: 12.051 distance: 271 - 274: 17.691 distance: 271 - 279: 10.271 distance: 272 - 273: 5.950 distance: 272 - 284: 11.572 distance: 274 - 275: 21.130 distance: 274 - 280: 22.870 distance: 274 - 281: 12.099 distance: 275 - 276: 8.501 distance: 275 - 277: 36.377 distance: 277 - 282: 9.874 distance: 284 - 285: 13.139 distance: 284 - 295: 13.875 distance: 285 - 286: 23.018 distance: 285 - 288: 3.652 distance: 285 - 296: 12.436 distance: 286 - 287: 19.297 distance: 286 - 304: 19.383 distance: 288 - 289: 5.160 distance: 288 - 297: 10.919 distance: 288 - 298: 13.100 distance: 289 - 290: 11.187 distance: 289 - 291: 21.395 distance: 290 - 292: 11.344 distance: 290 - 299: 12.914 distance: 291 - 293: 11.242 distance: 291 - 300: 12.842 distance: 292 - 294: 23.325 distance: 292 - 301: 11.205 distance: 293 - 294: 13.124 distance: 293 - 302: 13.143 distance: 304 - 305: 19.104 distance: 304 - 312: 5.206 distance: 304 - 385: 21.453 distance: 305 - 306: 16.749 distance: 305 - 308: 8.053 distance: 305 - 313: 12.875 distance: 306 - 307: 5.043 distance: 306 - 323: 12.614 distance: 307 - 382: 8.381 distance: 308 - 309: 9.915 distance: 308 - 314: 16.612 distance: 308 - 315: 7.326 distance: 309 - 310: 21.350 distance: 309 - 311: 4.962 distance: 309 - 316: 16.609 distance: 310 - 317: 9.317 distance: 310 - 318: 6.062 distance: 310 - 319: 5.377 distance: 311 - 320: 8.535 distance: 311 - 321: 6.129 distance: 311 - 322: 6.942