Starting phenix.real_space_refine on Fri Nov 17 15:50:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/11_2023/7rye_24735.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/11_2023/7rye_24735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/11_2023/7rye_24735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/11_2023/7rye_24735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/11_2023/7rye_24735.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/11_2023/7rye_24735.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 12445 2.51 5 N 3227 2.21 5 O 4006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "B ASP 11": "OD1" <-> "OD2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "C ASP 10": "OD1" <-> "OD2" Residue "C PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "E ASP 10": "OD1" <-> "OD2" Residue "E ASP 11": "OD1" <-> "OD2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 17": "OD1" <-> "OD2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I ASP 32": "OD1" <-> "OD2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 17": "OD1" <-> "OD2" Residue "J PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 17": "OD1" <-> "OD2" Residue "K ASP 21": "OD1" <-> "OD2" Residue "K GLU 29": "OE1" <-> "OE2" Residue "K TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "L ASP 21": "OD1" <-> "OD2" Residue "L PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 21": "OD1" <-> "OD2" Residue "M TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 32": "OD1" <-> "OD2" Residue "N TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 70": "OD1" <-> "OD2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "O TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 162": "OD1" <-> "OD2" Residue "O TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 277": "OD1" <-> "OD2" Residue "O TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 11": "OD1" <-> "OD2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "Q TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 133": "OE1" <-> "OE2" Residue "R TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 154": "OE1" <-> "OE2" Residue "R ASP 162": "OD1" <-> "OD2" Residue "R PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 283": "OD1" <-> "OD2" Residue "S ASP 17": "OD1" <-> "OD2" Residue "S ASP 21": "OD1" <-> "OD2" Residue "S ASP 32": "OD1" <-> "OD2" Residue "T ASP 10": "OD1" <-> "OD2" Residue "T ASP 21": "OD1" <-> "OD2" Residue "T ASP 72": "OD1" <-> "OD2" Residue "U TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 53": "OE1" <-> "OE2" Residue "V TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 162": "OD1" <-> "OD2" Residue "V ASP 190": "OD1" <-> "OD2" Residue "V TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 267": "OD1" <-> "OD2" Residue "V ASP 269": "OD1" <-> "OD2" Residue "V TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 320": "OD1" <-> "OD2" Residue "W TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 11": "OD1" <-> "OD2" Residue "W ASP 32": "OD1" <-> "OD2" Residue "W ASP 40": "OD1" <-> "OD2" Residue "X GLU 154": "OE1" <-> "OE2" Residue "X ASP 183": "OD1" <-> "OD2" Residue "X PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 230": "OE1" <-> "OE2" Residue "X TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 19708 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "C" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "D" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "E" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "H" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "I" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "J" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "K" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "L" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "M" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "N" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "O" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Q" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "R" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "U" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "V" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.60, per 1000 atoms: 0.49 Number of scatterers: 19708 At special positions: 0 Unit cell: (99.47, 96.04, 214.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 4006 8.00 N 3227 7.00 C 12445 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.32 Conformation dependent library (CDL) restraints added in 3.5 seconds 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4854 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 10 sheets defined 79.4% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 40 through 77 removed outlier: 3.887A pdb=" N ALA A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 20 Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 40 through 78 Processing helix chain 'C' and resid 7 through 20 Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 40 through 78 removed outlier: 3.733A pdb=" N ASN C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 Processing helix chain 'D' and resid 17 through 21 removed outlier: 3.644A pdb=" N ASP D 21 " --> pdb=" O THR D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 37 Processing helix chain 'D' and resid 40 through 77 Processing helix chain 'E' and resid 8 through 16 Processing helix chain 'E' and resid 17 through 35 removed outlier: 3.918A pdb=" N ASN E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR E 25 " --> pdb=" O ASP E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 78 removed outlier: 4.047A pdb=" N LEU E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 68 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS E 69 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP E 72 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE E 75 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 147 removed outlier: 3.662A pdb=" N SER F 143 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP F 147 " --> pdb=" O SER F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 175 Processing helix chain 'F' and resid 190 through 206 removed outlier: 3.894A pdb=" N LEU F 194 " --> pdb=" O ASP F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 removed outlier: 3.677A pdb=" N ALA F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU F 237 " --> pdb=" O GLN F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 268 Processing helix chain 'F' and resid 283 through 311 Processing helix chain 'F' and resid 311 through 323 removed outlier: 4.591A pdb=" N SER F 317 " --> pdb=" O SER F 313 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 332 through 340 removed outlier: 3.607A pdb=" N GLU F 335 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR F 336 " --> pdb=" O SER F 333 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 337 " --> pdb=" O LEU F 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 37 removed outlier: 3.976A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 78 removed outlier: 4.166A pdb=" N LEU G 44 " --> pdb=" O ASP G 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE G 75 " --> pdb=" O ILE G 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 37 removed outlier: 3.611A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR H 18 " --> pdb=" O ALA H 14 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS H 33 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 78 removed outlier: 3.867A pdb=" N ALA H 45 " --> pdb=" O PRO H 41 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE H 71 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP H 72 " --> pdb=" O PHE H 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 37 removed outlier: 4.192A pdb=" N GLY I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU I 23 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU I 29 " --> pdb=" O THR I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 78 removed outlier: 4.347A pdb=" N LEU I 44 " --> pdb=" O ASP I 40 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE I 75 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 43 through 79 Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.514A pdb=" N VAL K 20 " --> pdb=" O PHE K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 Processing helix chain 'K' and resid 40 through 77 Processing helix chain 'L' and resid 7 through 20 Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 40 through 77 Processing helix chain 'M' and resid 7 through 20 Processing helix chain 'M' and resid 22 through 37 Processing helix chain 'M' and resid 40 through 78 Processing helix chain 'N' and resid 7 through 20 Processing helix chain 'N' and resid 22 through 37 Processing helix chain 'N' and resid 40 through 78 removed outlier: 3.709A pdb=" N ASN N 78 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 149 removed outlier: 3.925A pdb=" N TRP O 135 " --> pdb=" O ASP O 131 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP O 136 " --> pdb=" O ALA O 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 174 removed outlier: 3.541A pdb=" N TYR O 153 " --> pdb=" O TYR O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 207 removed outlier: 3.852A pdb=" N GLN O 207 " --> pdb=" O ASN O 203 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 239 removed outlier: 3.766A pdb=" N GLU O 237 " --> pdb=" O GLN O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 269 removed outlier: 3.817A pdb=" N ASP O 269 " --> pdb=" O VAL O 265 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 272 No H-bonds generated for 'chain 'O' and resid 270 through 272' Processing helix chain 'O' and resid 283 through 311 Processing helix chain 'O' and resid 311 through 323 removed outlier: 4.351A pdb=" N SER O 317 " --> pdb=" O SER O 313 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU O 318 " --> pdb=" O ASN O 314 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN O 321 " --> pdb=" O SER O 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 331 Processing helix chain 'O' and resid 333 through 340 removed outlier: 3.881A pdb=" N THR O 336 " --> pdb=" O SER O 333 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA O 337 " --> pdb=" O LEU O 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'P' and resid 22 through 37 Processing helix chain 'P' and resid 40 through 78 removed outlier: 3.711A pdb=" N ASN P 78 " --> pdb=" O ALA P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.637A pdb=" N VAL Q 20 " --> pdb=" O PHE Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 4.128A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 79 Processing helix chain 'R' and resid 131 through 145 removed outlier: 4.193A pdb=" N SER R 143 " --> pdb=" O SER R 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE R 145 " --> pdb=" O ASN R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 175 removed outlier: 3.588A pdb=" N TYR R 153 " --> pdb=" O TYR R 149 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 205 removed outlier: 3.575A pdb=" N LEU R 194 " --> pdb=" O ASP R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 239 removed outlier: 3.529A pdb=" N ALA R 231 " --> pdb=" O THR R 227 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU R 237 " --> pdb=" O GLN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 268 Processing helix chain 'R' and resid 269 through 272 removed outlier: 3.722A pdb=" N GLY R 272 " --> pdb=" O ASP R 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 269 through 272' Processing helix chain 'R' and resid 283 through 323 removed outlier: 4.117A pdb=" N ALA R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER R 313 " --> pdb=" O THR R 309 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER R 317 " --> pdb=" O SER R 313 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU R 318 " --> pdb=" O ASN R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 334 removed outlier: 4.193A pdb=" N SER R 332 " --> pdb=" O SER R 328 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 340 Processing helix chain 'S' and resid 7 through 20 removed outlier: 3.638A pdb=" N PHE S 16 " --> pdb=" O VAL S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 37 removed outlier: 3.963A pdb=" N THR S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 80 removed outlier: 3.745A pdb=" N ARG S 80 " --> pdb=" O ILE S 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 37 removed outlier: 3.593A pdb=" N PHE T 16 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR T 18 " --> pdb=" O ALA T 14 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN T 22 " --> pdb=" O THR T 18 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU T 29 " --> pdb=" O THR T 25 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS T 33 " --> pdb=" O GLU T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 78 removed outlier: 4.033A pdb=" N LEU T 44 " --> pdb=" O ASP T 40 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS T 66 " --> pdb=" O SER T 62 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE T 68 " --> pdb=" O THR T 64 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 20 Processing helix chain 'U' and resid 22 through 37 removed outlier: 4.283A pdb=" N THR U 28 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS U 37 " --> pdb=" O LYS U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 80 Processing helix chain 'V' and resid 132 through 147 removed outlier: 3.527A pdb=" N ASP V 136 " --> pdb=" O ALA V 132 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 175 removed outlier: 3.521A pdb=" N TYR V 153 " --> pdb=" O TYR V 149 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY V 175 " --> pdb=" O LEU V 171 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 206 Processing helix chain 'V' and resid 227 through 239 Processing helix chain 'V' and resid 258 through 268 Processing helix chain 'V' and resid 269 through 272 Processing helix chain 'V' and resid 283 through 323 removed outlier: 4.133A pdb=" N TYR V 312 " --> pdb=" O LEU V 308 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER V 313 " --> pdb=" O THR V 309 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN V 314 " --> pdb=" O GLN V 310 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER V 317 " --> pdb=" O SER V 313 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU V 318 " --> pdb=" O ASN V 314 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 331 Processing helix chain 'V' and resid 335 through 340 Processing helix chain 'W' and resid 7 through 37 removed outlier: 4.215A pdb=" N GLY W 19 " --> pdb=" O LYS W 15 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN W 22 " --> pdb=" O THR W 18 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 78 removed outlier: 3.775A pdb=" N LEU W 44 " --> pdb=" O ASP W 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE W 71 " --> pdb=" O VAL W 67 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP W 72 " --> pdb=" O PHE W 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 147 removed outlier: 3.949A pdb=" N ASP X 136 " --> pdb=" O ALA X 132 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP X 147 " --> pdb=" O SER X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 175 removed outlier: 3.759A pdb=" N GLY X 175 " --> pdb=" O LEU X 171 " (cutoff:3.500A) Processing helix chain 'X' and resid 191 through 206 Processing helix chain 'X' and resid 227 through 239 Processing helix chain 'X' and resid 258 through 269 Processing helix chain 'X' and resid 270 through 272 No H-bonds generated for 'chain 'X' and resid 270 through 272' Processing helix chain 'X' and resid 283 through 311 removed outlier: 3.708A pdb=" N ALA X 289 " --> pdb=" O ALA X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 315 through 323 Processing helix chain 'X' and resid 326 through 334 removed outlier: 3.794A pdb=" N SER X 332 " --> pdb=" O SER X 328 " (cutoff:3.500A) Processing helix chain 'X' and resid 335 through 340 Processing sheet with id=AA1, first strand: chain 'F' and resid 178 through 180 removed outlier: 3.636A pdb=" N LEU F 179 " --> pdb=" O LYS F 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 245 through 248 removed outlier: 3.916A pdb=" N GLY F 251 " --> pdb=" O TYR F 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 178 through 181 removed outlier: 3.785A pdb=" N THR O 186 " --> pdb=" O GLY O 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 213 through 215 removed outlier: 3.897A pdb=" N PHE O 215 " --> pdb=" O VAL O 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 178 through 180 removed outlier: 3.920A pdb=" N LEU R 179 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 245 through 248 removed outlier: 4.025A pdb=" N GLY R 251 " --> pdb=" O TYR R 248 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 178 through 180 removed outlier: 3.614A pdb=" N LEU V 179 " --> pdb=" O LYS V 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 245 through 246 Processing sheet with id=AA9, first strand: chain 'X' and resid 178 through 181 removed outlier: 3.623A pdb=" N LEU X 179 " --> pdb=" O LYS X 188 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR X 186 " --> pdb=" O GLY X 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'X' and resid 245 through 248 removed outlier: 4.033A pdb=" N GLY X 251 " --> pdb=" O TYR X 248 " (cutoff:3.500A) 1524 hydrogen bonds defined for protein. 4512 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: 6.36 Time building geometry restraints manager: 8.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6046 1.34 - 1.45: 2762 1.45 - 1.57: 11189 1.57 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 20052 Sorted by residual: bond pdb=" CA LYS K 37 " pdb=" CB LYS K 37 " ideal model delta sigma weight residual 1.526 1.540 -0.013 9.30e-03 1.16e+04 2.05e+00 bond pdb=" CG1 ILE G 71 " pdb=" CD1 ILE G 71 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.62e+00 bond pdb=" CA LYS O 311 " pdb=" C LYS O 311 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.34e-02 5.57e+03 1.44e+00 bond pdb=" CG1 ILE A 71 " pdb=" CD1 ILE A 71 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.40e+00 bond pdb=" CB ASN W 63 " pdb=" CG ASN W 63 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.28e+00 ... (remaining 20047 not shown) Histogram of bond angle deviations from ideal: 98.41 - 106.14: 318 106.14 - 113.86: 11470 113.86 - 121.58: 11502 121.58 - 129.31: 3869 129.31 - 137.03: 84 Bond angle restraints: 27243 Sorted by residual: angle pdb=" C PHE R 215 " pdb=" N PRO R 216 " pdb=" CA PRO R 216 " ideal model delta sigma weight residual 127.00 137.03 -10.03 2.40e+00 1.74e-01 1.75e+01 angle pdb=" N LEU J 43 " pdb=" CA LEU J 43 " pdb=" C LEU J 43 " ideal model delta sigma weight residual 114.04 108.93 5.11 1.24e+00 6.50e-01 1.70e+01 angle pdb=" C PHE R 215 " pdb=" N PRO R 216 " pdb=" CD PRO R 216 " ideal model delta sigma weight residual 120.60 112.51 8.09 2.20e+00 2.07e-01 1.35e+01 angle pdb=" N PRO H 41 " pdb=" CA PRO H 41 " pdb=" C PRO H 41 " ideal model delta sigma weight residual 114.92 111.15 3.77 1.19e+00 7.06e-01 1.00e+01 angle pdb=" N VAL R 325 " pdb=" CA VAL R 325 " pdb=" C VAL R 325 " ideal model delta sigma weight residual 112.04 107.62 4.42 1.40e+00 5.10e-01 9.98e+00 ... (remaining 27238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10932 17.96 - 35.91: 944 35.91 - 53.87: 176 53.87 - 71.83: 44 71.83 - 89.78: 17 Dihedral angle restraints: 12113 sinusoidal: 4622 harmonic: 7491 Sorted by residual: dihedral pdb=" CA LYS O 311 " pdb=" C LYS O 311 " pdb=" N TYR O 312 " pdb=" CA TYR O 312 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU V 281 " pdb=" C GLU V 281 " pdb=" N MET V 282 " pdb=" CA MET V 282 " ideal model delta harmonic sigma weight residual 180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLU F 228 " pdb=" C GLU F 228 " pdb=" N ALA F 229 " pdb=" CA ALA F 229 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 12110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2054 0.035 - 0.070: 794 0.070 - 0.104: 224 0.104 - 0.139: 41 0.139 - 0.174: 6 Chirality restraints: 3119 Sorted by residual: chirality pdb=" CA GLU P 29 " pdb=" N GLU P 29 " pdb=" C GLU P 29 " pdb=" CB GLU P 29 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CA GLN O 266 " pdb=" N GLN O 266 " pdb=" C GLN O 266 " pdb=" CB GLN O 266 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA GLU L 29 " pdb=" N GLU L 29 " pdb=" C GLU L 29 " pdb=" CB GLU L 29 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 3116 not shown) Planarity restraints: 3524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP X 177 " 0.018 2.00e-02 2.50e+03 1.58e-02 6.24e+00 pdb=" CG TRP X 177 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP X 177 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP X 177 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP X 177 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP X 177 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP X 177 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 177 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 177 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP X 177 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 25 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C THR P 25 " 0.036 2.00e-02 2.50e+03 pdb=" O THR P 25 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN P 26 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 164 " 0.021 2.00e-02 2.50e+03 1.38e-02 3.79e+00 pdb=" CG TYR V 164 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR V 164 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR V 164 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR V 164 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR V 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR V 164 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR V 164 " 0.003 2.00e-02 2.50e+03 ... (remaining 3521 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 310 2.65 - 3.21: 20461 3.21 - 3.78: 33044 3.78 - 4.34: 41246 4.34 - 4.90: 67330 Nonbonded interactions: 162391 Sorted by model distance: nonbonded pdb=" OD1 ASP D 17 " pdb=" OH TYR D 57 " model vdw 2.090 2.440 nonbonded pdb=" O SER O 328 " pdb=" OG SER O 332 " model vdw 2.095 2.440 nonbonded pdb=" OH TYR I 54 " pdb=" OD2 ASP V 131 " model vdw 2.136 2.440 nonbonded pdb=" O SER R 328 " pdb=" OG SER R 332 " model vdw 2.159 2.440 nonbonded pdb=" OD1 ASN V 314 " pdb=" ND2 ASN X 316 " model vdw 2.176 2.520 ... (remaining 162386 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' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'B' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'C' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'D' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = (chain 'J' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'K' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'L' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'M' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'N' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'P' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'Q' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'S' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = chain 'T' selection = (chain 'U' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = chain 'W' } ncs_group { reference = chain 'F' selection = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'X' } 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.330 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 50.820 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 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 : 0.003 0.050 20052 Z= 0.221 Angle : 0.649 10.032 27243 Z= 0.359 Chirality : 0.040 0.174 3119 Planarity : 0.003 0.040 3524 Dihedral : 14.566 89.782 7259 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2487 helix: 1.59 (0.12), residues: 1813 sheet: -1.31 (0.58), residues: 75 loop : -1.76 (0.23), residues: 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 866 time to evaluate : 2.303 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: 0 outliers final: 0 residues processed: 866 average time/residue: 0.2960 time to fit residues: 392.7257 Evaluate side-chains 495 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 2.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN B 78 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 59 ASN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 63 ASN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 ASN N 24 GLN ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 239 ASN O 288 GLN ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN Q 48 GLN Q 63 ASN R 196 ASN ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 233 GLN ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 199 ASN ** V 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20052 Z= 0.199 Angle : 0.638 10.937 27243 Z= 0.328 Chirality : 0.041 0.205 3119 Planarity : 0.004 0.060 3524 Dihedral : 4.348 24.951 2693 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.48 % Allowed : 17.99 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.17), residues: 2487 helix: 1.61 (0.12), residues: 1847 sheet: -1.33 (0.58), residues: 75 loop : -1.69 (0.25), residues: 565 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 568 time to evaluate : 2.294 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: 75 outliers final: 39 residues processed: 605 average time/residue: 0.2847 time to fit residues: 273.7874 Evaluate side-chains 502 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 463 time to evaluate : 2.228 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.1981 time to fit residues: 17.3974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN I 55 ASN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 239 ASN O 288 GLN O 291 GLN ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 GLN ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 291 GLN V 300 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 141 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20052 Z= 0.195 Angle : 0.601 8.858 27243 Z= 0.312 Chirality : 0.040 0.180 3119 Planarity : 0.004 0.052 3524 Dihedral : 4.206 22.521 2693 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.64 % Allowed : 19.61 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2487 helix: 1.67 (0.12), residues: 1857 sheet: -1.57 (0.78), residues: 50 loop : -1.59 (0.25), residues: 580 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 545 time to evaluate : 2.271 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: 57 outliers final: 25 residues processed: 570 average time/residue: 0.2885 time to fit residues: 257.9512 Evaluate side-chains 500 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 475 time to evaluate : 2.298 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2083 time to fit residues: 12.1649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 8.9990 chunk 162 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 63 ASN ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 GLN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 297 GLN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20052 Z= 0.214 Angle : 0.625 9.522 27243 Z= 0.320 Chirality : 0.041 0.233 3119 Planarity : 0.003 0.035 3524 Dihedral : 4.189 21.864 2693 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.25 % Allowed : 22.48 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2487 helix: 1.66 (0.12), residues: 1899 sheet: -1.71 (0.77), residues: 50 loop : -1.61 (0.25), residues: 538 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 531 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 41 residues processed: 570 average time/residue: 0.2839 time to fit residues: 257.1467 Evaluate side-chains 507 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 466 time to evaluate : 2.272 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1940 time to fit residues: 17.6100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 206 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN F 288 GLN ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 ASN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 ASN ** O 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 GLN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 291 GLN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20052 Z= 0.188 Angle : 0.623 12.715 27243 Z= 0.316 Chirality : 0.040 0.242 3119 Planarity : 0.003 0.046 3524 Dihedral : 4.173 18.786 2693 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.60 % Allowed : 24.01 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.17), residues: 2487 helix: 1.71 (0.12), residues: 1920 sheet: -1.59 (0.80), residues: 50 loop : -1.58 (0.26), residues: 517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 515 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 27 residues processed: 535 average time/residue: 0.2787 time to fit residues: 236.9692 Evaluate side-chains 497 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 470 time to evaluate : 2.419 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2226 time to fit residues: 13.3922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 8.9990 chunk 207 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 0.0070 chunk 230 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN K 55 ASN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN U 22 ASN U 26 GLN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 77 GLN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 63 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20052 Z= 0.176 Angle : 0.621 13.763 27243 Z= 0.316 Chirality : 0.040 0.185 3119 Planarity : 0.003 0.045 3524 Dihedral : 4.149 19.278 2693 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.04 % Allowed : 26.24 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.17), residues: 2487 helix: 1.76 (0.12), residues: 1905 sheet: -1.54 (0.81), residues: 50 loop : -1.49 (0.26), residues: 532 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 523 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 17 residues processed: 544 average time/residue: 0.2839 time to fit residues: 243.7630 Evaluate side-chains 494 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 477 time to evaluate : 2.215 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2018 time to fit residues: 9.0669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 131 optimal weight: 0.0970 chunk 168 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 229 optimal weight: 0.0070 chunk 143 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 78 ASN ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN J 24 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 GLN U 63 ASN U 77 GLN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 297 GLN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.6867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20052 Z= 0.176 Angle : 0.642 9.671 27243 Z= 0.326 Chirality : 0.041 0.211 3119 Planarity : 0.003 0.044 3524 Dihedral : 4.141 21.818 2693 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.81 % Allowed : 27.68 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.17), residues: 2487 helix: 1.78 (0.12), residues: 1892 sheet: -1.50 (0.81), residues: 50 loop : -1.47 (0.25), residues: 545 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 513 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 530 average time/residue: 0.2896 time to fit residues: 244.6475 Evaluate side-chains 480 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 460 time to evaluate : 2.427 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2071 time to fit residues: 10.7325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN U 26 GLN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 77 GLN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 284 ASN ** W 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 321 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.7293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20052 Z= 0.191 Angle : 0.666 10.902 27243 Z= 0.339 Chirality : 0.041 0.214 3119 Planarity : 0.003 0.049 3524 Dihedral : 4.190 23.463 2693 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.30 % Allowed : 27.96 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.17), residues: 2487 helix: 1.76 (0.12), residues: 1898 sheet: -1.56 (0.79), residues: 50 loop : -1.48 (0.25), residues: 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 496 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 507 average time/residue: 0.2791 time to fit residues: 223.7654 Evaluate side-chains 469 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 456 time to evaluate : 2.260 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1985 time to fit residues: 7.6314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 213 optimal weight: 0.0470 chunk 128 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 59 ASN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 GLN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 77 GLN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.7590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20052 Z= 0.195 Angle : 0.685 11.176 27243 Z= 0.349 Chirality : 0.042 0.245 3119 Planarity : 0.003 0.047 3524 Dihedral : 4.228 22.673 2693 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.02 % Allowed : 29.62 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.17), residues: 2487 helix: 1.65 (0.12), residues: 1918 sheet: -1.57 (0.78), residues: 50 loop : -1.51 (0.26), residues: 519 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 479 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 490 average time/residue: 0.2841 time to fit residues: 221.5035 Evaluate side-chains 463 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 453 time to evaluate : 2.393 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2088 time to fit residues: 6.7876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN ** P 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 GLN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 78 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.8169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20052 Z= 0.233 Angle : 0.712 14.899 27243 Z= 0.369 Chirality : 0.043 0.322 3119 Planarity : 0.004 0.049 3524 Dihedral : 4.348 24.586 2693 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.60 % Allowed : 30.27 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2487 helix: 1.56 (0.12), residues: 1906 sheet: None (None), residues: 0 loop : -1.50 (0.24), residues: 581 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 496 time to evaluate : 2.122 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: 13 outliers final: 7 residues processed: 502 average time/residue: 0.2761 time to fit residues: 221.9948 Evaluate side-chains 458 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 451 time to evaluate : 2.321 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2282 time to fit residues: 5.6055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 63 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN U 24 GLN U 26 GLN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.087940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.076942 restraints weight = 65670.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.078947 restraints weight = 35371.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.080294 restraints weight = 22070.677| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.8466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20052 Z= 0.214 Angle : 0.721 17.788 27243 Z= 0.371 Chirality : 0.043 0.322 3119 Planarity : 0.004 0.055 3524 Dihedral : 4.387 26.652 2693 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.51 % Allowed : 31.11 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2487 helix: 1.53 (0.12), residues: 1913 sheet: None (None), residues: 0 loop : -1.45 (0.25), residues: 574 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4551.53 seconds wall clock time: 86 minutes 59.49 seconds (5219.49 seconds total)