Starting phenix.real_space_refine on Fri Feb 23 14:39:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f29_28809/02_2024/8f29_28809_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f29_28809/02_2024/8f29_28809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f29_28809/02_2024/8f29_28809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f29_28809/02_2024/8f29_28809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f29_28809/02_2024/8f29_28809_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f29_28809/02_2024/8f29_28809_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 24871 2.51 5 N 6561 2.21 5 O 7358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y ASP 34": "OD1" <-> "OD2" Residue "Y GLU 44": "OE1" <-> "OE2" Residue "Y ASP 72": "OD1" <-> "OD2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "Y PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 156": "OE1" <-> "OE2" Residue "Y GLU 170": "OE1" <-> "OE2" Residue "Y ASP 173": "OD1" <-> "OD2" Residue "G TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "Z ASP 90": "OD1" <-> "OD2" Residue "Z GLU 202": "OE1" <-> "OE2" Residue "7 PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 83": "OD1" <-> "OD2" Residue "6 GLU 87": "OE1" <-> "OE2" Residue "U PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 45": "OD1" <-> "OD2" Residue "K PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 45": "OD1" <-> "OD2" Residue "L PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 45": "OD1" <-> "OD2" Residue "P PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 45": "OD1" <-> "OD2" Residue "Q PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 59": "OE1" <-> "OE2" Residue "R PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 38": "OD1" <-> "OD2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "E PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38906 Number of models: 1 Model: "" Number of chains: 32 Chain: "Y" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1414 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2028 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 990 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "I" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 392 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1231 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "7" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1363 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 710 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 8, 'TRANS': 80} Chain: "U" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 639 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "T" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "K" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "L" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "M" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "P" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Q" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "R" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "8" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 356 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "X" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1750 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3858 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 486} Chain: "B" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3846 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 20, 'TRANS': 485} Chain: "C" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3844 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 484} Chain: "D" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 449} Chain: "E" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 449} Chain: "F" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3566 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 448} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.30, per 1000 atoms: 0.50 Number of scatterers: 38906 At special positions: 0 Unit cell: (122, 148, 239, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 11 15.00 Mg 5 11.99 O 7358 8.00 N 6561 7.00 C 24871 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: 18.04 Conformation dependent library (CDL) restraints added in 6.7 seconds 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9350 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 26 sheets defined 51.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.41 Creating SS restraints... Processing helix chain 'Y' and resid 15 through 30 removed outlier: 4.012A pdb=" N TYR Y 19 " --> pdb=" O VAL Y 15 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA Y 20 " --> pdb=" O GLU Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 49 Processing helix chain 'Y' and resid 51 through 58 Processing helix chain 'Y' and resid 64 through 76 Processing helix chain 'Y' and resid 85 through 95 Processing helix chain 'Y' and resid 98 through 115 removed outlier: 3.814A pdb=" N PHE Y 101 " --> pdb=" O LEU Y 98 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU Y 102 " --> pdb=" O GLY Y 99 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP Y 113 " --> pdb=" O VAL Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 131 through 143 removed outlier: 3.530A pdb=" N ARG Y 136 " --> pdb=" O LYS Y 132 " (cutoff:3.500A) Processing helix chain 'Y' and resid 180 through 191 removed outlier: 3.685A pdb=" N ILE Y 188 " --> pdb=" O ILE Y 184 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS Y 189 " --> pdb=" O GLN Y 185 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL Y 190 " --> pdb=" O LYS Y 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 13 Processing helix chain 'G' and resid 18 through 54 removed outlier: 3.549A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 101 Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'G' and resid 185 through 189 Processing helix chain 'G' and resid 205 through 273 removed outlier: 3.501A pdb=" N MET G 218 " --> pdb=" O LEU G 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 111 Processing helix chain 'H' and resid 117 through 137 removed outlier: 3.748A pdb=" N GLU H 122 " --> pdb=" O ARG H 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 23 Processing helix chain 'I' and resid 32 through 38 Processing helix chain 'Z' and resid 54 through 110 removed outlier: 3.569A pdb=" N LEU Z 58 " --> pdb=" O ASP Z 54 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU Z 59 " --> pdb=" O GLU Z 55 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix Processing helix chain 'Z' and resid 117 through 132 Processing helix chain 'Z' and resid 134 through 183 Processing helix chain 'Z' and resid 190 through 206 Processing helix chain '7' and resid 4 through 16 Processing helix chain '7' and resid 27 through 46 Processing helix chain '7' and resid 68 through 76 Processing helix chain '7' and resid 92 through 125 Processing helix chain '7' and resid 135 through 141 Processing helix chain '7' and resid 144 through 154 Processing helix chain '6' and resid 5 through 16 removed outlier: 4.348A pdb=" N LEU 6 11 " --> pdb=" O TYR 6 7 " (cutoff:3.500A) Processing helix chain '6' and resid 46 through 50 Processing helix chain '6' and resid 75 through 90 Processing helix chain 'U' and resid 18 through 29 removed outlier: 4.107A pdb=" N ILE U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS U 29 " --> pdb=" O ALA U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 54 Processing helix chain 'U' and resid 63 through 84 removed outlier: 3.643A pdb=" N SER U 79 " --> pdb=" O ALA U 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 38 removed outlier: 4.208A pdb=" N ILE S 17 " --> pdb=" O GLY S 13 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLY S 18 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU S 20 " --> pdb=" O THR S 16 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA S 22 " --> pdb=" O GLY S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 73 Proline residue: S 49 - end of helix Processing helix chain 'T' and resid 2 through 39 removed outlier: 4.641A pdb=" N GLY T 18 " --> pdb=" O ILE T 14 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU T 19 " --> pdb=" O SER T 15 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU T 20 " --> pdb=" O THR T 16 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLY T 21 " --> pdb=" O ILE T 17 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ALA T 22 " --> pdb=" O GLY T 18 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA T 27 " --> pdb=" O GLY T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 73 removed outlier: 4.966A pdb=" N ASP T 45 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE T 48 " --> pdb=" O ASP T 45 " (cutoff:3.500A) Proline residue: T 49 - end of helix removed outlier: 3.559A pdb=" N PHE T 55 " --> pdb=" O ILE T 52 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA T 56 " --> pdb=" O LEU T 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 39 removed outlier: 4.584A pdb=" N GLY K 18 " --> pdb=" O ILE K 14 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU K 19 " --> pdb=" O SER K 15 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY K 21 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE K 30 " --> pdb=" O ILE K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 73 removed outlier: 3.885A pdb=" N LYS K 44 " --> pdb=" O PRO K 41 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP K 45 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE K 48 " --> pdb=" O ASP K 45 " (cutoff:3.500A) Proline residue: K 49 - end of helix Processing helix chain 'L' and resid 2 through 39 removed outlier: 4.001A pdb=" N THR L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE L 17 " --> pdb=" O GLY L 13 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY L 18 " --> pdb=" O ILE L 14 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU L 19 " --> pdb=" O SER L 15 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLY L 21 " --> pdb=" O ILE L 17 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 73 Proline residue: L 49 - end of helix Processing helix chain 'M' and resid 2 through 39 removed outlier: 4.385A pdb=" N ILE M 17 " --> pdb=" O GLY M 13 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLY M 18 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU M 19 " --> pdb=" O SER M 15 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLY M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA M 27 " --> pdb=" O GLY M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 73 removed outlier: 4.785A pdb=" N ASP M 45 " --> pdb=" O SER M 42 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE M 48 " --> pdb=" O ASP M 45 " (cutoff:3.500A) Proline residue: M 49 - end of helix removed outlier: 3.955A pdb=" N ALA M 60 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL M 68 " --> pdb=" O CYS M 65 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE M 70 " --> pdb=" O MET M 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU M 71 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU M 72 " --> pdb=" O SER M 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 39 removed outlier: 4.518A pdb=" N ILE N 17 " --> pdb=" O GLY N 13 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY N 18 " --> pdb=" O ILE N 14 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLY N 21 " --> pdb=" O ILE N 17 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 63 removed outlier: 3.700A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 73 Processing helix chain 'O' and resid 3 through 39 removed outlier: 3.871A pdb=" N ILE O 17 " --> pdb=" O GLY O 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY O 18 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU O 19 " --> pdb=" O SER O 15 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU O 20 " --> pdb=" O THR O 16 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY O 21 " --> pdb=" O ILE O 17 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA O 22 " --> pdb=" O GLY O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 72 removed outlier: 3.999A pdb=" N LYS O 44 " --> pdb=" O PRO O 41 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASP O 45 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE O 48 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Proline residue: O 49 - end of helix removed outlier: 3.856A pdb=" N THR O 61 " --> pdb=" O SER O 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 39 removed outlier: 4.206A pdb=" N THR P 16 " --> pdb=" O ALA P 12 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE P 17 " --> pdb=" O GLY P 13 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY P 18 " --> pdb=" O ILE P 14 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU P 19 " --> pdb=" O SER P 15 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU P 20 " --> pdb=" O THR P 16 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY P 21 " --> pdb=" O ILE P 17 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 73 removed outlier: 4.262A pdb=" N ASP P 45 " --> pdb=" O SER P 42 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE P 48 " --> pdb=" O ASP P 45 " (cutoff:3.500A) Proline residue: P 49 - end of helix removed outlier: 3.510A pdb=" N PHE P 55 " --> pdb=" O ILE P 52 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU P 59 " --> pdb=" O ALA P 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 39 removed outlier: 4.458A pdb=" N GLY Q 18 " --> pdb=" O ILE Q 14 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU Q 19 " --> pdb=" O SER Q 15 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU Q 20 " --> pdb=" O THR Q 16 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLY Q 21 " --> pdb=" O ILE Q 17 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA Q 27 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 73 removed outlier: 4.550A pdb=" N ASP Q 45 " --> pdb=" O SER Q 42 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE Q 48 " --> pdb=" O ASP Q 45 " (cutoff:3.500A) Proline residue: Q 49 - end of helix removed outlier: 3.600A pdb=" N LEU Q 57 " --> pdb=" O GLY Q 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU Q 59 " --> pdb=" O ALA Q 56 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE Q 64 " --> pdb=" O THR Q 61 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET Q 67 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL Q 68 " --> pdb=" O CYS Q 65 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU Q 71 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 39 removed outlier: 4.156A pdb=" N ILE R 17 " --> pdb=" O GLY R 13 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY R 18 " --> pdb=" O ILE R 14 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU R 19 " --> pdb=" O SER R 15 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLY R 21 " --> pdb=" O ILE R 17 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA R 27 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE R 30 " --> pdb=" O ILE R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 73 removed outlier: 4.016A pdb=" N LYS R 44 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP R 45 " --> pdb=" O SER R 42 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE R 48 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Proline residue: R 49 - end of helix removed outlier: 3.656A pdb=" N ALA R 60 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR R 61 " --> pdb=" O SER R 58 " (cutoff:3.500A) Processing helix chain '8' and resid 14 through 46 removed outlier: 3.859A pdb=" N SER 8 28 " --> pdb=" O LEU 8 24 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU 8 32 " --> pdb=" O SER 8 28 " (cutoff:3.500A) Proline residue: 8 33 - end of helix Processing helix chain 'X' and resid 30 through 41 removed outlier: 3.783A pdb=" N VAL X 36 " --> pdb=" O TYR X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 76 removed outlier: 4.253A pdb=" N ILE X 65 " --> pdb=" O SER X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 103 removed outlier: 3.958A pdb=" N SER X 103 " --> pdb=" O ALA X 99 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 114 No H-bonds generated for 'chain 'X' and resid 111 through 114' Processing helix chain 'X' and resid 116 through 136 Processing helix chain 'X' and resid 138 through 145 removed outlier: 3.529A pdb=" N PHE X 145 " --> pdb=" O PHE X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 168 Proline residue: X 156 - end of helix removed outlier: 4.242A pdb=" N ILE X 160 " --> pdb=" O PRO X 156 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU X 164 " --> pdb=" O ILE X 160 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER X 165 " --> pdb=" O ILE X 161 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR X 166 " --> pdb=" O GLU X 162 " (cutoff:3.500A) Processing helix chain 'X' and resid 172 through 194 removed outlier: 3.765A pdb=" N LEU X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 211 through 246 Processing helix chain 'J' and resid 14 through 31 Processing helix chain 'A' and resid 5 through 15 removed outlier: 4.126A pdb=" N GLU A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 153 through 156 No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.851A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 242 through 262 Proline residue: A 249 - end of helix removed outlier: 3.590A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.722A pdb=" N ARG A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.750A pdb=" N GLY A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 removed outlier: 4.050A pdb=" N GLY A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N SER A 410 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 411 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 412 " --> pdb=" O GLY A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 412' Processing helix chain 'A' and resid 414 through 429 Processing helix chain 'A' and resid 440 through 451 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 464 through 476 Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'B' and resid 5 through 23 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 155 through 158 No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.774A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.850A pdb=" N LEU B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 3.548A pdb=" N PHE B 301 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU B 309 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.602A pdb=" N VAL B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 392 through 408 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 418 through 429 Processing helix chain 'B' and resid 441 through 451 removed outlier: 3.955A pdb=" N VAL B 444 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 460 through 477 removed outlier: 4.520A pdb=" N GLY B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLU B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 493 through 506 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.694A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 242 through 261 Proline residue: C 249 - end of helix removed outlier: 3.567A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 301 through 308 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 377 through 380 removed outlier: 3.627A pdb=" N ALA C 380 " --> pdb=" O GLY C 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 380' Processing helix chain 'C' and resid 383 through 408 removed outlier: 3.921A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 430 Processing helix chain 'C' and resid 440 through 451 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 460 through 476 removed outlier: 4.750A pdb=" N GLY C 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 469 " --> pdb=" O PHE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 488 Processing helix chain 'C' and resid 493 through 509 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 163 through 177 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 226 through 245 removed outlier: 4.548A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 271 Processing helix chain 'D' and resid 285 through 295 removed outlier: 3.544A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 328 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 365 through 390 removed outlier: 4.481A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 414 Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 463 through 477 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 163 through 176 Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 226 through 246 removed outlier: 4.086A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 284 through 294 removed outlier: 3.944A pdb=" N THR E 287 " --> pdb=" O THR E 284 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET E 289 " --> pdb=" O ALA E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 365 through 391 removed outlier: 3.844A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 414 Processing helix chain 'E' and resid 434 through 446 Processing helix chain 'E' and resid 454 through 457 No H-bonds generated for 'chain 'E' and resid 454 through 457' Processing helix chain 'E' and resid 463 through 476 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 163 through 178 removed outlier: 4.162A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 226 through 245 removed outlier: 4.270A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 271 removed outlier: 3.508A pdb=" N VAL F 268 " --> pdb=" O GLY F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 327 removed outlier: 3.521A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 340 No H-bonds generated for 'chain 'F' and resid 337 through 340' Processing helix chain 'F' and resid 365 through 383 Processing helix chain 'F' and resid 385 through 389 Processing helix chain 'F' and resid 398 through 414 Processing helix chain 'F' and resid 422 through 425 No H-bonds generated for 'chain 'F' and resid 422 through 425' Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 477 Processing sheet with id= A, first strand: chain 'Y' and resid 152 through 159 removed outlier: 3.576A pdb=" N LEU Y 119 " --> pdb=" O SER Y 152 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY Y 121 " --> pdb=" O LYS Y 154 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR Y 124 " --> pdb=" O LEU Y 168 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 161 through 165 removed outlier: 3.543A pdb=" N ILE G 77 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 106 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE G 74 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR G 109 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER G 129 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 10 through 12 Processing sheet with id= D, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.525A pdb=" N GLN H 29 " --> pdb=" O MET H 60 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.764A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 43 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 62 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= G, first strand: chain 'A' and resid 168 through 170 Processing sheet with id= H, first strand: chain 'A' and resid 232 through 236 Processing sheet with id= I, first strand: chain 'B' and resid 40 through 43 removed outlier: 7.142A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE B 78 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLY B 63 " --> pdb=" O PHE B 78 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 55 through 57 Processing sheet with id= K, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= L, first strand: chain 'B' and resid 204 through 207 removed outlier: 6.147A pdb=" N SER B 322 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE B 268 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR B 324 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N TYR B 270 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.153A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE C 44 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL C 33 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 98 through 101 Processing sheet with id= O, first strand: chain 'C' and resid 109 through 111 removed outlier: 7.855A pdb=" N VAL C 110 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE C 233 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ILE C 232 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS C 265 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL C 204 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL C 206 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL C 269 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL C 208 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 350 through 354 removed outlier: 3.512A pdb=" N ILE C 329 " --> pdb=" O ILE C 169 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.988A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 85 through 87 removed outlier: 3.517A pdb=" N LYS D 115 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 152 through 157 removed outlier: 7.513A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLY D 157 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL D 310 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.055A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR E 41 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.672A pdb=" N VAL E 85 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS E 115 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 332 through 335 removed outlier: 8.450A pdb=" N THR E 333 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY E 154 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU E 335 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE E 156 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE E 153 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER E 306 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU E 155 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN E 308 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLY E 157 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 75 through 78 removed outlier: 4.658A pdb=" N ILE F 9 " --> pdb=" O ASP F 78 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.608A pdb=" N LYS F 115 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 152 through 154 removed outlier: 6.463A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 215 through 220 removed outlier: 6.935A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU F 252 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR F 185 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE F 254 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL F 187 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASP F 256 " --> pdb=" O VAL F 187 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z 1937 hydrogen bonds defined for protein. 5124 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: 12.38 Time building geometry restraints manager: 18.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10786 1.33 - 1.46: 6615 1.46 - 1.58: 21928 1.58 - 1.70: 17 1.70 - 1.82: 184 Bond restraints: 39530 Sorted by residual: bond pdb=" CG PRO 7 50 " pdb=" CD PRO 7 50 " ideal model delta sigma weight residual 1.503 1.245 0.258 3.40e-02 8.65e+02 5.78e+01 bond pdb=" N PRO 7 50 " pdb=" CD PRO 7 50 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.75e+01 bond pdb=" CB PRO 7 50 " pdb=" CG PRO 7 50 " ideal model delta sigma weight residual 1.492 1.665 -0.173 5.00e-02 4.00e+02 1.20e+01 bond pdb=" O4 PO4 D 503 " pdb=" P PO4 D 503 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.74e+00 bond pdb=" O3 PO4 D 503 " pdb=" P PO4 D 503 " ideal model delta sigma weight residual 1.569 1.511 0.058 2.00e-02 2.50e+03 8.52e+00 ... (remaining 39525 not shown) Histogram of bond angle deviations from ideal: 85.22 - 95.38: 3 95.38 - 105.53: 748 105.53 - 115.69: 24972 115.69 - 125.85: 27456 125.85 - 136.01: 376 Bond angle restraints: 53555 Sorted by residual: angle pdb=" CA PRO 7 50 " pdb=" N PRO 7 50 " pdb=" CD PRO 7 50 " ideal model delta sigma weight residual 112.00 94.77 17.23 1.40e+00 5.10e-01 1.52e+02 angle pdb=" N PRO 7 50 " pdb=" CD PRO 7 50 " pdb=" CG PRO 7 50 " ideal model delta sigma weight residual 103.20 85.22 17.98 1.50e+00 4.44e-01 1.44e+02 angle pdb=" CA PRO 7 50 " pdb=" CB PRO 7 50 " pdb=" CG PRO 7 50 " ideal model delta sigma weight residual 104.50 90.07 14.43 1.90e+00 2.77e-01 5.77e+01 angle pdb=" CA LEU X 187 " pdb=" CB LEU X 187 " pdb=" CG LEU X 187 " ideal model delta sigma weight residual 116.30 134.87 -18.57 3.50e+00 8.16e-02 2.82e+01 angle pdb=" C VAL B 382 " pdb=" N LYS B 383 " pdb=" CA LYS B 383 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.24e+01 ... (remaining 53550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.49: 22825 34.49 - 68.97: 934 68.97 - 103.46: 94 103.46 - 137.95: 3 137.95 - 172.44: 1 Dihedral angle restraints: 23857 sinusoidal: 9291 harmonic: 14566 Sorted by residual: dihedral pdb=" C2' ADP B 601 " pdb=" C1' ADP B 601 " pdb=" N9 ADP B 601 " pdb=" C4 ADP B 601 " ideal model delta sinusoidal sigma weight residual 91.55 -96.02 -172.44 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -176.80 116.80 1 2.00e+01 2.50e-03 3.48e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 -171.85 111.85 1 2.00e+01 2.50e-03 3.29e+01 ... (remaining 23854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5570 0.071 - 0.142: 733 0.142 - 0.213: 33 0.213 - 0.284: 6 0.284 - 0.355: 3 Chirality restraints: 6345 Sorted by residual: chirality pdb=" CB ILE A 169 " pdb=" CA ILE A 169 " pdb=" CG1 ILE A 169 " pdb=" CG2 ILE A 169 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CG LEU C 471 " pdb=" CB LEU C 471 " pdb=" CD1 LEU C 471 " pdb=" CD2 LEU C 471 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CG LEU M 66 " pdb=" CB LEU M 66 " pdb=" CD1 LEU M 66 " pdb=" CD2 LEU M 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 6342 not shown) Planarity restraints: 6837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN 7 49 " 0.080 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO 7 50 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO 7 50 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO 7 50 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 40 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO R 41 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO R 41 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO R 41 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN S 40 " -0.064 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO S 41 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " -0.051 5.00e-02 4.00e+02 ... (remaining 6834 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 494 2.60 - 3.18: 36322 3.18 - 3.75: 70425 3.75 - 4.33: 92477 4.33 - 4.90: 146017 Nonbonded interactions: 345735 Sorted by model distance: nonbonded pdb=" O2B ADP B 601 " pdb="MG MG B 602 " model vdw 2.025 2.170 nonbonded pdb=" O SER Q 58 " pdb=" OG1 THR Q 61 " model vdw 2.066 2.440 nonbonded pdb=" O2B ADP A 601 " pdb="MG MG A 602 " model vdw 2.071 2.170 nonbonded pdb="MG MG D 502 " pdb=" O3 PO4 D 503 " model vdw 2.082 2.170 nonbonded pdb=" OD1 ASP C 172 " pdb=" N ARG C 173 " model vdw 2.150 2.520 ... (remaining 345730 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 6 through 509 or resid 601 through 602)) selection = (chain 'B' and (resid 6 through 509 or resid 601 through 602)) selection = (chain 'C' and (resid 6 through 509 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and resid 7 through 478) selection = (chain 'E' and resid 7 through 478) selection = (chain 'F' and resid 7 through 478) } ncs_group { reference = (chain 'K' and resid 1 through 74) selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 1 through 74) selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 0.850 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: 0.030 Extract box with map and model: 5.850 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 98.470 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.004 0.258 39530 Z= 0.243 Angle : 0.785 18.573 53555 Z= 0.392 Chirality : 0.046 0.355 6345 Planarity : 0.005 0.107 6837 Dihedral : 18.210 172.436 14507 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 0.24 % Allowed : 33.65 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 5060 helix: 0.78 (0.10), residues: 2641 sheet: -1.05 (0.24), residues: 478 loop : -1.13 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 234 HIS 0.007 0.001 HIS B 478 PHE 0.053 0.002 PHE M 64 TYR 0.024 0.001 TYR B 473 ARG 0.012 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 615 time to evaluate : 4.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: G 159 TYR cc_start: 0.8721 (m-80) cc_final: 0.8378 (m-80) REVERT: Z 85 MET cc_start: 0.7408 (mmt) cc_final: 0.6842 (mmt) REVERT: 7 8 ASN cc_start: 0.5749 (m-40) cc_final: 0.5193 (p0) REVERT: 6 79 TRP cc_start: 0.8841 (p-90) cc_final: 0.8631 (p-90) REVERT: U 17 SER cc_start: 0.8533 (m) cc_final: 0.8322 (p) REVERT: T 53 LEU cc_start: 0.5298 (pp) cc_final: 0.4837 (mp) REVERT: K 66 LEU cc_start: 0.8012 (mt) cc_final: 0.7734 (mt) REVERT: L 48 PHE cc_start: 0.7341 (t80) cc_final: 0.6658 (t80) REVERT: M 64 PHE cc_start: 0.8602 (m-80) cc_final: 0.8330 (m-80) REVERT: Q 70 PHE cc_start: 0.8080 (m-80) cc_final: 0.7652 (m-80) REVERT: Q 72 LEU cc_start: 0.8151 (mm) cc_final: 0.7878 (mm) REVERT: 8 43 LEU cc_start: 0.9360 (tp) cc_final: 0.9058 (tp) REVERT: X 104 MET cc_start: 0.7350 (tpt) cc_final: 0.6697 (mmm) REVERT: X 126 TRP cc_start: 0.8924 (t60) cc_final: 0.8672 (t60) REVERT: X 176 ARG cc_start: 0.9137 (ttm-80) cc_final: 0.8752 (mtm-85) REVERT: X 241 TYR cc_start: 0.8783 (m-80) cc_final: 0.8010 (m-80) REVERT: A 38 ASP cc_start: 0.8472 (m-30) cc_final: 0.7735 (p0) REVERT: C 167 GLU cc_start: 0.8875 (tp30) cc_final: 0.8296 (tp30) REVERT: F 369 ASP cc_start: 0.8959 (m-30) cc_final: 0.8726 (m-30) outliers start: 10 outliers final: 6 residues processed: 620 average time/residue: 0.4858 time to fit residues: 502.1838 Evaluate side-chains 532 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 526 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain F residue 312 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 422 optimal weight: 9.9990 chunk 378 optimal weight: 9.9990 chunk 210 optimal weight: 0.0030 chunk 129 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 202 optimal weight: 0.0010 chunk 391 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 238 optimal weight: 2.9990 chunk 291 optimal weight: 8.9990 chunk 454 optimal weight: 2.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 25 GLN Y 185 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN ** 7 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 39530 Z= 0.221 Angle : 0.662 11.811 53555 Z= 0.324 Chirality : 0.043 0.284 6345 Planarity : 0.005 0.070 6837 Dihedral : 5.640 171.965 5491 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 3.80 % Allowed : 29.02 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.12), residues: 5060 helix: 0.78 (0.10), residues: 2631 sheet: -1.19 (0.23), residues: 502 loop : -1.02 (0.15), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP U 67 HIS 0.005 0.001 HIS Y 78 PHE 0.064 0.002 PHE L 55 TYR 0.025 0.001 TYR D 458 ARG 0.008 0.000 ARG 8 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 553 time to evaluate : 4.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: G 159 TYR cc_start: 0.8748 (m-80) cc_final: 0.8394 (m-80) REVERT: G 248 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7960 (mt) REVERT: G 257 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7474 (tmm160) REVERT: H 102 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8616 (tttp) REVERT: 7 41 ARG cc_start: 0.7670 (mmt180) cc_final: 0.7405 (mmt180) REVERT: 7 100 MET cc_start: 0.8930 (mpp) cc_final: 0.8515 (mpp) REVERT: 6 22 GLN cc_start: 0.1353 (OUTLIER) cc_final: 0.0933 (pt0) REVERT: 6 79 TRP cc_start: 0.8788 (p-90) cc_final: 0.8564 (p-90) REVERT: U 4 LEU cc_start: 0.3211 (OUTLIER) cc_final: 0.2137 (mp) REVERT: U 6 PRO cc_start: 0.3542 (Cg_exo) cc_final: 0.3241 (Cg_endo) REVERT: U 67 TRP cc_start: 0.3326 (m-10) cc_final: 0.2989 (m-90) REVERT: S 19 LEU cc_start: 0.7061 (mm) cc_final: 0.6825 (pt) REVERT: T 53 LEU cc_start: 0.5337 (pp) cc_final: 0.5117 (mp) REVERT: L 48 PHE cc_start: 0.7332 (t80) cc_final: 0.6655 (t80) REVERT: L 57 LEU cc_start: 0.5307 (OUTLIER) cc_final: 0.4643 (pp) REVERT: M 50 MET cc_start: 0.4938 (mmp) cc_final: 0.4496 (mmp) REVERT: N 26 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8136 (pp) REVERT: N 30 PHE cc_start: 0.8250 (m-80) cc_final: 0.7835 (m-80) REVERT: O 67 MET cc_start: 0.8725 (ppp) cc_final: 0.8519 (ppp) REVERT: P 19 LEU cc_start: 0.8794 (mm) cc_final: 0.8456 (mt) REVERT: P 67 MET cc_start: 0.8561 (mmm) cc_final: 0.8163 (mmm) REVERT: Q 70 PHE cc_start: 0.8203 (m-80) cc_final: 0.7770 (m-80) REVERT: X 215 MET cc_start: 0.4318 (ptt) cc_final: 0.3938 (ptt) REVERT: X 241 TYR cc_start: 0.8872 (m-80) cc_final: 0.8279 (m-80) REVERT: A 38 ASP cc_start: 0.8628 (m-30) cc_final: 0.7696 (p0) REVERT: A 85 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7201 (mtpp) REVERT: B 330 GLU cc_start: 0.8755 (tt0) cc_final: 0.8132 (mm-30) REVERT: B 335 ASP cc_start: 0.8105 (t0) cc_final: 0.7899 (t0) REVERT: B 343 ASN cc_start: 0.8821 (m-40) cc_final: 0.8592 (m-40) REVERT: B 378 SER cc_start: 0.7138 (p) cc_final: 0.6901 (p) REVERT: C 40 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9047 (mt) REVERT: C 159 VAL cc_start: 0.9670 (OUTLIER) cc_final: 0.9430 (p) REVERT: C 172 ASP cc_start: 0.8304 (t0) cc_final: 0.8058 (t0) REVERT: D 12 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7442 (mtmm) outliers start: 157 outliers final: 70 residues processed: 679 average time/residue: 0.4757 time to fit residues: 543.0233 Evaluate side-chains 577 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 498 time to evaluate : 4.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 135 LYS Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 6 residue 22 GLN Chi-restraints excluded: chain 6 residue 39 LEU Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 252 optimal weight: 0.0050 chunk 140 optimal weight: 6.9990 chunk 377 optimal weight: 6.9990 chunk 309 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 454 optimal weight: 5.9990 chunk 491 optimal weight: 20.0000 chunk 405 optimal weight: 7.9990 chunk 451 optimal weight: 1.9990 chunk 155 optimal weight: 30.0000 chunk 364 optimal weight: 0.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39530 Z= 0.190 Angle : 0.649 10.611 53555 Z= 0.313 Chirality : 0.043 0.267 6345 Planarity : 0.004 0.063 6837 Dihedral : 5.537 172.624 5483 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.26 % Rotamer: Outliers : 4.43 % Allowed : 28.81 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 5060 helix: 0.71 (0.10), residues: 2652 sheet: -1.09 (0.23), residues: 501 loop : -1.02 (0.15), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 6 79 HIS 0.004 0.001 HIS Y 78 PHE 0.045 0.002 PHE L 55 TYR 0.023 0.001 TYR 6 7 ARG 0.004 0.000 ARG Y 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 546 time to evaluate : 4.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 MET cc_start: 0.7291 (tmm) cc_final: 0.6875 (ttt) REVERT: G 102 GLN cc_start: 0.6655 (pp30) cc_final: 0.6378 (pp30) REVERT: G 159 TYR cc_start: 0.8727 (m-80) cc_final: 0.8383 (m-80) REVERT: G 257 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7396 (tmm160) REVERT: H 102 LYS cc_start: 0.8914 (ttpp) cc_final: 0.8687 (tttp) REVERT: 7 100 MET cc_start: 0.9029 (mpp) cc_final: 0.8775 (mpp) REVERT: 6 22 GLN cc_start: 0.1361 (OUTLIER) cc_final: 0.0940 (pt0) REVERT: 6 79 TRP cc_start: 0.8791 (p-90) cc_final: 0.8565 (p-90) REVERT: U 4 LEU cc_start: 0.3135 (OUTLIER) cc_final: 0.2053 (mp) REVERT: U 6 PRO cc_start: 0.3558 (Cg_exo) cc_final: 0.3249 (Cg_endo) REVERT: U 8 LYS cc_start: 0.1783 (OUTLIER) cc_final: 0.1537 (tptp) REVERT: S 19 LEU cc_start: 0.7022 (mm) cc_final: 0.6623 (pt) REVERT: S 71 LEU cc_start: 0.6610 (mm) cc_final: 0.6368 (mm) REVERT: T 30 PHE cc_start: 0.8677 (m-80) cc_final: 0.8444 (m-80) REVERT: T 53 LEU cc_start: 0.5191 (pp) cc_final: 0.4961 (mp) REVERT: L 48 PHE cc_start: 0.7300 (t80) cc_final: 0.6625 (t80) REVERT: L 57 LEU cc_start: 0.5430 (OUTLIER) cc_final: 0.4886 (pp) REVERT: M 9 TYR cc_start: 0.8115 (m-10) cc_final: 0.7810 (m-10) REVERT: N 26 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.7891 (pp) REVERT: N 30 PHE cc_start: 0.8298 (m-80) cc_final: 0.7743 (m-80) REVERT: O 67 MET cc_start: 0.8733 (ppp) cc_final: 0.8523 (ppp) REVERT: P 67 MET cc_start: 0.8612 (mmm) cc_final: 0.8261 (mmm) REVERT: Q 70 PHE cc_start: 0.8302 (m-80) cc_final: 0.7799 (m-80) REVERT: 8 34 MET cc_start: 0.8023 (ppp) cc_final: 0.7811 (ppp) REVERT: 8 35 ILE cc_start: 0.9010 (mm) cc_final: 0.8782 (mm) REVERT: X 215 MET cc_start: 0.4591 (ptt) cc_final: 0.4173 (ptt) REVERT: X 241 TYR cc_start: 0.8855 (m-10) cc_final: 0.8242 (m-80) REVERT: A 38 ASP cc_start: 0.8715 (m-30) cc_final: 0.7708 (p0) REVERT: A 40 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8918 (mt) REVERT: A 339 TYR cc_start: 0.7660 (t80) cc_final: 0.7429 (t80) REVERT: B 323 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8886 (tt) REVERT: B 330 GLU cc_start: 0.8660 (tt0) cc_final: 0.8101 (mm-30) REVERT: B 335 ASP cc_start: 0.8236 (t0) cc_final: 0.7905 (t0) REVERT: B 343 ASN cc_start: 0.8943 (m-40) cc_final: 0.8664 (m110) REVERT: B 378 SER cc_start: 0.7101 (OUTLIER) cc_final: 0.6875 (p) REVERT: C 40 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9020 (mt) REVERT: C 159 VAL cc_start: 0.9689 (OUTLIER) cc_final: 0.9451 (p) REVERT: C 172 ASP cc_start: 0.8498 (t0) cc_final: 0.8213 (t0) REVERT: D 267 GLU cc_start: 0.8460 (tp30) cc_final: 0.8254 (tp30) REVERT: D 271 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8760 (mm) REVERT: D 349 ASP cc_start: 0.8394 (t0) cc_final: 0.8188 (t0) REVERT: E 267 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7676 (mp0) REVERT: E 269 SER cc_start: 0.9253 (OUTLIER) cc_final: 0.8988 (p) outliers start: 183 outliers final: 94 residues processed: 681 average time/residue: 0.4776 time to fit residues: 549.3004 Evaluate side-chains 598 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 492 time to evaluate : 4.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 147 VAL Chi-restraints excluded: chain Y residue 158 VAL Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 98 HIS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 6 residue 22 GLN Chi-restraints excluded: chain 6 residue 39 LEU Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 352 ASP Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 449 optimal weight: 8.9990 chunk 341 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 50 optimal weight: 30.0000 chunk 217 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 456 optimal weight: 5.9990 chunk 483 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 432 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 78 HIS G 98 HIS ** G 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 118 GLN ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 ASN ** X 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN C 225 HIS ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 ASN ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 39530 Z= 0.283 Angle : 0.682 10.587 53555 Z= 0.331 Chirality : 0.044 0.269 6345 Planarity : 0.004 0.059 6837 Dihedral : 5.620 172.898 5483 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.12 % Favored : 94.82 % Rotamer: Outliers : 5.20 % Allowed : 28.52 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 5060 helix: 0.73 (0.10), residues: 2641 sheet: -1.08 (0.23), residues: 517 loop : -0.96 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP U 67 HIS 0.006 0.001 HIS Y 78 PHE 0.038 0.002 PHE L 55 TYR 0.024 0.002 TYR D 458 ARG 0.010 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 523 time to evaluate : 4.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: G 23 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7023 (ttt) REVERT: G 159 TYR cc_start: 0.8708 (m-80) cc_final: 0.8409 (m-80) REVERT: 7 166 ARG cc_start: 0.7632 (ptp90) cc_final: 0.7321 (ptp90) REVERT: 6 22 GLN cc_start: 0.1106 (OUTLIER) cc_final: 0.0640 (pt0) REVERT: 6 79 TRP cc_start: 0.8820 (p-90) cc_final: 0.8587 (p-90) REVERT: U 4 LEU cc_start: 0.3145 (OUTLIER) cc_final: 0.2082 (mp) REVERT: U 6 PRO cc_start: 0.3425 (Cg_exo) cc_final: 0.3113 (Cg_endo) REVERT: U 8 LYS cc_start: 0.1962 (OUTLIER) cc_final: 0.1622 (tptp) REVERT: S 30 PHE cc_start: 0.8647 (m-80) cc_final: 0.8063 (m-10) REVERT: L 48 PHE cc_start: 0.7295 (t80) cc_final: 0.6623 (t80) REVERT: L 57 LEU cc_start: 0.5357 (OUTLIER) cc_final: 0.4709 (pp) REVERT: M 9 TYR cc_start: 0.8266 (m-10) cc_final: 0.7983 (m-10) REVERT: M 50 MET cc_start: 0.5414 (mmp) cc_final: 0.4928 (mmp) REVERT: N 26 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8252 (pp) REVERT: N 30 PHE cc_start: 0.8261 (m-80) cc_final: 0.7846 (m-80) REVERT: O 67 MET cc_start: 0.8751 (ppp) cc_final: 0.8542 (ppp) REVERT: P 19 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8299 (mt) REVERT: P 67 MET cc_start: 0.8631 (mmm) cc_final: 0.8241 (mmm) REVERT: Q 70 PHE cc_start: 0.8369 (m-80) cc_final: 0.7854 (m-80) REVERT: R 53 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8477 (mm) REVERT: R 55 PHE cc_start: 0.8390 (t80) cc_final: 0.7946 (t80) REVERT: R 59 GLU cc_start: 0.8126 (mp0) cc_final: 0.7765 (mp0) REVERT: 8 34 MET cc_start: 0.8076 (ppp) cc_final: 0.7865 (ppp) REVERT: 8 35 ILE cc_start: 0.9034 (mm) cc_final: 0.8783 (mm) REVERT: X 94 MET cc_start: 0.9229 (mpp) cc_final: 0.8970 (mpp) REVERT: X 215 MET cc_start: 0.4663 (ptt) cc_final: 0.4267 (ptt) REVERT: X 220 MET cc_start: 0.3783 (mmm) cc_final: 0.3551 (mmm) REVERT: X 241 TYR cc_start: 0.8868 (m-10) cc_final: 0.8277 (m-80) REVERT: A 339 TYR cc_start: 0.7763 (t80) cc_final: 0.7563 (t80) REVERT: A 351 GLN cc_start: 0.8365 (pm20) cc_final: 0.8001 (pm20) REVERT: B 330 GLU cc_start: 0.8623 (tt0) cc_final: 0.8076 (mm-30) REVERT: B 335 ASP cc_start: 0.8462 (t0) cc_final: 0.8080 (t0) REVERT: B 343 ASN cc_start: 0.9017 (m-40) cc_final: 0.8747 (m110) REVERT: B 481 LEU cc_start: 0.2360 (OUTLIER) cc_final: 0.1895 (pp) REVERT: C 172 ASP cc_start: 0.8547 (t0) cc_final: 0.8329 (t0) REVERT: D 271 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8832 (mm) REVERT: E 267 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7742 (mp0) REVERT: F 38 GLU cc_start: 0.7635 (mp0) cc_final: 0.7402 (mp0) outliers start: 215 outliers final: 137 residues processed: 685 average time/residue: 0.4631 time to fit residues: 537.6457 Evaluate side-chains 619 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 472 time to evaluate : 4.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 147 VAL Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 6 residue 22 GLN Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 65 CYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 67 ASP Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 352 ASP Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 402 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 359 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 chunk 412 optimal weight: 10.0000 chunk 334 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 246 optimal weight: 7.9990 chunk 433 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 55 HIS G 98 HIS ** G 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS B 245 GLN B 443 GLN B 454 HIS ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 365 GLN E 127 GLN ** F 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 39530 Z= 0.343 Angle : 0.722 10.846 53555 Z= 0.355 Chirality : 0.045 0.340 6345 Planarity : 0.005 0.056 6837 Dihedral : 5.836 173.413 5483 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 6.03 % Allowed : 28.25 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.12), residues: 5060 helix: 0.58 (0.10), residues: 2638 sheet: -1.20 (0.23), residues: 530 loop : -0.98 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP U 67 HIS 0.005 0.001 HIS C 225 PHE 0.032 0.002 PHE S 55 TYR 0.029 0.002 TYR D 345 ARG 0.006 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 501 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 33 ILE cc_start: 0.9051 (mp) cc_final: 0.8812 (mp) REVERT: Y 189 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8934 (mmtm) REVERT: G 23 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7028 (ttt) REVERT: H 102 LYS cc_start: 0.8904 (tttp) cc_final: 0.8628 (ptmm) REVERT: 7 133 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7259 (mt) REVERT: 7 152 MET cc_start: 0.6762 (ppp) cc_final: 0.6538 (ppp) REVERT: U 4 LEU cc_start: 0.3263 (OUTLIER) cc_final: 0.2228 (mp) REVERT: U 6 PRO cc_start: 0.3654 (Cg_exo) cc_final: 0.3330 (Cg_endo) REVERT: U 8 LYS cc_start: 0.2168 (OUTLIER) cc_final: 0.1568 (tptp) REVERT: U 67 TRP cc_start: 0.3508 (m-10) cc_final: 0.3135 (m-10) REVERT: L 48 PHE cc_start: 0.7356 (t80) cc_final: 0.6677 (t80) REVERT: L 57 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.4797 (pp) REVERT: M 9 TYR cc_start: 0.8383 (m-10) cc_final: 0.8103 (m-10) REVERT: N 26 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8125 (pp) REVERT: N 30 PHE cc_start: 0.8342 (m-80) cc_final: 0.7930 (m-80) REVERT: P 19 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8463 (mt) REVERT: P 55 PHE cc_start: 0.8070 (p90) cc_final: 0.7676 (p90) REVERT: P 67 MET cc_start: 0.8642 (mmm) cc_final: 0.8270 (mmm) REVERT: Q 70 PHE cc_start: 0.8481 (m-80) cc_final: 0.8049 (m-80) REVERT: R 35 ASN cc_start: 0.8753 (m-40) cc_final: 0.8487 (m110) REVERT: R 55 PHE cc_start: 0.8530 (t80) cc_final: 0.7946 (t80) REVERT: R 59 GLU cc_start: 0.8074 (mp0) cc_final: 0.7434 (mp0) REVERT: R 61 THR cc_start: 0.6946 (OUTLIER) cc_final: 0.5838 (p) REVERT: R 64 PHE cc_start: 0.7820 (m-80) cc_final: 0.7142 (m-80) REVERT: 8 36 LEU cc_start: 0.9267 (tt) cc_final: 0.9021 (pp) REVERT: X 215 MET cc_start: 0.4695 (ptt) cc_final: 0.4338 (ptt) REVERT: X 241 TYR cc_start: 0.8914 (m-80) cc_final: 0.8344 (m-80) REVERT: A 69 GLU cc_start: 0.7987 (mp0) cc_final: 0.7744 (mp0) REVERT: A 351 GLN cc_start: 0.8648 (pm20) cc_final: 0.8215 (pm20) REVERT: A 357 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8656 (tm-30) REVERT: A 394 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9015 (tt) REVERT: B 281 ARG cc_start: 0.8359 (mtp180) cc_final: 0.8151 (mtp180) REVERT: B 323 LEU cc_start: 0.9314 (tp) cc_final: 0.9044 (tt) REVERT: B 335 ASP cc_start: 0.8543 (t0) cc_final: 0.8170 (t0) REVERT: B 343 ASN cc_start: 0.9198 (m-40) cc_final: 0.8903 (m110) REVERT: B 383 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8825 (tptp) REVERT: C 210 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8606 (mm-40) REVERT: C 383 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8718 (ttpp) REVERT: D 292 LEU cc_start: 0.9484 (tp) cc_final: 0.9175 (tt) REVERT: E 267 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7655 (mp0) REVERT: E 281 TYR cc_start: 0.7593 (t80) cc_final: 0.7219 (t80) REVERT: E 326 PHE cc_start: 0.5953 (m-80) cc_final: 0.5725 (m-80) REVERT: E 459 MET cc_start: 0.6953 (tpt) cc_final: 0.6718 (tpt) REVERT: F 345 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7622 (t80) outliers start: 249 outliers final: 147 residues processed: 695 average time/residue: 0.4806 time to fit residues: 565.4281 Evaluate side-chains 622 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 462 time to evaluate : 4.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 257 ARG Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain 7 residue 32 PHE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 108 SER Chi-restraints excluded: chain 7 residue 133 LEU Chi-restraints excluded: chain 7 residue 160 VAL Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 65 CYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 77 ILE Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 116 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 352 ASP Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 9.9990 chunk 435 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 483 optimal weight: 3.9990 chunk 401 optimal weight: 10.0000 chunk 223 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 HIS ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN P 2 GLN ** Q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 ASN ** X 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 443 GLN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39530 Z= 0.227 Angle : 0.696 14.071 53555 Z= 0.333 Chirality : 0.044 0.357 6345 Planarity : 0.004 0.052 6837 Dihedral : 5.826 173.495 5483 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 4.55 % Allowed : 29.58 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.12), residues: 5060 helix: 0.58 (0.10), residues: 2634 sheet: -1.25 (0.23), residues: 523 loop : -0.95 (0.15), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 6 79 HIS 0.005 0.001 HIS F 328 PHE 0.029 0.002 PHE M 64 TYR 0.025 0.001 TYR D 345 ARG 0.005 0.000 ARG Y 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 509 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 33 ILE cc_start: 0.9052 (mp) cc_final: 0.8819 (mp) REVERT: Y 72 ASP cc_start: 0.9203 (m-30) cc_final: 0.8633 (p0) REVERT: G 23 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7024 (ttt) REVERT: I 30 GLN cc_start: 0.4519 (OUTLIER) cc_final: 0.4270 (tp-100) REVERT: Z 85 MET cc_start: 0.7833 (mmt) cc_final: 0.7532 (mmt) REVERT: 7 152 MET cc_start: 0.6706 (ppp) cc_final: 0.6494 (ppp) REVERT: 6 79 TRP cc_start: 0.8836 (p-90) cc_final: 0.8612 (p-90) REVERT: U 6 PRO cc_start: 0.3533 (Cg_exo) cc_final: 0.3191 (Cg_endo) REVERT: U 8 LYS cc_start: 0.1843 (OUTLIER) cc_final: 0.1167 (tptp) REVERT: S 30 PHE cc_start: 0.8688 (m-80) cc_final: 0.8078 (m-10) REVERT: L 48 PHE cc_start: 0.7291 (t80) cc_final: 0.6662 (t80) REVERT: L 57 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4501 (pp) REVERT: M 9 TYR cc_start: 0.8356 (m-10) cc_final: 0.8034 (m-10) REVERT: N 26 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.7408 (pp) REVERT: N 30 PHE cc_start: 0.8297 (m-80) cc_final: 0.7455 (m-80) REVERT: P 19 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8522 (mt) REVERT: P 55 PHE cc_start: 0.8146 (p90) cc_final: 0.7796 (p90) REVERT: P 67 MET cc_start: 0.8633 (mmm) cc_final: 0.8279 (mmm) REVERT: Q 70 PHE cc_start: 0.8504 (m-80) cc_final: 0.7990 (m-80) REVERT: R 35 ASN cc_start: 0.8742 (m-40) cc_final: 0.8482 (m110) REVERT: R 53 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8516 (mm) REVERT: R 55 PHE cc_start: 0.8560 (t80) cc_final: 0.8058 (t80) REVERT: R 59 GLU cc_start: 0.8121 (mp0) cc_final: 0.7520 (mp0) REVERT: R 61 THR cc_start: 0.6890 (OUTLIER) cc_final: 0.5903 (p) REVERT: R 64 PHE cc_start: 0.7925 (m-80) cc_final: 0.7297 (m-80) REVERT: 8 27 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7717 (t80) REVERT: 8 36 LEU cc_start: 0.9264 (tt) cc_final: 0.8989 (pp) REVERT: X 126 TRP cc_start: 0.8856 (t60) cc_final: 0.8576 (t60) REVERT: X 215 MET cc_start: 0.4714 (ptt) cc_final: 0.4225 (ptt) REVERT: X 241 TYR cc_start: 0.8909 (m-10) cc_final: 0.8333 (m-80) REVERT: A 69 GLU cc_start: 0.7998 (mp0) cc_final: 0.7711 (mp0) REVERT: A 245 GLN cc_start: 0.9002 (mt0) cc_final: 0.8766 (mt0) REVERT: A 276 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8661 (tp40) REVERT: A 351 GLN cc_start: 0.8592 (pm20) cc_final: 0.8153 (pm20) REVERT: A 357 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 394 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9005 (tt) REVERT: B 52 GLU cc_start: 0.7682 (pm20) cc_final: 0.7249 (pm20) REVERT: B 323 LEU cc_start: 0.9288 (tp) cc_final: 0.8989 (tt) REVERT: B 335 ASP cc_start: 0.8393 (t0) cc_final: 0.7987 (t0) REVERT: B 343 ASN cc_start: 0.9168 (m-40) cc_final: 0.8841 (m110) REVERT: D 292 LEU cc_start: 0.9457 (tp) cc_final: 0.9166 (tt) REVERT: E 267 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7832 (mp0) REVERT: E 459 MET cc_start: 0.7163 (tpt) cc_final: 0.6929 (tpt) outliers start: 188 outliers final: 136 residues processed: 653 average time/residue: 0.4735 time to fit residues: 525.1530 Evaluate side-chains 619 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 472 time to evaluate : 4.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 30 GLN Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 36 LYS Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 65 CYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 27 PHE Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 466 optimal weight: 8.9990 chunk 54 optimal weight: 30.0000 chunk 275 optimal weight: 0.7980 chunk 353 optimal weight: 0.9990 chunk 273 optimal weight: 0.7980 chunk 407 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 481 optimal weight: 0.8980 chunk 301 optimal weight: 9.9990 chunk 293 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 HIS G 100 ASN ** G 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 39530 Z= 0.194 Angle : 0.692 12.649 53555 Z= 0.328 Chirality : 0.044 0.308 6345 Planarity : 0.004 0.052 6837 Dihedral : 5.744 173.297 5483 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.74 % Rotamer: Outliers : 4.48 % Allowed : 30.14 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.12), residues: 5060 helix: 0.59 (0.10), residues: 2621 sheet: -1.23 (0.23), residues: 522 loop : -0.94 (0.15), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 6 79 HIS 0.006 0.001 HIS F 328 PHE 0.046 0.001 PHE Z 65 TYR 0.019 0.001 TYR G 166 ARG 0.005 0.000 ARG 7 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 501 time to evaluate : 4.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 33 ILE cc_start: 0.9051 (mp) cc_final: 0.8820 (mp) REVERT: Y 72 ASP cc_start: 0.9226 (m-30) cc_final: 0.8726 (p0) REVERT: Y 189 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8821 (mmtm) REVERT: G 23 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6981 (ttt) REVERT: Z 85 MET cc_start: 0.7939 (mmt) cc_final: 0.7655 (mmt) REVERT: 7 152 MET cc_start: 0.6694 (ppp) cc_final: 0.6491 (ppp) REVERT: 6 79 TRP cc_start: 0.8837 (p-90) cc_final: 0.8611 (p-90) REVERT: U 6 PRO cc_start: 0.3391 (Cg_exo) cc_final: 0.3043 (Cg_endo) REVERT: U 8 LYS cc_start: 0.1705 (OUTLIER) cc_final: 0.1200 (tptp) REVERT: S 30 PHE cc_start: 0.8652 (m-80) cc_final: 0.8148 (m-80) REVERT: L 48 PHE cc_start: 0.7247 (t80) cc_final: 0.6674 (t80) REVERT: L 57 LEU cc_start: 0.4931 (OUTLIER) cc_final: 0.4370 (pp) REVERT: M 9 TYR cc_start: 0.8411 (m-10) cc_final: 0.8164 (m-10) REVERT: M 70 PHE cc_start: 0.7512 (m-10) cc_final: 0.7055 (m-80) REVERT: N 26 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8272 (pp) REVERT: N 30 PHE cc_start: 0.8261 (m-80) cc_final: 0.7862 (m-80) REVERT: P 19 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8516 (mt) REVERT: P 55 PHE cc_start: 0.8116 (p90) cc_final: 0.7788 (p90) REVERT: P 67 MET cc_start: 0.8663 (mmm) cc_final: 0.8278 (mmm) REVERT: Q 70 PHE cc_start: 0.8467 (m-80) cc_final: 0.7976 (m-80) REVERT: R 35 ASN cc_start: 0.8652 (m-40) cc_final: 0.8409 (m-40) REVERT: R 53 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8408 (mm) REVERT: R 55 PHE cc_start: 0.8530 (t80) cc_final: 0.7904 (t80) REVERT: R 59 GLU cc_start: 0.8069 (mp0) cc_final: 0.7070 (mp0) REVERT: R 61 THR cc_start: 0.6676 (OUTLIER) cc_final: 0.5660 (p) REVERT: R 64 PHE cc_start: 0.7968 (m-80) cc_final: 0.7327 (m-80) REVERT: 8 36 LEU cc_start: 0.9255 (tt) cc_final: 0.8957 (pp) REVERT: X 126 TRP cc_start: 0.8902 (t60) cc_final: 0.8539 (t60) REVERT: X 215 MET cc_start: 0.4841 (ptt) cc_final: 0.4460 (ptt) REVERT: X 241 TYR cc_start: 0.8894 (m-10) cc_final: 0.8299 (m-80) REVERT: A 69 GLU cc_start: 0.8022 (mp0) cc_final: 0.7779 (mp0) REVERT: A 245 GLN cc_start: 0.8962 (mt0) cc_final: 0.8712 (mt0) REVERT: A 276 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8695 (tp40) REVERT: A 357 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8569 (tm-30) REVERT: A 394 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9020 (tt) REVERT: B 52 GLU cc_start: 0.7647 (pm20) cc_final: 0.7188 (pm20) REVERT: B 323 LEU cc_start: 0.9255 (tp) cc_final: 0.8983 (tt) REVERT: B 335 ASP cc_start: 0.8376 (t0) cc_final: 0.7957 (t0) REVERT: B 343 ASN cc_start: 0.9157 (m-40) cc_final: 0.8829 (m110) REVERT: B 383 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8562 (tptm) REVERT: D 292 LEU cc_start: 0.9443 (tp) cc_final: 0.9166 (tt) REVERT: E 267 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7814 (mp0) REVERT: F 301 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8983 (mppt) outliers start: 185 outliers final: 143 residues processed: 641 average time/residue: 0.4704 time to fit residues: 512.0607 Evaluate side-chains 624 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 470 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain U residue 31 TYR Chi-restraints excluded: chain U residue 57 ASP Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 65 CYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 26 LEU Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 298 optimal weight: 5.9990 chunk 192 optimal weight: 50.0000 chunk 287 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 chunk 328 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 44 optimal weight: 30.0000 chunk 378 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 41 GLN G 98 HIS ** G 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 39530 Z= 0.218 Angle : 0.701 13.581 53555 Z= 0.334 Chirality : 0.044 0.388 6345 Planarity : 0.004 0.056 6837 Dihedral : 5.710 172.622 5483 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 4.77 % Allowed : 30.21 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 5060 helix: 0.61 (0.10), residues: 2618 sheet: -1.22 (0.23), residues: 525 loop : -0.91 (0.15), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 6 79 HIS 0.006 0.001 HIS F 328 PHE 0.045 0.002 PHE Z 65 TYR 0.029 0.001 TYR G 166 ARG 0.006 0.000 ARG 7 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 485 time to evaluate : 4.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 33 ILE cc_start: 0.9085 (mp) cc_final: 0.8857 (mp) REVERT: Y 72 ASP cc_start: 0.9197 (m-30) cc_final: 0.8690 (p0) REVERT: G 23 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7027 (ttt) REVERT: G 222 MET cc_start: 0.8355 (tmm) cc_final: 0.8126 (tmm) REVERT: Z 85 MET cc_start: 0.7973 (mmt) cc_final: 0.7677 (mmt) REVERT: 6 79 TRP cc_start: 0.8846 (p-90) cc_final: 0.8618 (p-90) REVERT: U 6 PRO cc_start: 0.3470 (Cg_exo) cc_final: 0.3123 (Cg_endo) REVERT: U 8 LYS cc_start: 0.1764 (OUTLIER) cc_final: 0.1311 (tptp) REVERT: S 30 PHE cc_start: 0.8602 (m-80) cc_final: 0.8100 (m-80) REVERT: T 33 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8334 (mm) REVERT: L 48 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6695 (t80) REVERT: L 57 LEU cc_start: 0.5090 (OUTLIER) cc_final: 0.4496 (pp) REVERT: M 67 MET cc_start: 0.7813 (ppp) cc_final: 0.7069 (ppp) REVERT: M 70 PHE cc_start: 0.7674 (m-10) cc_final: 0.7119 (m-80) REVERT: N 26 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8238 (pp) REVERT: N 30 PHE cc_start: 0.8298 (m-80) cc_final: 0.7932 (m-80) REVERT: P 19 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8491 (mt) REVERT: P 55 PHE cc_start: 0.7999 (p90) cc_final: 0.7785 (p90) REVERT: P 67 MET cc_start: 0.8699 (mmm) cc_final: 0.8302 (mmm) REVERT: Q 70 PHE cc_start: 0.8485 (m-80) cc_final: 0.7969 (m-80) REVERT: R 35 ASN cc_start: 0.8593 (m-40) cc_final: 0.8367 (m-40) REVERT: R 53 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8470 (mm) REVERT: R 61 THR cc_start: 0.6680 (OUTLIER) cc_final: 0.5691 (p) REVERT: R 64 PHE cc_start: 0.7997 (m-80) cc_final: 0.7349 (m-80) REVERT: 8 36 LEU cc_start: 0.9255 (tt) cc_final: 0.8958 (pp) REVERT: X 104 MET cc_start: 0.7560 (tpt) cc_final: 0.6718 (mmp) REVERT: X 215 MET cc_start: 0.4983 (ptt) cc_final: 0.4616 (ptt) REVERT: X 241 TYR cc_start: 0.8893 (m-10) cc_final: 0.8301 (m-80) REVERT: A 69 GLU cc_start: 0.8036 (mp0) cc_final: 0.7757 (mp0) REVERT: A 245 GLN cc_start: 0.8962 (mt0) cc_final: 0.8733 (mt0) REVERT: A 276 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8709 (tp40) REVERT: A 357 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8598 (tm-30) REVERT: A 394 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9034 (tt) REVERT: B 52 GLU cc_start: 0.7671 (pm20) cc_final: 0.7291 (pm20) REVERT: B 323 LEU cc_start: 0.9279 (tp) cc_final: 0.8992 (tt) REVERT: B 335 ASP cc_start: 0.8409 (t0) cc_final: 0.7983 (t0) REVERT: B 343 ASN cc_start: 0.9113 (m-40) cc_final: 0.8816 (m110) REVERT: B 383 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8594 (tptm) REVERT: E 204 THR cc_start: 0.7073 (OUTLIER) cc_final: 0.6578 (m) REVERT: E 267 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7822 (mp0) outliers start: 197 outliers final: 155 residues processed: 632 average time/residue: 0.4767 time to fit residues: 510.4473 Evaluate side-chains 634 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 465 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 160 VAL Chi-restraints excluded: chain 7 residue 170 LEU Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 39 LEU Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain U residue 57 ASP Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 65 CYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 27 PHE Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 160 ILE Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 438 optimal weight: 20.0000 chunk 461 optimal weight: 0.6980 chunk 421 optimal weight: 7.9990 chunk 449 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 352 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 405 optimal weight: 9.9990 chunk 424 optimal weight: 8.9990 chunk 447 optimal weight: 6.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 116 ASN G 98 HIS ** G 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 ASN ** X 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN B 434 GLN ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS D 257 ASN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 39530 Z= 0.305 Angle : 0.745 14.620 53555 Z= 0.359 Chirality : 0.046 0.343 6345 Planarity : 0.004 0.058 6837 Dihedral : 5.866 171.232 5483 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.85 % Favored : 94.11 % Rotamer: Outliers : 4.79 % Allowed : 30.38 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.12), residues: 5060 helix: 0.52 (0.10), residues: 2652 sheet: -1.06 (0.24), residues: 499 loop : -0.94 (0.15), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 126 HIS 0.012 0.001 HIS F 328 PHE 0.041 0.002 PHE Z 65 TYR 0.026 0.002 TYR G 166 ARG 0.008 0.001 ARG 7 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 484 time to evaluate : 4.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 72 ASP cc_start: 0.9251 (m-30) cc_final: 0.8814 (p0) REVERT: G 23 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7138 (ttt) REVERT: 6 15 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8809 (mmmt) REVERT: 6 79 TRP cc_start: 0.8850 (p-90) cc_final: 0.8616 (p-90) REVERT: U 6 PRO cc_start: 0.3696 (Cg_exo) cc_final: 0.3349 (Cg_endo) REVERT: U 8 LYS cc_start: 0.1915 (OUTLIER) cc_final: 0.1043 (tptp) REVERT: S 30 PHE cc_start: 0.8651 (m-80) cc_final: 0.8151 (m-10) REVERT: T 33 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8400 (mm) REVERT: L 48 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6698 (t80) REVERT: L 57 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.4593 (pp) REVERT: M 67 MET cc_start: 0.7839 (ppp) cc_final: 0.7070 (ppp) REVERT: M 70 PHE cc_start: 0.7601 (m-10) cc_final: 0.7009 (m-80) REVERT: N 26 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.7803 (pp) REVERT: N 30 PHE cc_start: 0.8328 (m-80) cc_final: 0.7942 (m-80) REVERT: O 1 MET cc_start: 0.2375 (pmm) cc_final: 0.1638 (pmm) REVERT: P 19 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8483 (mt) REVERT: P 55 PHE cc_start: 0.7975 (p90) cc_final: 0.7756 (p90) REVERT: P 67 MET cc_start: 0.8821 (mmm) cc_final: 0.8446 (mmm) REVERT: Q 70 PHE cc_start: 0.8598 (m-80) cc_final: 0.8071 (m-80) REVERT: R 35 ASN cc_start: 0.8606 (m-40) cc_final: 0.8392 (m110) REVERT: R 61 THR cc_start: 0.6671 (OUTLIER) cc_final: 0.5665 (p) REVERT: R 64 PHE cc_start: 0.7973 (m-80) cc_final: 0.7360 (m-80) REVERT: X 126 TRP cc_start: 0.8802 (t60) cc_final: 0.8514 (t60) REVERT: X 215 MET cc_start: 0.5032 (ptt) cc_final: 0.4560 (ptt) REVERT: X 241 TYR cc_start: 0.8899 (m-10) cc_final: 0.8315 (m-80) REVERT: A 276 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8797 (tp40) REVERT: A 357 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8660 (tm-30) REVERT: A 394 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9036 (tt) REVERT: B 52 GLU cc_start: 0.7827 (pm20) cc_final: 0.7423 (pm20) REVERT: B 323 LEU cc_start: 0.9347 (tp) cc_final: 0.9052 (tt) REVERT: B 335 ASP cc_start: 0.8447 (t0) cc_final: 0.8014 (t0) REVERT: B 343 ASN cc_start: 0.9105 (m-40) cc_final: 0.8801 (m110) REVERT: B 378 SER cc_start: 0.7580 (p) cc_final: 0.7378 (p) REVERT: B 383 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8672 (tptm) REVERT: E 267 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7807 (mp0) outliers start: 198 outliers final: 155 residues processed: 629 average time/residue: 0.4769 time to fit residues: 509.2178 Evaluate side-chains 634 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 466 time to evaluate : 4.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 32 PHE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 160 VAL Chi-restraints excluded: chain 6 residue 15 LYS Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 39 LEU Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain U residue 57 ASP Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 65 CYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 27 PHE Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 81 ASN Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 294 optimal weight: 9.9990 chunk 474 optimal weight: 9.9990 chunk 289 optimal weight: 0.9980 chunk 225 optimal weight: 30.0000 chunk 330 optimal weight: 0.7980 chunk 498 optimal weight: 0.0020 chunk 458 optimal weight: 5.9990 chunk 396 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 HIS ** G 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 35 ASN ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.299 39530 Z= 0.367 Angle : 0.845 59.192 53555 Z= 0.429 Chirality : 0.047 0.690 6345 Planarity : 0.005 0.058 6837 Dihedral : 5.872 171.203 5483 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 4.53 % Allowed : 30.55 % Favored : 64.92 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.12), residues: 5060 helix: 0.51 (0.10), residues: 2651 sheet: -1.08 (0.24), residues: 499 loop : -0.96 (0.15), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP X 126 HIS 0.012 0.001 HIS F 328 PHE 0.044 0.002 PHE R 55 TYR 0.091 0.002 TYR 6 7 ARG 0.009 0.000 ARG 7 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 469 time to evaluate : 4.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7131 (ttt) REVERT: G 266 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7850 (pp20) REVERT: Z 85 MET cc_start: 0.7748 (mmt) cc_final: 0.7317 (mmt) REVERT: 6 15 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8805 (mmmt) REVERT: 6 79 TRP cc_start: 0.8848 (p-90) cc_final: 0.8613 (p-90) REVERT: U 6 PRO cc_start: 0.3689 (Cg_exo) cc_final: 0.3340 (Cg_endo) REVERT: U 8 LYS cc_start: 0.1905 (OUTLIER) cc_final: 0.1040 (tptp) REVERT: S 30 PHE cc_start: 0.8646 (m-80) cc_final: 0.8150 (m-10) REVERT: T 33 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8395 (mm) REVERT: L 48 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6696 (t80) REVERT: L 57 LEU cc_start: 0.5251 (OUTLIER) cc_final: 0.4594 (pp) REVERT: M 67 MET cc_start: 0.7842 (ppp) cc_final: 0.7049 (ppp) REVERT: M 70 PHE cc_start: 0.7611 (m-10) cc_final: 0.7009 (m-80) REVERT: N 26 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.7801 (pp) REVERT: N 30 PHE cc_start: 0.8324 (m-80) cc_final: 0.7937 (m-80) REVERT: O 1 MET cc_start: 0.2319 (pmm) cc_final: 0.1562 (pmm) REVERT: P 19 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8484 (mt) REVERT: P 33 LEU cc_start: 0.9130 (tp) cc_final: 0.8836 (tt) REVERT: P 55 PHE cc_start: 0.7968 (p90) cc_final: 0.7761 (p90) REVERT: P 67 MET cc_start: 0.8837 (mmm) cc_final: 0.8483 (mmm) REVERT: Q 70 PHE cc_start: 0.8595 (m-80) cc_final: 0.8250 (m-80) REVERT: R 61 THR cc_start: 0.6660 (OUTLIER) cc_final: 0.5663 (p) REVERT: R 64 PHE cc_start: 0.7970 (m-80) cc_final: 0.7357 (m-80) REVERT: X 126 TRP cc_start: 0.8799 (t60) cc_final: 0.8515 (t60) REVERT: X 215 MET cc_start: 0.5037 (ptt) cc_final: 0.4674 (ptt) REVERT: X 241 TYR cc_start: 0.8898 (m-10) cc_final: 0.8313 (m-80) REVERT: A 182 LEU cc_start: 0.9303 (mp) cc_final: 0.9046 (mt) REVERT: A 357 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8656 (tm-30) REVERT: A 394 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9034 (tt) REVERT: B 52 GLU cc_start: 0.7806 (pm20) cc_final: 0.7385 (pm20) REVERT: B 323 LEU cc_start: 0.9340 (tp) cc_final: 0.9042 (tt) REVERT: B 335 ASP cc_start: 0.8442 (t0) cc_final: 0.8007 (t0) REVERT: B 343 ASN cc_start: 0.9082 (m-40) cc_final: 0.8790 (m110) REVERT: B 383 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8666 (tptm) REVERT: D 292 LEU cc_start: 0.9515 (tp) cc_final: 0.9244 (tt) REVERT: E 267 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7794 (mp0) outliers start: 187 outliers final: 158 residues processed: 605 average time/residue: 0.4786 time to fit residues: 492.3777 Evaluate side-chains 633 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 463 time to evaluate : 4.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 91 VAL Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 124 THR Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain 7 residue 32 PHE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 39 LEU Chi-restraints excluded: chain 6 residue 83 ASP Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain U residue 29 HIS Chi-restraints excluded: chain U residue 31 TYR Chi-restraints excluded: chain U residue 57 ASP Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 65 CYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 30 PHE Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain 8 residue 23 LEU Chi-restraints excluded: chain 8 residue 27 PHE Chi-restraints excluded: chain 8 residue 32 LEU Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 127 LEU Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 328 HIS Chi-restraints excluded: chain F residue 345 TYR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 393 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 315 optimal weight: 6.9990 chunk 422 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 365 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 397 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 407 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 98 HIS ** G 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.088418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.063742 restraints weight = 184923.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063711 restraints weight = 111289.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.064280 restraints weight = 81372.795| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.299 39530 Z= 0.367 Angle : 0.845 59.192 53555 Z= 0.429 Chirality : 0.047 0.690 6345 Planarity : 0.005 0.058 6837 Dihedral : 5.872 171.203 5483 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 27.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 4.14 % Allowed : 30.99 % Favored : 64.88 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.12), residues: 5060 helix: 0.51 (0.10), residues: 2651 sheet: -1.08 (0.24), residues: 499 loop : -0.96 (0.15), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP X 126 HIS 0.012 0.001 HIS F 328 PHE 0.044 0.002 PHE R 55 TYR 0.091 0.002 TYR 6 7 ARG 0.009 0.000 ARG 7 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9224.40 seconds wall clock time: 169 minutes 29.82 seconds (10169.82 seconds total)