Starting phenix.real_space_refine on Tue Apr 16 10:03:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f39_28835/04_2024/8f39_28835_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f39_28835/04_2024/8f39_28835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f39_28835/04_2024/8f39_28835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f39_28835/04_2024/8f39_28835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f39_28835/04_2024/8f39_28835_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f39_28835/04_2024/8f39_28835_updated.pdb" } resolution = 3.5 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 10 5.49 5 Mg 4 5.21 5 S 100 5.16 5 C 24788 2.51 5 N 6540 2.21 5 O 7325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 112": "OD1" <-> "OD2" Residue "G PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 266": "OE1" <-> "OE2" Residue "Z TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 69": "OD1" <-> "OD2" Residue "7 GLU 96": "OE1" <-> "OE2" Residue "7 GLU 150": "OE1" <-> "OE2" Residue "6 GLU 41": "OE1" <-> "OE2" Residue "6 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X ASP 67": "OD1" <-> "OD2" Residue "Y ASP 34": "OD1" <-> "OD2" Residue "Y PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 66": "OD1" <-> "OD2" Residue "Y ASP 72": "OD1" <-> "OD2" Residue "Y PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 130": "OD1" <-> "OD2" Residue "Y GLU 138": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 271": "OD1" <-> "OD2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ASP 124": "OD1" <-> "OD2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 299": "OD1" <-> "OD2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 465": "OD1" <-> "OD2" Residue "E PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E ASP 330": "OD1" <-> "OD2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "F TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F ASP 349": "OD1" <-> "OD2" Residue "F TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 376": "OE1" <-> "OE2" Residue "F TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "I PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38767 Number of models: 1 Model: "" Number of chains: 32 Chain: "G" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2032 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "Z" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 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: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1772 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} 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: "Y" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1254 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} 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: {'PCIS': 1, 'PTRANS': 22, '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: "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: "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: "E" 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: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.55, per 1000 atoms: 0.53 Number of scatterers: 38767 At special positions: 0 Unit cell: (130, 149, 237, 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 10 15.00 Mg 4 11.99 O 7325 8.00 N 6540 7.00 C 24788 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 Atom "HETATM38737 O5' ADP E 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.14 Conformation dependent library (CDL) restraints added in 7.5 seconds 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9318 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 178 helices and 27 sheets defined 53.3% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.64 Creating SS restraints... Processing helix chain 'G' and resid 6 through 54 removed outlier: 5.250A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ALA G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 101 removed outlier: 4.054A pdb=" N LEU G 91 " --> pdb=" O ILE G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 185 through 188 No H-bonds generated for 'chain 'G' and resid 185 through 188' Processing helix chain 'G' and resid 205 through 273 Processing helix chain 'Z' and resid 56 through 113 removed outlier: 3.797A pdb=" N LEU Z 63 " --> pdb=" O LEU Z 59 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY Z 64 " --> pdb=" O LEU Z 60 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.566A pdb=" N ARG Z 84 " --> pdb=" O PHE Z 80 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN Z 112 " --> pdb=" O ASP Z 108 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU Z 113 " --> pdb=" O SER Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 185 removed outlier: 3.969A pdb=" N VAL Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS Z 128 " --> pdb=" O PHE Z 124 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU Z 134 " --> pdb=" O THR Z 130 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER Z 135 " --> pdb=" O VAL Z 131 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU Z 136 " --> pdb=" O GLU Z 132 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA Z 137 " --> pdb=" O LEU Z 133 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN Z 142 " --> pdb=" O PHE Z 138 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS Z 143 " --> pdb=" O GLU Z 139 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE Z 177 " --> pdb=" O ALA Z 173 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER Z 178 " --> pdb=" O LYS Z 174 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU Z 183 " --> pdb=" O ARG Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 191 through 206 removed outlier: 3.683A pdb=" N SER Z 206 " --> pdb=" O GLU Z 202 " (cutoff:3.500A) Processing helix chain '7' and resid 5 through 19 removed outlier: 4.025A pdb=" N LEU 7 19 " --> pdb=" O VAL 7 15 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 47 Processing helix chain '7' and resid 68 through 77 Processing helix chain '7' and resid 91 through 126 removed outlier: 3.979A pdb=" N SER 7 126 " --> pdb=" O ASP 7 122 " (cutoff:3.500A) Processing helix chain '7' and resid 135 through 141 Processing helix chain '7' and resid 143 through 155 Processing helix chain '6' and resid 5 through 16 removed outlier: 3.768A pdb=" N ARG 6 9 " --> pdb=" O ASP 6 5 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU 6 10 " --> pdb=" O LEU 6 6 " (cutoff:3.500A) Processing helix chain '6' and resid 46 through 50 Processing helix chain '6' and resid 76 through 91 removed outlier: 3.768A pdb=" N GLU 6 90 " --> pdb=" O GLU 6 86 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER 6 91 " --> pdb=" O GLU 6 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 27 removed outlier: 3.941A pdb=" N LYS U 22 " --> pdb=" O ALA U 18 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 54 Processing helix chain 'U' and resid 64 through 84 removed outlier: 4.195A pdb=" N SER U 79 " --> pdb=" O ALA U 75 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N MET U 80 " --> pdb=" O PHE U 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 39 removed outlier: 4.238A pdb=" N ILE S 17 " --> pdb=" O GLY S 13 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLY S 18 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU S 20 " --> pdb=" O THR S 16 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 73 removed outlier: 4.492A pdb=" N ASP S 45 " --> pdb=" O SER S 42 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE S 48 " --> pdb=" O ASP S 45 " (cutoff:3.500A) Proline residue: S 49 - end of helix removed outlier: 3.567A pdb=" N PHE S 55 " --> pdb=" O ILE S 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 39 removed outlier: 3.627A pdb=" N ILE T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLY T 18 " --> pdb=" O ILE T 14 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU T 19 " --> pdb=" O SER T 15 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU T 20 " --> pdb=" O THR T 16 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLY T 21 " --> pdb=" O ILE T 17 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA T 22 " --> pdb=" O GLY T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 73 removed outlier: 3.736A pdb=" N LYS T 44 " --> pdb=" O PRO T 41 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP T 45 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE T 48 " --> pdb=" O ASP T 45 " (cutoff:3.500A) Proline residue: T 49 - end of helix Processing helix chain 'K' and resid 2 through 39 removed outlier: 4.185A pdb=" N ILE K 17 " --> pdb=" O GLY K 13 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLY K 18 " --> pdb=" O ILE K 14 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU K 19 " --> pdb=" O SER K 15 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY K 21 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 74 removed outlier: 3.802A pdb=" N LYS K 44 " --> pdb=" O PRO K 41 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP K 45 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE K 48 " --> pdb=" O ASP K 45 " (cutoff:3.500A) Proline residue: K 49 - end of helix removed outlier: 4.005A pdb=" N PHE K 74 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 39 removed outlier: 3.563A pdb=" N THR L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE L 17 " --> pdb=" O GLY L 13 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLY L 18 " --> pdb=" O ILE L 14 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU L 19 " --> pdb=" O SER L 15 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY L 21 " --> pdb=" O ILE L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 73 removed outlier: 4.143A pdb=" N LYS L 44 " --> pdb=" O PRO L 41 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP L 45 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE L 48 " --> pdb=" O ASP L 45 " (cutoff:3.500A) Proline residue: L 49 - end of helix Processing helix chain 'M' and resid 2 through 39 removed outlier: 4.202A pdb=" N ILE M 17 " --> pdb=" O GLY M 13 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY M 18 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU M 19 " --> pdb=" O SER M 15 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 73 Proline residue: M 49 - end of helix removed outlier: 3.946A pdb=" N THR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY M 62 " --> pdb=" O SER M 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 39 removed outlier: 4.294A pdb=" N ILE N 17 " --> pdb=" O GLY N 13 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLY N 18 " --> pdb=" O ILE N 14 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY N 21 " --> pdb=" O ILE N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 71 removed outlier: 3.514A pdb=" N ASP N 45 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE N 48 " --> pdb=" O ASP N 45 " (cutoff:3.500A) Proline residue: N 49 - end of helix removed outlier: 3.589A pdb=" N LEU N 71 " --> pdb=" O VAL N 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 39 removed outlier: 3.655A pdb=" N THR O 16 " --> pdb=" O ALA O 12 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE O 17 " --> pdb=" O GLY O 13 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLY O 18 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU O 19 " --> pdb=" O SER O 15 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU O 20 " --> pdb=" O THR O 16 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY O 21 " --> pdb=" O ILE O 17 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA O 22 " --> pdb=" O GLY O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 71 removed outlier: 3.779A pdb=" N ASP O 45 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE O 48 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Proline residue: O 49 - end of helix Processing helix chain 'P' and resid 2 through 39 removed outlier: 4.389A pdb=" N ILE P 17 " --> pdb=" O GLY P 13 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLY P 18 " --> pdb=" O ILE P 14 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU P 19 " --> pdb=" O SER P 15 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU P 20 " --> pdb=" O THR P 16 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY P 21 " --> pdb=" O ILE P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 74 removed outlier: 4.053A pdb=" N ASP P 45 " --> pdb=" O SER P 42 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE P 48 " --> pdb=" O ASP P 45 " (cutoff:3.500A) Proline residue: P 49 - end of helix removed outlier: 3.537A pdb=" N GLU P 59 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE P 74 " --> pdb=" O LEU P 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 39 removed outlier: 4.868A pdb=" N GLY Q 18 " --> pdb=" O ILE Q 14 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU Q 19 " --> pdb=" O SER Q 15 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU Q 20 " --> pdb=" O THR Q 16 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLY Q 21 " --> pdb=" O ILE Q 17 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 71 removed outlier: 4.558A pdb=" N ASP Q 45 " --> pdb=" O SER Q 42 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE Q 48 " --> pdb=" O ASP Q 45 " (cutoff:3.500A) Proline residue: Q 49 - end of helix removed outlier: 3.916A pdb=" N LEU Q 71 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 39 removed outlier: 3.615A pdb=" N THR R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE R 17 " --> pdb=" O GLY R 13 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY R 18 " --> pdb=" O ILE R 14 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU R 19 " --> pdb=" O SER R 15 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY R 21 " --> pdb=" O ILE R 17 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 73 removed outlier: 4.382A pdb=" N ASP R 45 " --> pdb=" O SER R 42 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE R 48 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Proline residue: R 49 - end of helix removed outlier: 3.571A pdb=" N GLU R 59 " --> pdb=" O ALA R 56 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 46 removed outlier: 4.995A 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 28 through 45 removed outlier: 3.748A pdb=" N TYR X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 77 Processing helix chain 'X' and resid 82 through 101 Proline residue: X 87 - end of helix Processing helix chain 'X' and resid 111 through 113 No H-bonds generated for 'chain 'X' and resid 111 through 113' Processing helix chain 'X' and resid 116 through 136 Processing helix chain 'X' and resid 138 through 145 Processing helix chain 'X' and resid 152 through 172 Proline residue: X 156 - end of helix removed outlier: 3.645A pdb=" N ILE X 171 " --> pdb=" O PHE X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 174 through 194 removed outlier: 5.799A pdb=" N SER X 179 " --> pdb=" O LEU X 175 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 246 Proline residue: X 212 - end of helix Processing helix chain 'J' and resid 14 through 31 Processing helix chain 'Y' and resid 18 through 30 removed outlier: 3.976A pdb=" N ASN Y 30 " --> pdb=" O ALA Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 49 Processing helix chain 'Y' and resid 51 through 54 No H-bonds generated for 'chain 'Y' and resid 51 through 54' Processing helix chain 'Y' and resid 64 through 74 Processing helix chain 'Y' and resid 85 through 93 Processing helix chain 'Y' and resid 101 through 114 Processing helix chain 'Y' and resid 138 through 148 Processing helix chain 'Y' and resid 160 through 171 Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' 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 178 through 192 removed outlier: 3.815A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.616A 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 261 Proline residue: A 249 - end of helix removed outlier: 3.691A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 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 308 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 377 through 380 No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 392 through 405 removed outlier: 4.329A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 4.338A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 460 through 476 removed outlier: 3.504A pdb=" N ILE A 463 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 493 through 507 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 153 through 158 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.996A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.942A 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 262 Proline residue: B 249 - end of helix removed outlier: 3.546A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 286 Processing helix chain 'B' and resid 298 through 310 removed outlier: 4.216A pdb=" N PHE B 301 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR B 302 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 309 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 310 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 383 through 386 No H-bonds generated for 'chain 'B' and resid 383 through 386' Processing helix chain 'B' and resid 395 through 404 Processing helix chain 'B' and resid 414 through 429 Processing helix chain 'B' and resid 440 through 449 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.554A pdb=" N GLY B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 467 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' 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 158 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.776A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.761A 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 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 262 Proline residue: C 249 - end of helix removed outlier: 3.695A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 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 300 through 309 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 Processing helix chain 'C' and resid 383 through 407 removed outlier: 3.987A pdb=" N GLY C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN C 407 " --> pdb=" O ALA C 403 " (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: 5.278A pdb=" N GLY C 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 488 Processing helix chain 'C' and resid 493 through 508 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 141 through 144 No H-bonds generated for 'chain 'D' and resid 141 through 144' Processing helix chain 'D' and resid 163 through 177 Processing helix chain 'D' and resid 193 through 203 Processing helix chain 'D' and resid 228 through 247 removed outlier: 4.359A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 269 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 326 Processing helix chain 'D' and resid 365 through 390 removed outlier: 4.518A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 5.293A 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 419 through 425 removed outlier: 4.291A pdb=" N VAL D 423 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR D 425 " --> pdb=" O GLU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 446 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 463 through 477 Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 163 through 177 removed outlier: 4.416A pdb=" N LYS E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA E 177 " --> pdb=" O ASN E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 226 through 245 removed outlier: 4.593A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 271 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 283 through 295 removed outlier: 4.456A pdb=" N ALA E 286 " --> pdb=" O PRO E 283 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP E 288 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU E 294 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 327 removed outlier: 4.321A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.592A pdb=" N LEU E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 363 No H-bonds generated for 'chain 'E' and resid 360 through 363' Processing helix chain 'E' and resid 367 through 390 removed outlier: 4.642A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.266A 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 419 through 425 removed outlier: 3.951A pdb=" N GLU E 422 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL E 423 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR E 425 " --> pdb=" O GLU E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'E' and resid 454 through 457 Processing helix chain 'E' and resid 463 through 475 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: 4.302A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 226 through 245 removed outlier: 4.491A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 271 removed outlier: 3.756A pdb=" N ALA F 270 " --> pdb=" O GLU F 267 " (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 295 removed outlier: 3.881A pdb=" N ARG F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) 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 328 removed outlier: 4.288A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 365 through 390 removed outlier: 5.123A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 398 through 414 Processing helix chain 'F' and resid 419 through 425 removed outlier: 3.701A pdb=" N GLU F 422 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL F 423 " --> pdb=" O VAL F 420 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR F 425 " --> pdb=" O GLU F 422 " (cutoff:3.500A) 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 helix chain 'H' and resid 99 through 114 removed outlier: 4.051A pdb=" N ASN H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 137 removed outlier: 3.628A pdb=" N ALA H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE H 125 " --> pdb=" O ALA H 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 23 removed outlier: 3.803A pdb=" N ILE I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 38 Processing helix chain 'I' and resid 48 through 51 No H-bonds generated for 'chain 'I' and resid 48 through 51' Processing sheet with id= A, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.654A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE A 78 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY A 63 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 101 Processing sheet with id= C, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.607A pdb=" N ASP A 271 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 208 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.719A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.119A pdb=" N PHE B 44 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL B 33 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 55 through 57 Processing sheet with id= G, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= H, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.378A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 231 through 236 removed outlier: 8.539A pdb=" N ILE B 232 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS B 265 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL B 204 " --> pdb=" O HIS B 265 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B 267 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL B 206 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 269 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL B 208 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER B 322 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE B 268 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR B 324 " --> pdb=" O ILE B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.324A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE C 44 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL C 33 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 98 through 101 Processing sheet with id= L, first strand: chain 'C' and resid 108 through 110 removed outlier: 4.017A pdb=" N ARG C 108 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 169 through 172 Processing sheet with id= N, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.310A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D 46 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 84 through 87 removed outlier: 3.509A pdb=" N LYS D 115 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 152 through 155 removed outlier: 7.948A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.371A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.546A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 215 through 217 removed outlier: 6.318A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU E 252 " --> pdb=" O VAL E 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'F' and resid 9 through 12 removed outlier: 4.783A pdb=" N ILE F 9 " --> pdb=" O ASP F 78 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS F 75 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS F 40 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR F 41 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N HIS F 24 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL F 13 " --> pdb=" O HIS F 24 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 84 through 87 removed outlier: 4.314A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 306 through 311 removed outlier: 6.842A pdb=" N ALA F 331 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE F 156 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR F 333 " --> pdb=" O PHE F 156 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 215 through 220 removed outlier: 7.146A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL F 187 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.741A pdb=" N SER H 25 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA H 15 " --> pdb=" O VAL H 85 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 49 through 52 removed outlier: 4.250A pdb=" N GLY H 73 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 56 through 60 removed outlier: 3.611A pdb=" N LYS H 66 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 43 through 45 1958 hydrogen bonds defined for protein. 4971 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: 15.18 Time building geometry restraints manager: 18.40 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: 10966 1.33 - 1.46: 6357 1.46 - 1.58: 21867 1.58 - 1.70: 19 1.70 - 1.82: 184 Bond restraints: 39393 Sorted by residual: bond pdb=" CG PRO G 123 " pdb=" CD PRO G 123 " ideal model delta sigma weight residual 1.503 1.319 0.184 3.40e-02 8.65e+02 2.91e+01 bond pdb=" CB PRO G 123 " pdb=" CG PRO G 123 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.59e+00 bond pdb=" N PRO G 123 " pdb=" CA PRO G 123 " ideal model delta sigma weight residual 1.473 1.435 0.037 1.33e-02 5.65e+03 7.87e+00 bond pdb=" N PRO G 123 " pdb=" CD PRO G 123 " ideal model delta sigma weight residual 1.473 1.505 -0.032 1.40e-02 5.10e+03 5.28e+00 bond pdb=" CB GLU A 294 " pdb=" CG GLU A 294 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.58e+00 ... (remaining 39388 not shown) Histogram of bond angle deviations from ideal: 92.51 - 101.27: 59 101.27 - 110.02: 4938 110.02 - 118.78: 27493 118.78 - 127.54: 20621 127.54 - 136.29: 259 Bond angle restraints: 53370 Sorted by residual: angle pdb=" CA PRO G 123 " pdb=" N PRO G 123 " pdb=" CD PRO G 123 " ideal model delta sigma weight residual 112.00 92.84 19.16 1.40e+00 5.10e-01 1.87e+02 angle pdb=" CA MET X 72 " pdb=" CB MET X 72 " pdb=" CG MET X 72 " ideal model delta sigma weight residual 114.10 132.11 -18.01 2.00e+00 2.50e-01 8.11e+01 angle pdb=" N PRO G 123 " pdb=" CD PRO G 123 " pdb=" CG PRO G 123 " ideal model delta sigma weight residual 103.20 92.51 10.69 1.50e+00 4.44e-01 5.08e+01 angle pdb=" CA PRO 6 40 " pdb=" N PRO 6 40 " pdb=" CD PRO 6 40 " ideal model delta sigma weight residual 112.00 102.67 9.33 1.40e+00 5.10e-01 4.44e+01 angle pdb=" C SER E 123 " pdb=" CA SER E 123 " pdb=" CB SER E 123 " ideal model delta sigma weight residual 116.63 110.47 6.16 1.16e+00 7.43e-01 2.82e+01 ... (remaining 53365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.81: 23049 32.81 - 65.63: 652 65.63 - 98.44: 68 98.44 - 131.26: 2 131.26 - 164.07: 3 Dihedral angle restraints: 23774 sinusoidal: 9258 harmonic: 14516 Sorted by residual: dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 104.07 -164.07 1 2.00e+01 2.50e-03 4.71e+01 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 -108.81 -159.65 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 77.10 -137.10 1 2.00e+01 2.50e-03 4.16e+01 ... (remaining 23771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5583 0.069 - 0.137: 708 0.137 - 0.206: 24 0.206 - 0.274: 5 0.274 - 0.343: 2 Chirality restraints: 6322 Sorted by residual: chirality pdb=" C1' ADP E 501 " pdb=" C2' ADP E 501 " pdb=" N9 ADP E 501 " pdb=" O4' ADP E 501 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CG LEU 7 114 " pdb=" CB LEU 7 114 " pdb=" CD1 LEU 7 114 " pdb=" CD2 LEU 7 114 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE C 345 " pdb=" CA ILE C 345 " pdb=" CG1 ILE C 345 " pdb=" CG2 ILE C 345 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 6319 not shown) Planarity restraints: 6814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS G 122 " -0.120 5.00e-02 4.00e+02 1.65e-01 4.35e+01 pdb=" N PRO G 123 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO G 123 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO G 123 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 6 39 " -0.083 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO 6 40 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO 6 40 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO 6 40 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Q 40 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO Q 41 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO Q 41 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO Q 41 " -0.062 5.00e-02 4.00e+02 ... (remaining 6811 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 392 2.54 - 3.13: 32899 3.13 - 3.72: 68277 3.72 - 4.31: 91089 4.31 - 4.90: 147555 Nonbonded interactions: 340212 Sorted by model distance: nonbonded pdb=" O2B ADP B 601 " pdb="MG MG B 602 " model vdw 1.955 2.170 nonbonded pdb=" O3B ADP A 601 " pdb="MG MG A 602 " model vdw 2.006 2.170 nonbonded pdb=" OG1 THR B 30 " pdb=" O VAL B 90 " model vdw 2.031 2.440 nonbonded pdb=" O3B ADP C 601 " pdb="MG MG C 602 " model vdw 2.036 2.170 nonbonded pdb=" O ALA 7 39 " pdb=" NE2 GLN 7 42 " model vdw 2.074 2.520 ... (remaining 340207 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.170 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 106.990 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.280 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 39393 Z= 0.216 Angle : 0.741 19.162 53370 Z= 0.379 Chirality : 0.044 0.343 6322 Planarity : 0.005 0.165 6814 Dihedral : 15.477 164.071 14456 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.16 % Favored : 94.63 % Rotamer: Outliers : 0.22 % Allowed : 16.09 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 5042 helix: 1.22 (0.10), residues: 2613 sheet: -0.74 (0.25), residues: 454 loop : -0.91 (0.15), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 234 HIS 0.010 0.001 HIS D 328 PHE 0.042 0.001 PHE 7 32 TYR 0.049 0.001 TYR 7 58 ARG 0.011 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 591 time to evaluate : 4.694 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: G 136 ASP cc_start: 0.7715 (m-30) cc_final: 0.7513 (m-30) REVERT: Z 128 LYS cc_start: 0.2761 (mmmt) cc_final: 0.2141 (mmtt) REVERT: K 39 ARG cc_start: 0.7869 (ptm160) cc_final: 0.7365 (ptm-80) REVERT: Y 81 LEU cc_start: 0.9410 (mm) cc_final: 0.9105 (mp) REVERT: A 52 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8020 (mm-30) REVERT: A 294 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 335 ASP cc_start: 0.8742 (t0) cc_final: 0.8536 (t0) REVERT: C 396 LEU cc_start: 0.9730 (OUTLIER) cc_final: 0.9507 (mm) REVERT: D 291 LEU cc_start: 0.9385 (mm) cc_final: 0.9166 (mm) REVERT: E 420 VAL cc_start: 0.9410 (m) cc_final: 0.9138 (p) REVERT: E 458 TYR cc_start: 0.8502 (t80) cc_final: 0.8278 (t80) REVERT: F 200 GLU cc_start: 0.9046 (tt0) cc_final: 0.8800 (tm-30) REVERT: F 201 MET cc_start: 0.9331 (mtt) cc_final: 0.9113 (mtm) outliers start: 9 outliers final: 6 residues processed: 596 average time/residue: 0.5100 time to fit residues: 501.6873 Evaluate side-chains 508 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 501 time to evaluate : 4.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 8 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 385 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 5.9990 chunk 377 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 390 optimal weight: 1.9990 chunk 151 optimal weight: 40.0000 chunk 237 optimal weight: 8.9990 chunk 290 optimal weight: 0.0870 chunk 452 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 196 GLN 7 118 GLN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 ASN P 40 ASN Y 68 ASN ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 GLN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 39393 Z= 0.237 Angle : 0.634 14.114 53370 Z= 0.318 Chirality : 0.042 0.256 6322 Planarity : 0.005 0.069 6814 Dihedral : 6.251 158.066 5480 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.04 % Favored : 94.72 % Rotamer: Outliers : 2.48 % Allowed : 15.67 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.18 (0.12), residues: 5042 helix: 1.04 (0.10), residues: 2620 sheet: -0.84 (0.24), residues: 473 loop : -0.82 (0.15), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP X 82 HIS 0.007 0.001 HIS G 88 PHE 0.029 0.001 PHE 7 32 TYR 0.029 0.001 TYR G 226 ARG 0.005 0.000 ARG Z 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 521 time to evaluate : 4.664 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 237 MET cc_start: 0.6938 (mmt) cc_final: 0.6330 (mmt) REVERT: Z 128 LYS cc_start: 0.2659 (mmmt) cc_final: 0.2274 (mmtt) REVERT: Z 151 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7678 (ptpt) REVERT: Z 166 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8359 (mm-40) REVERT: U 4 LEU cc_start: 0.4973 (OUTLIER) cc_final: 0.4525 (tt) REVERT: K 39 ARG cc_start: 0.7862 (ptm160) cc_final: 0.7318 (ttp80) REVERT: L 50 MET cc_start: -0.0735 (OUTLIER) cc_final: -0.1092 (mmt) REVERT: X 70 MET cc_start: 0.4770 (OUTLIER) cc_final: 0.3571 (tmm) REVERT: Y 81 LEU cc_start: 0.9403 (mm) cc_final: 0.9103 (mp) REVERT: Y 90 LYS cc_start: 0.9540 (mmtt) cc_final: 0.9180 (mttt) REVERT: Y 107 ASP cc_start: 0.9126 (m-30) cc_final: 0.8843 (m-30) REVERT: Y 116 ASN cc_start: 0.8589 (t0) cc_final: 0.8374 (t0) REVERT: A 89 LEU cc_start: 0.9010 (tp) cc_final: 0.8800 (tp) REVERT: A 294 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8362 (tm-30) REVERT: B 82 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.8038 (ttm110) REVERT: B 240 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8292 (mt-10) REVERT: B 299 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8066 (p0) REVERT: B 335 ASP cc_start: 0.8834 (t0) cc_final: 0.8612 (t0) REVERT: B 355 GLU cc_start: 0.8150 (pm20) cc_final: 0.7487 (pm20) REVERT: B 357 GLU cc_start: 0.8775 (tp30) cc_final: 0.8508 (tp30) REVERT: B 442 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8809 (mp0) REVERT: C 90 VAL cc_start: 0.9494 (OUTLIER) cc_final: 0.9269 (p) REVERT: C 396 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9502 (mm) REVERT: D 191 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7855 (p) REVERT: D 291 LEU cc_start: 0.9470 (mm) cc_final: 0.9060 (mm) REVERT: D 375 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8792 (mm-40) REVERT: E 339 ILE cc_start: 0.9527 (mt) cc_final: 0.9020 (mt) REVERT: E 420 VAL cc_start: 0.9459 (m) cc_final: 0.9212 (p) REVERT: F 189 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7266 (mm-30) REVERT: F 200 GLU cc_start: 0.9054 (tt0) cc_final: 0.8808 (tm-30) REVERT: F 256 ASP cc_start: 0.8596 (t0) cc_final: 0.8382 (t0) outliers start: 102 outliers final: 51 residues processed: 593 average time/residue: 0.4874 time to fit residues: 484.1175 Evaluate side-chains 526 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 466 time to evaluate : 5.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 74 TYR Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 8 LEU Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain X residue 70 MET Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 38 GLN Chi-restraints excluded: chain Y residue 66 ASP Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 10.0000 chunk 140 optimal weight: 50.0000 chunk 376 optimal weight: 9.9990 chunk 307 optimal weight: 0.9990 chunk 124 optimal weight: 40.0000 chunk 453 optimal weight: 5.9990 chunk 489 optimal weight: 40.0000 chunk 403 optimal weight: 9.9990 chunk 449 optimal weight: 6.9990 chunk 154 optimal weight: 40.0000 chunk 363 optimal weight: 0.6980 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 ASN O 35 ASN ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 478 HIS B 282 GLN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 39393 Z= 0.346 Angle : 0.662 11.355 53370 Z= 0.331 Chirality : 0.043 0.171 6322 Planarity : 0.005 0.054 6814 Dihedral : 6.074 158.970 5472 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.39 % Favored : 94.37 % Rotamer: Outliers : 3.45 % Allowed : 15.58 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.09 (0.12), residues: 5042 helix: 0.90 (0.10), residues: 2620 sheet: -0.89 (0.23), residues: 497 loop : -0.75 (0.15), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP X 82 HIS 0.006 0.001 HIS F 367 PHE 0.026 0.002 PHE X 198 TYR 0.026 0.002 TYR K 9 ARG 0.004 0.000 ARG Y 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 484 time to evaluate : 4.772 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: G 8 MET cc_start: 0.8475 (ppp) cc_final: 0.8225 (ppp) REVERT: G 250 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.8232 (ttp-110) REVERT: Z 128 LYS cc_start: 0.2770 (mmmt) cc_final: 0.2347 (mmtt) REVERT: Z 151 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7819 (ptpt) REVERT: Z 166 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8389 (mm-40) REVERT: U 4 LEU cc_start: 0.4996 (OUTLIER) cc_final: 0.4544 (tt) REVERT: K 39 ARG cc_start: 0.7939 (ptm160) cc_final: 0.7427 (ptm-80) REVERT: L 50 MET cc_start: -0.0455 (OUTLIER) cc_final: -0.1056 (mmt) REVERT: Y 68 ASN cc_start: 0.9554 (m-40) cc_final: 0.9277 (m110) REVERT: Y 81 LEU cc_start: 0.9442 (mm) cc_final: 0.9145 (mp) REVERT: Y 90 LYS cc_start: 0.9564 (OUTLIER) cc_final: 0.9189 (mttt) REVERT: Y 107 ASP cc_start: 0.9134 (m-30) cc_final: 0.8735 (m-30) REVERT: A 89 LEU cc_start: 0.9126 (tp) cc_final: 0.8897 (tp) REVERT: B 82 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.8029 (ttm110) REVERT: B 240 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8334 (mt-10) REVERT: B 271 ASP cc_start: 0.8830 (t70) cc_final: 0.8428 (t0) REVERT: B 299 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8186 (p0) REVERT: B 335 ASP cc_start: 0.8987 (t0) cc_final: 0.8718 (t0) REVERT: B 355 GLU cc_start: 0.8308 (pm20) cc_final: 0.7906 (pm20) REVERT: B 357 GLU cc_start: 0.8785 (tp30) cc_final: 0.8396 (tp30) REVERT: B 442 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8820 (mp0) REVERT: C 396 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9504 (mm) REVERT: D 291 LEU cc_start: 0.9485 (mm) cc_final: 0.9034 (mm) REVERT: D 311 TYR cc_start: 0.9018 (t80) cc_final: 0.8641 (t80) REVERT: D 375 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8848 (mm-40) REVERT: E 458 TYR cc_start: 0.8879 (t80) cc_final: 0.8618 (t80) REVERT: F 189 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7652 (mm-30) REVERT: F 200 GLU cc_start: 0.9085 (tt0) cc_final: 0.8880 (tm-30) REVERT: F 201 MET cc_start: 0.9547 (mtt) cc_final: 0.9287 (mtt) outliers start: 142 outliers final: 71 residues processed: 585 average time/residue: 0.4992 time to fit residues: 491.8567 Evaluate side-chains 513 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 435 time to evaluate : 4.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 8 LEU Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain T residue 40 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 48 PHE Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 50 optimal weight: 40.0000 chunk 216 optimal weight: 0.9990 chunk 304 optimal weight: 5.9990 chunk 454 optimal weight: 6.9990 chunk 481 optimal weight: 30.0000 chunk 237 optimal weight: 4.9990 chunk 430 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN F 52 GLN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 39393 Z= 0.228 Angle : 0.625 12.515 53370 Z= 0.309 Chirality : 0.042 0.187 6322 Planarity : 0.004 0.054 6814 Dihedral : 6.144 157.599 5472 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.36 % Favored : 94.41 % Rotamer: Outliers : 3.01 % Allowed : 17.04 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: 0.03 (0.12), residues: 5042 helix: 0.84 (0.10), residues: 2615 sheet: -0.91 (0.24), residues: 491 loop : -0.76 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 82 HIS 0.007 0.001 HIS E 367 PHE 0.024 0.001 PHE N 30 TYR 0.023 0.001 TYR D 242 ARG 0.005 0.000 ARG S 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 497 time to evaluate : 4.621 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: G 8 MET cc_start: 0.8377 (ppp) cc_final: 0.8073 (ppp) REVERT: G 9 ARG cc_start: 0.8469 (tmm-80) cc_final: 0.8202 (tmm-80) REVERT: G 124 ASN cc_start: 0.9358 (t0) cc_final: 0.8894 (p0) REVERT: G 222 MET cc_start: 0.8598 (tmm) cc_final: 0.8303 (tmm) REVERT: G 247 MET cc_start: 0.8850 (ttt) cc_final: 0.8592 (ttt) REVERT: G 250 ARG cc_start: 0.8437 (ttp-110) cc_final: 0.8193 (ttp-110) REVERT: G 262 VAL cc_start: 0.8886 (p) cc_final: 0.8425 (p) REVERT: Z 128 LYS cc_start: 0.2597 (mmmt) cc_final: 0.2193 (mmtt) REVERT: Z 151 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7820 (ptpt) REVERT: Z 166 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8326 (mm-40) REVERT: U 4 LEU cc_start: 0.4953 (OUTLIER) cc_final: 0.4493 (tt) REVERT: K 39 ARG cc_start: 0.7946 (ptm160) cc_final: 0.7443 (ptm-80) REVERT: L 50 MET cc_start: -0.0551 (OUTLIER) cc_final: -0.1142 (mmt) REVERT: Y 68 ASN cc_start: 0.9539 (m-40) cc_final: 0.9151 (m110) REVERT: Y 81 LEU cc_start: 0.9404 (mm) cc_final: 0.9118 (mp) REVERT: Y 90 LYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9175 (mttt) REVERT: Y 107 ASP cc_start: 0.9179 (m-30) cc_final: 0.8651 (m-30) REVERT: B 67 ASN cc_start: 0.8845 (m110) cc_final: 0.8389 (m-40) REVERT: B 82 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.7998 (ttm110) REVERT: B 240 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8332 (mt-10) REVERT: B 271 ASP cc_start: 0.8809 (t70) cc_final: 0.8408 (t70) REVERT: B 294 GLU cc_start: 0.8806 (pm20) cc_final: 0.8572 (pm20) REVERT: B 299 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8121 (p0) REVERT: B 335 ASP cc_start: 0.8996 (t0) cc_final: 0.8737 (t0) REVERT: B 355 GLU cc_start: 0.8251 (pm20) cc_final: 0.7788 (pm20) REVERT: B 357 GLU cc_start: 0.8680 (tp30) cc_final: 0.8274 (tp30) REVERT: B 471 LEU cc_start: 0.9469 (mm) cc_final: 0.9230 (mm) REVERT: C 173 ARG cc_start: 0.9549 (OUTLIER) cc_final: 0.8538 (ptp90) REVERT: C 178 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8875 (m) REVERT: C 204 VAL cc_start: 0.9832 (t) cc_final: 0.9542 (m) REVERT: C 331 THR cc_start: 0.9663 (OUTLIER) cc_final: 0.9314 (t) REVERT: D 257 ASN cc_start: 0.8643 (t0) cc_final: 0.8212 (t0) REVERT: D 281 TYR cc_start: 0.7805 (m-80) cc_final: 0.7442 (m-80) REVERT: D 291 LEU cc_start: 0.9469 (mm) cc_final: 0.9002 (mm) REVERT: D 311 TYR cc_start: 0.9004 (t80) cc_final: 0.8581 (t80) REVERT: D 375 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8816 (mm-40) REVERT: E 299 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8749 (p) REVERT: F 189 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7570 (mm-30) REVERT: F 400 ASP cc_start: 0.8920 (m-30) cc_final: 0.8610 (m-30) outliers start: 124 outliers final: 73 residues processed: 586 average time/residue: 0.5228 time to fit residues: 515.4463 Evaluate side-chains 533 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 451 time to evaluate : 4.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain T residue 40 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 48 PHE Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 6 optimal weight: 40.0000 chunk 358 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 410 optimal weight: 0.9990 chunk 332 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 432 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN G 260 GLN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 118 GLN ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 ASN ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 39393 Z= 0.322 Angle : 0.656 11.011 53370 Z= 0.325 Chirality : 0.043 0.247 6322 Planarity : 0.004 0.055 6814 Dihedral : 6.086 156.987 5468 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 3.45 % Allowed : 18.30 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.00 (0.12), residues: 5042 helix: 0.81 (0.10), residues: 2631 sheet: -1.00 (0.23), residues: 491 loop : -0.74 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 82 HIS 0.006 0.001 HIS E 367 PHE 0.024 0.001 PHE K 48 TYR 0.027 0.002 TYR C 270 ARG 0.004 0.000 ARG Y 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 462 time to evaluate : 4.481 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: G 8 MET cc_start: 0.8406 (ppp) cc_final: 0.8114 (ppp) REVERT: G 9 ARG cc_start: 0.8521 (tmm-80) cc_final: 0.8304 (tmm-80) REVERT: G 124 ASN cc_start: 0.9368 (t0) cc_final: 0.8929 (p0) REVERT: G 222 MET cc_start: 0.8596 (tmm) cc_final: 0.8260 (tmm) REVERT: G 262 VAL cc_start: 0.8865 (p) cc_final: 0.8647 (p) REVERT: Z 128 LYS cc_start: 0.2601 (mmmt) cc_final: 0.2388 (mmtt) REVERT: Z 166 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8346 (mm-40) REVERT: Z 203 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6673 (tp-100) REVERT: U 4 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4529 (tt) REVERT: K 39 ARG cc_start: 0.7984 (ptm160) cc_final: 0.7478 (ptm-80) REVERT: L 50 MET cc_start: -0.0594 (OUTLIER) cc_final: -0.1197 (mmt) REVERT: 8 10 MET cc_start: -0.0076 (ptm) cc_final: -0.0410 (tmm) REVERT: Y 81 LEU cc_start: 0.9419 (mm) cc_final: 0.9141 (mp) REVERT: Y 90 LYS cc_start: 0.9557 (OUTLIER) cc_final: 0.9179 (mttt) REVERT: Y 107 ASP cc_start: 0.9195 (m-30) cc_final: 0.8679 (m-30) REVERT: B 82 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7935 (ttm110) REVERT: B 299 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8100 (p0) REVERT: B 335 ASP cc_start: 0.9059 (t0) cc_final: 0.8792 (t0) REVERT: B 355 GLU cc_start: 0.8305 (pm20) cc_final: 0.7792 (pm20) REVERT: B 357 GLU cc_start: 0.8684 (tp30) cc_final: 0.8231 (tp30) REVERT: B 442 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8789 (mp0) REVERT: C 178 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9006 (m) REVERT: C 270 TYR cc_start: 0.8882 (m-10) cc_final: 0.8324 (m-80) REVERT: C 331 THR cc_start: 0.9650 (OUTLIER) cc_final: 0.9329 (t) REVERT: C 401 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8679 (mp0) REVERT: D 281 TYR cc_start: 0.8169 (m-80) cc_final: 0.7707 (m-80) REVERT: D 311 TYR cc_start: 0.9079 (t80) cc_final: 0.8753 (t80) REVERT: D 375 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8832 (mm-40) REVERT: E 299 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8763 (p) REVERT: F 68 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8620 (mm-30) REVERT: F 74 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8654 (mm-30) REVERT: F 189 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7538 (mm-30) REVERT: F 400 ASP cc_start: 0.8914 (m-30) cc_final: 0.8591 (m-30) outliers start: 142 outliers final: 89 residues processed: 563 average time/residue: 0.5010 time to fit residues: 471.3337 Evaluate side-chains 527 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 427 time to evaluate : 4.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 100 MET Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain T residue 40 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 55 PHE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 48 PHE Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 163 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 161 optimal weight: 50.0000 chunk 433 optimal weight: 0.7980 chunk 95 optimal weight: 50.0000 chunk 282 optimal weight: 0.9990 chunk 118 optimal weight: 30.0000 chunk 481 optimal weight: 0.1980 chunk 399 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 260 GLN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 29 GLN Y 68 ASN ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39393 Z= 0.179 Angle : 0.631 11.907 53370 Z= 0.310 Chirality : 0.042 0.295 6322 Planarity : 0.004 0.087 6814 Dihedral : 6.025 156.462 5468 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.65 % Favored : 94.07 % Rotamer: Outliers : 2.89 % Allowed : 18.98 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % 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: -0.00 (0.12), residues: 5042 helix: 0.82 (0.10), residues: 2616 sheet: -0.93 (0.23), residues: 502 loop : -0.77 (0.15), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 82 HIS 0.008 0.001 HIS E 367 PHE 0.021 0.001 PHE S 55 TYR 0.027 0.001 TYR D 242 ARG 0.005 0.000 ARG S 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 515 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: G 8 MET cc_start: 0.8327 (ppp) cc_final: 0.8005 (ppp) REVERT: G 124 ASN cc_start: 0.9327 (t0) cc_final: 0.8926 (p0) REVERT: G 222 MET cc_start: 0.8555 (tmm) cc_final: 0.8210 (tmm) REVERT: G 250 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8176 (ptp90) REVERT: G 262 VAL cc_start: 0.8810 (p) cc_final: 0.8548 (p) REVERT: Z 128 LYS cc_start: 0.2618 (mmmt) cc_final: 0.2417 (mmtt) REVERT: U 4 LEU cc_start: 0.4899 (OUTLIER) cc_final: 0.4536 (tt) REVERT: K 39 ARG cc_start: 0.7965 (ptm160) cc_final: 0.7445 (ptm-80) REVERT: L 50 MET cc_start: -0.0677 (OUTLIER) cc_final: -0.1018 (mmm) REVERT: N 1 MET cc_start: 0.6007 (mmm) cc_final: 0.5799 (mmm) REVERT: 8 10 MET cc_start: -0.0372 (ptm) cc_final: -0.0668 (tmm) REVERT: Y 68 ASN cc_start: 0.9532 (m-40) cc_final: 0.9233 (m110) REVERT: Y 81 LEU cc_start: 0.9383 (mm) cc_final: 0.9098 (mp) REVERT: Y 90 LYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9156 (mttt) REVERT: A 355 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7464 (mm-30) REVERT: B 82 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.7898 (ttm110) REVERT: B 240 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8304 (mt-10) REVERT: B 286 LEU cc_start: 0.9512 (mp) cc_final: 0.9303 (mp) REVERT: B 294 GLU cc_start: 0.8852 (pm20) cc_final: 0.8577 (pm20) REVERT: B 299 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8061 (p0) REVERT: B 335 ASP cc_start: 0.9031 (t0) cc_final: 0.8787 (t0) REVERT: B 355 GLU cc_start: 0.8223 (pm20) cc_final: 0.7728 (pm20) REVERT: B 357 GLU cc_start: 0.8598 (tp30) cc_final: 0.8106 (tp30) REVERT: C 13 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7741 (mp) REVERT: C 178 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8827 (m) REVERT: C 270 TYR cc_start: 0.8818 (m-10) cc_final: 0.8245 (m-80) REVERT: C 331 THR cc_start: 0.9681 (OUTLIER) cc_final: 0.9356 (t) REVERT: D 200 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8389 (mm-30) REVERT: D 257 ASN cc_start: 0.8710 (t0) cc_final: 0.8199 (t0) REVERT: D 281 TYR cc_start: 0.8079 (m-80) cc_final: 0.7658 (m-80) REVERT: D 291 LEU cc_start: 0.9489 (mm) cc_final: 0.9036 (mm) REVERT: D 311 TYR cc_start: 0.9071 (t80) cc_final: 0.8620 (t80) REVERT: D 318 THR cc_start: 0.9589 (p) cc_final: 0.9357 (t) REVERT: D 352 ASP cc_start: 0.9179 (m-30) cc_final: 0.8852 (p0) REVERT: D 375 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8803 (mm-40) REVERT: E 299 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8735 (p) REVERT: E 324 THR cc_start: 0.9649 (m) cc_final: 0.9391 (p) REVERT: F 189 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7358 (mm-30) REVERT: F 400 ASP cc_start: 0.8921 (m-30) cc_final: 0.8599 (m-30) outliers start: 119 outliers final: 78 residues processed: 597 average time/residue: 0.4586 time to fit residues: 455.9299 Evaluate side-chains 541 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 454 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 57 HIS Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 100 MET Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain T residue 40 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 MET Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 55 PHE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 48 PHE Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain X residue 77 ILE Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 351 optimal weight: 9.9990 chunk 272 optimal weight: 3.9990 chunk 405 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 479 optimal weight: 9.9990 chunk 300 optimal weight: 4.9990 chunk 292 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: