Starting phenix.real_space_refine on Sun Feb 18 17:05:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/02_2024/7tap_25780_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/02_2024/7tap_25780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/02_2024/7tap_25780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/02_2024/7tap_25780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/02_2024/7tap_25780_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tap_25780/02_2024/7tap_25780_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.325 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 14821 2.51 5 N 3558 2.21 5 O 3998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "N ASP 248": "OD1" <-> "OD2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 47": "OD1" <-> "OD2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "H TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 137": "OE1" <-> "OE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 105": "OD1" <-> "OD2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22520 Number of models: 1 Model: "" Number of chains: 22 Chain: "D" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1145 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1473 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 195} Chain: "N" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 400 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 570 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2802 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 335} Chain: "A" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6089 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'KJL': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'KJL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.85, per 1000 atoms: 0.53 Number of scatterers: 22520 At special positions: 0 Unit cell: (123.6, 121.54, 133.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 143 16.00 O 3998 8.00 N 3558 7.00 C 14821 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 17 " - pdb=" SG CYS E 75 " distance=2.08 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 75 " distance=2.05 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 75 " distance=2.06 Simple disulfide: pdb=" SG CYS H 17 " - pdb=" SG CYS H 75 " distance=2.07 Simple disulfide: pdb=" SG CYS I 17 " - pdb=" SG CYS I 75 " distance=2.05 Simple disulfide: pdb=" SG CYS J 17 " - pdb=" SG CYS J 75 " distance=2.07 Simple disulfide: pdb=" SG CYS K 17 " - pdb=" SG CYS K 75 " distance=2.05 Simple disulfide: pdb=" SG CYS L 17 " - pdb=" SG CYS L 75 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.01 Conformation dependent library (CDL) restraints added in 4.0 seconds 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 3 sheets defined 73.7% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'D' and resid 15 through 50 removed outlier: 3.605A pdb=" N GLY D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 58 through 83 removed outlier: 3.974A pdb=" N ILE D 61 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Proline residue: D 62 - end of helix removed outlier: 3.560A pdb=" N MET D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR D 72 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 74 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 75 " --> pdb=" O TYR D 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 76 " --> pdb=" O GLY D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 126 Processing helix chain 'D' and resid 131 through 163 removed outlier: 3.524A pdb=" N PHE D 134 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 135 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 141 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 144 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D 150 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 153 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 154 " --> pdb=" O GLY D 151 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 161 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER D 163 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 38 Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 56 through 90 Processing helix chain 'C' and resid 94 through 124 removed outlier: 4.061A pdb=" N THR C 98 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN C 100 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE C 102 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS C 107 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C 109 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C 110 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 111 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 115 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 123 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 176 Processing helix chain 'C' and resid 178 through 205 removed outlier: 4.376A pdb=" N VAL C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 194 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 245 Processing helix chain 'N' and resid 251 through 253 No H-bonds generated for 'chain 'N' and resid 251 through 253' Processing helix chain 'M' and resid 4 through 24 Processing helix chain 'M' and resid 30 through 54 Processing helix chain 'E' and resid 9 through 43 removed outlier: 3.812A pdb=" N GLY E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 21 " --> pdb=" O CYS E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 53 removed outlier: 4.796A pdb=" N PHE E 51 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 77 removed outlier: 3.614A pdb=" N ILE E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 119 Processing helix chain 'E' and resid 123 through 153 removed outlier: 3.879A pdb=" N VAL E 127 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 131 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA E 136 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR E 142 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 146 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 150 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN E 151 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER E 152 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 32 removed outlier: 4.234A pdb=" N GLY O 20 " --> pdb=" O LEU O 16 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE O 23 " --> pdb=" O PHE O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 39 No H-bonds generated for 'chain 'O' and resid 36 through 39' Processing helix chain 'O' and resid 48 through 74 Processing helix chain 'F' and resid 9 through 43 removed outlier: 3.836A pdb=" N GLY F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE F 21 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 55 through 76 removed outlier: 3.752A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 119 Processing helix chain 'F' and resid 123 through 151 removed outlier: 3.698A pdb=" N VAL F 127 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR F 142 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 148 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 150 " --> pdb=" O ALA F 147 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN F 151 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 43 removed outlier: 3.812A pdb=" N GLY G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE G 21 " --> pdb=" O CYS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 55 through 75 removed outlier: 3.659A pdb=" N ILE G 63 " --> pdb=" O MET G 59 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 119 Processing helix chain 'G' and resid 123 through 151 removed outlier: 3.729A pdb=" N VAL G 127 " --> pdb=" O ARG G 124 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA G 136 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU G 141 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR G 142 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE G 145 " --> pdb=" O TYR G 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 43 removed outlier: 3.831A pdb=" N GLY H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE H 21 " --> pdb=" O CYS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 55 through 76 removed outlier: 3.670A pdb=" N ILE H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 119 Processing helix chain 'H' and resid 123 through 154 removed outlier: 3.759A pdb=" N VAL H 127 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE H 130 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H 131 " --> pdb=" O GLY H 128 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE H 132 " --> pdb=" O MET H 129 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE H 135 " --> pdb=" O ILE H 132 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA H 136 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY H 140 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU H 141 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR H 142 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 148 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU H 149 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN H 151 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER H 152 " --> pdb=" O LEU H 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 42 removed outlier: 3.816A pdb=" N GLY I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE I 21 " --> pdb=" O CYS I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 52 through 76 removed outlier: 3.721A pdb=" N VAL I 55 " --> pdb=" O LYS I 52 " (cutoff:3.500A) Proline residue: I 56 - end of helix removed outlier: 3.670A pdb=" N ALA I 60 " --> pdb=" O VAL I 57 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE I 62 " --> pdb=" O MET I 59 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL I 69 " --> pdb=" O TYR I 66 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL I 70 " --> pdb=" O GLY I 67 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER I 71 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL I 72 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU I 73 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL I 74 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS I 75 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR I 76 " --> pdb=" O LEU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 119 Processing helix chain 'I' and resid 123 through 153 removed outlier: 3.853A pdb=" N VAL I 127 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR I 142 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE I 145 " --> pdb=" O TYR I 142 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER I 152 " --> pdb=" O LEU I 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 43 removed outlier: 3.737A pdb=" N GLY J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 55 through 75 removed outlier: 4.000A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 119 Processing helix chain 'J' and resid 123 through 153 removed outlier: 3.877A pdb=" N VAL J 127 " --> pdb=" O ARG J 124 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR J 142 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL J 146 " --> pdb=" O GLY J 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU J 150 " --> pdb=" O ALA J 147 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN J 151 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER J 152 " --> pdb=" O LEU J 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 43 removed outlier: 3.704A pdb=" N GLY K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE K 21 " --> pdb=" O CYS K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 53 removed outlier: 4.592A pdb=" N PHE K 51 " --> pdb=" O ASP K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 76 removed outlier: 3.768A pdb=" N ILE K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 119 removed outlier: 3.606A pdb=" N ALA K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 151 removed outlier: 3.674A pdb=" N VAL K 127 " --> pdb=" O ARG K 124 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA K 136 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU K 137 " --> pdb=" O ILE K 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL K 138 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY K 140 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU K 149 " --> pdb=" O VAL K 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 43 removed outlier: 3.902A pdb=" N GLY L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 55 through 75 Processing helix chain 'L' and resid 84 through 119 Processing helix chain 'L' and resid 123 through 154 removed outlier: 3.544A pdb=" N VAL L 127 " --> pdb=" O ARG L 124 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE L 135 " --> pdb=" O ILE L 132 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA L 136 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU L 137 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL L 138 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE L 145 " --> pdb=" O TYR L 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 removed outlier: 4.219A pdb=" N ASN B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE B 8 " --> pdb=" O VAL B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 39 through 48 removed outlier: 3.595A pdb=" N SER B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 86 Processing helix chain 'B' and resid 90 through 115 removed outlier: 4.006A pdb=" N GLY B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 174 through 198 Processing helix chain 'B' and resid 204 through 229 removed outlier: 3.734A pdb=" N GLN B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 262 through 271 removed outlier: 3.814A pdb=" N ASN B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 284 through 300 Processing helix chain 'B' and resid 306 through 331 removed outlier: 3.755A pdb=" N ALA B 311 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP B 312 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 314 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B 315 " --> pdb=" O TRP B 312 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 316 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 317 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 320 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 36 removed outlier: 4.404A pdb=" N ARG A 27 " --> pdb=" O GLN A 23 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 56 through 78 Processing helix chain 'A' and resid 104 through 146 Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 193 through 207 removed outlier: 4.161A pdb=" N ALA A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 267 through 325 removed outlier: 4.106A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 360 removed outlier: 4.317A pdb=" N ALA A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 removed outlier: 4.217A pdb=" N TYR A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 423 removed outlier: 4.489A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 426 through 441 removed outlier: 3.536A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 462 through 479 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 528 through 561 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.648A pdb=" N ILE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 601 No H-bonds generated for 'chain 'A' and resid 598 through 601' Processing helix chain 'A' and resid 608 through 617 removed outlier: 3.621A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 658 Proline residue: A 646 - end of helix removed outlier: 5.176A pdb=" N LYS A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Proline residue: A 653 - end of helix Processing helix chain 'A' and resid 707 through 754 removed outlier: 3.913A pdb=" N VAL A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 734 " --> pdb=" O THR A 730 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 760 Processing helix chain 'A' and resid 763 through 783 Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 806 through 809 No H-bonds generated for 'chain 'A' and resid 806 through 809' Processing sheet with id= A, first strand: chain 'A' and resid 369 through 371 removed outlier: 4.221A pdb=" N LEU A 16 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 334 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 258 through 261 removed outlier: 4.358A pdb=" N THR A 188 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 222 through 224 1606 hydrogen bonds defined for protein. 4047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.73 Time building geometry restraints manager: 10.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3501 1.27 - 1.41: 5746 1.41 - 1.55: 13358 1.55 - 1.69: 167 1.69 - 1.82: 204 Bond restraints: 22976 Sorted by residual: bond pdb=" C SER G 96 " pdb=" O SER G 96 " ideal model delta sigma weight residual 1.236 1.135 0.101 1.16e-02 7.43e+03 7.62e+01 bond pdb=" C LEU I 141 " pdb=" O LEU I 141 " ideal model delta sigma weight residual 1.237 1.135 0.102 1.17e-02 7.31e+03 7.54e+01 bond pdb=" C ILE G 134 " pdb=" O ILE G 134 " ideal model delta sigma weight residual 1.237 1.141 0.097 1.17e-02 7.31e+03 6.83e+01 bond pdb=" C ILE K 134 " pdb=" O ILE K 134 " ideal model delta sigma weight residual 1.237 1.140 0.096 1.19e-02 7.06e+03 6.57e+01 bond pdb=" C ILE E 134 " pdb=" O ILE E 134 " ideal model delta sigma weight residual 1.237 1.142 0.095 1.19e-02 7.06e+03 6.38e+01 ... (remaining 22971 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.12: 269 104.12 - 111.69: 10451 111.69 - 119.27: 8589 119.27 - 126.84: 11665 126.84 - 134.41: 228 Bond angle restraints: 31202 Sorted by residual: angle pdb=" CA ALA F 20 " pdb=" C ALA F 20 " pdb=" O ALA F 20 " ideal model delta sigma weight residual 120.82 112.05 8.77 1.05e+00 9.07e-01 6.98e+01 angle pdb=" CA ALA H 20 " pdb=" C ALA H 20 " pdb=" O ALA H 20 " ideal model delta sigma weight residual 120.82 112.49 8.33 1.05e+00 9.07e-01 6.30e+01 angle pdb=" CA ALA E 20 " pdb=" C ALA E 20 " pdb=" O ALA E 20 " ideal model delta sigma weight residual 120.82 112.68 8.14 1.05e+00 9.07e-01 6.01e+01 angle pdb=" N LEU L 68 " pdb=" CA LEU L 68 " pdb=" C LEU L 68 " ideal model delta sigma weight residual 112.23 102.59 9.64 1.26e+00 6.30e-01 5.86e+01 angle pdb=" CA GLU G 137 " pdb=" C GLU G 137 " pdb=" N VAL G 138 " ideal model delta sigma weight residual 117.30 125.78 -8.48 1.16e+00 7.43e-01 5.34e+01 ... (remaining 31197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 12878 24.54 - 49.07: 608 49.07 - 73.61: 118 73.61 - 98.14: 38 98.14 - 122.68: 4 Dihedral angle restraints: 13646 sinusoidal: 5372 harmonic: 8274 Sorted by residual: dihedral pdb=" CB CYS I 17 " pdb=" SG CYS I 17 " pdb=" SG CYS I 75 " pdb=" CB CYS I 75 " ideal model delta sinusoidal sigma weight residual -86.00 -167.40 81.40 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS E 17 " pdb=" SG CYS E 17 " pdb=" SG CYS E 75 " pdb=" CB CYS E 75 " ideal model delta sinusoidal sigma weight residual -86.00 -165.14 79.14 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CB CYS G 17 " pdb=" SG CYS G 17 " pdb=" SG CYS G 75 " pdb=" CB CYS G 75 " ideal model delta sinusoidal sigma weight residual -86.00 -129.63 43.63 1 1.00e+01 1.00e-02 2.65e+01 ... (remaining 13643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2950 0.074 - 0.148: 570 0.148 - 0.223: 145 0.223 - 0.297: 28 0.297 - 0.371: 18 Chirality restraints: 3711 Sorted by residual: chirality pdb=" CB THR I 24 " pdb=" CA THR I 24 " pdb=" OG1 THR I 24 " pdb=" CG2 THR I 24 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" C09 KJL F 201 " pdb=" C08 KJL F 201 " pdb=" C10 KJL F 201 " pdb=" O48 KJL F 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.74 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C09 KJL E 201 " pdb=" C08 KJL E 201 " pdb=" C10 KJL E 201 " pdb=" O48 KJL E 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.74 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3708 not shown) Planarity restraints: 3879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 67 " 0.025 2.00e-02 2.50e+03 5.18e-02 2.68e+01 pdb=" C GLY G 67 " -0.090 2.00e-02 2.50e+03 pdb=" O GLY G 67 " 0.033 2.00e-02 2.50e+03 pdb=" N LEU G 68 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY K 67 " -0.025 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C GLY K 67 " 0.088 2.00e-02 2.50e+03 pdb=" O GLY K 67 " -0.033 2.00e-02 2.50e+03 pdb=" N LEU K 68 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 71 " -0.023 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C SER L 71 " 0.084 2.00e-02 2.50e+03 pdb=" O SER L 71 " -0.032 2.00e-02 2.50e+03 pdb=" N VAL L 72 " -0.029 2.00e-02 2.50e+03 ... (remaining 3876 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3514 2.76 - 3.30: 24347 3.30 - 3.83: 40365 3.83 - 4.37: 52706 4.37 - 4.90: 85132 Nonbonded interactions: 206064 Sorted by model distance: nonbonded pdb=" OG SER B 315 " pdb=" OH TYR B 345 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR A 116 " pdb=" NH1 ARG A 120 " model vdw 2.238 2.520 nonbonded pdb=" O LEU A 38 " pdb=" OH TYR A 817 " model vdw 2.240 2.440 nonbonded pdb=" O LEU N 254 " pdb=" NE2 GLN K 121 " model vdw 2.250 2.520 nonbonded pdb=" O ASP A 224 " pdb=" N ARG A 228 " model vdw 2.251 2.520 ... (remaining 206059 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 'E' and resid 1 through 159) selection = (chain 'F' and resid 1 through 159) selection = (chain 'G' and resid 1 through 159) selection = (chain 'H' and resid 1 through 159) selection = (chain 'I' and resid 1 through 159) selection = (chain 'J' and resid 1 through 159) selection = chain 'K' selection = chain 'L' } 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 individual isotropic 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.280 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 58.760 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.170 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.013 0.134 22976 Z= 0.830 Angle : 1.473 14.522 31202 Z= 1.031 Chirality : 0.069 0.371 3711 Planarity : 0.008 0.084 3879 Dihedral : 15.279 122.681 8370 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.28 % Favored : 98.65 % Rotamer: Outliers : 1.37 % Allowed : 3.59 % Favored : 95.05 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.35 % 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: 0.26 (0.15), residues: 2881 helix: 0.31 (0.11), residues: 2131 sheet: -0.63 (0.78), residues: 42 loop : 0.24 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 312 HIS 0.009 0.001 HIS A 801 PHE 0.029 0.002 PHE L 23 TYR 0.026 0.002 TYR F 66 ARG 0.007 0.001 ARG K 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 328 time to evaluate : 2.168 Fit side-chains REVERT: D 40 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7730 (tttp) REVERT: C 134 TYR cc_start: 0.8927 (m-80) cc_final: 0.8605 (m-80) REVERT: M 43 MET cc_start: 0.7303 (mtp) cc_final: 0.7023 (mtp) REVERT: G 19 SER cc_start: 0.8750 (m) cc_final: 0.8421 (m) REVERT: G 58 ILE cc_start: 0.8746 (mt) cc_final: 0.8325 (mt) REVERT: G 59 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8495 (mmt) REVERT: H 59 MET cc_start: 0.8748 (mmt) cc_final: 0.8010 (mmt) REVERT: H 131 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7929 (tp) REVERT: J 59 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8040 (mmm) REVERT: L 30 TYR cc_start: 0.8676 (t80) cc_final: 0.8472 (t80) REVERT: B 185 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: B 186 LYS cc_start: 0.8377 (tttm) cc_final: 0.8017 (tttt) REVERT: B 194 ASN cc_start: 0.7340 (m-40) cc_final: 0.6849 (m-40) outliers start: 32 outliers final: 3 residues processed: 350 average time/residue: 1.1071 time to fit residues: 452.7303 Evaluate side-chains 268 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 260 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain J residue 59 MET Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain B residue 185 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 72 optimal weight: 0.0770 chunk 143 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 151 ASN A 210 ASN A 442 ASN A 499 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22976 Z= 0.209 Angle : 0.529 5.682 31202 Z= 0.282 Chirality : 0.039 0.149 3711 Planarity : 0.004 0.058 3879 Dihedral : 10.027 120.591 3645 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.18 % Favored : 98.79 % Rotamer: Outliers : 2.18 % Allowed : 8.88 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.16), residues: 2881 helix: 1.30 (0.11), residues: 2107 sheet: -0.54 (0.72), residues: 52 loop : 0.15 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 737 HIS 0.003 0.001 HIS A 801 PHE 0.029 0.002 PHE C 80 TYR 0.015 0.001 TYR D 127 ARG 0.007 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 280 time to evaluate : 2.334 Fit side-chains REVERT: D 94 ASN cc_start: 0.8302 (t0) cc_final: 0.8090 (t160) REVERT: C 134 TYR cc_start: 0.8980 (m-80) cc_final: 0.8632 (m-80) REVERT: E 129 MET cc_start: 0.8449 (ttp) cc_final: 0.8164 (ttp) REVERT: G 8 TYR cc_start: 0.8707 (p90) cc_final: 0.8480 (p90) REVERT: G 131 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7359 (mp) REVERT: H 59 MET cc_start: 0.8366 (mmt) cc_final: 0.7838 (mmt) REVERT: K 131 LEU cc_start: 0.8373 (tp) cc_final: 0.7901 (mm) REVERT: B 185 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: B 194 ASN cc_start: 0.7304 (m-40) cc_final: 0.6751 (m-40) REVERT: B 313 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7542 (tpt) REVERT: A 23 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6883 (tt0) REVERT: A 195 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.6828 (mtpp) REVERT: A 746 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8413 (mp) REVERT: A 762 ARG cc_start: 0.7386 (mmt-90) cc_final: 0.6657 (mmp80) REVERT: A 804 GLU cc_start: 0.8322 (mp0) cc_final: 0.8005 (mp0) outliers start: 51 outliers final: 10 residues processed: 310 average time/residue: 1.1688 time to fit residues: 422.2495 Evaluate side-chains 263 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 247 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 746 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 255 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 253 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 ASN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN B 334 GLN A 210 ASN A 499 HIS A 533 ASN A 634 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 22976 Z= 0.416 Angle : 0.603 9.258 31202 Z= 0.313 Chirality : 0.043 0.271 3711 Planarity : 0.005 0.053 3879 Dihedral : 9.550 115.116 3627 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.70 % Favored : 98.26 % Rotamer: Outliers : 2.78 % Allowed : 11.19 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.98 (0.15), residues: 2881 helix: 1.03 (0.11), residues: 2131 sheet: -0.66 (0.79), residues: 38 loop : -0.17 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 340 HIS 0.008 0.001 HIS D 98 PHE 0.029 0.002 PHE C 80 TYR 0.015 0.002 TYR L 30 ARG 0.006 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 282 time to evaluate : 2.534 Fit side-chains REVERT: D 23 CYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8204 (m) REVERT: G 131 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7460 (mp) REVERT: H 157 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6600 (t70) REVERT: J 3 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6616 (tm-30) REVERT: K 124 ARG cc_start: 0.8745 (mtp180) cc_final: 0.8503 (mtp180) REVERT: K 127 VAL cc_start: 0.8491 (t) cc_final: 0.8199 (p) REVERT: K 131 LEU cc_start: 0.8414 (tp) cc_final: 0.8027 (mm) REVERT: L 46 ARG cc_start: 0.8258 (mmm-85) cc_final: 0.7910 (mtp180) REVERT: L 82 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7885 (pt0) REVERT: B 14 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.6845 (tp30) REVERT: B 123 ILE cc_start: 0.7977 (mt) cc_final: 0.7739 (mp) REVERT: B 145 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7563 (tp) REVERT: B 175 MET cc_start: 0.6220 (mmm) cc_final: 0.5974 (mpp) REVERT: B 194 ASN cc_start: 0.7451 (m-40) cc_final: 0.6797 (m-40) REVERT: B 313 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7543 (tpt) REVERT: A 23 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: A 195 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.6950 (mtpp) REVERT: A 746 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8536 (mp) REVERT: A 761 PHE cc_start: 0.7714 (m-10) cc_final: 0.7453 (m-10) REVERT: A 762 ARG cc_start: 0.7438 (mmt-90) cc_final: 0.6782 (mmp80) outliers start: 65 outliers final: 22 residues processed: 322 average time/residue: 1.2076 time to fit residues: 451.8523 Evaluate side-chains 302 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 269 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain A residue 776 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 132 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 256 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 243 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 ASN C 100 ASN E 82 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 258 GLN A 210 ASN A 442 ASN A 499 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22976 Z= 0.183 Angle : 0.468 7.693 31202 Z= 0.250 Chirality : 0.037 0.148 3711 Planarity : 0.004 0.045 3879 Dihedral : 8.927 111.342 3627 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.15 % Favored : 98.82 % Rotamer: Outliers : 2.09 % Allowed : 13.24 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.15), residues: 2881 helix: 1.28 (0.11), residues: 2131 sheet: -0.60 (0.77), residues: 42 loop : -0.06 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 737 HIS 0.003 0.000 HIS A 801 PHE 0.025 0.001 PHE C 80 TYR 0.014 0.001 TYR L 30 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 288 time to evaluate : 2.628 Fit side-chains REVERT: D 23 CYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8044 (m) REVERT: C 134 TYR cc_start: 0.9012 (m-80) cc_final: 0.8717 (m-80) REVERT: K 127 VAL cc_start: 0.8402 (t) cc_final: 0.8112 (p) REVERT: L 46 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.8005 (mtp180) REVERT: B 145 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7435 (tp) REVERT: B 194 ASN cc_start: 0.7433 (m-40) cc_final: 0.6792 (m-40) REVERT: B 313 MET cc_start: 0.7915 (mmm) cc_final: 0.7578 (tpt) REVERT: A 27 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7956 (ttp80) REVERT: A 195 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.6914 (mtpp) REVERT: A 247 LYS cc_start: 0.8295 (tppt) cc_final: 0.8086 (tppp) REVERT: A 746 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 761 PHE cc_start: 0.7694 (m-10) cc_final: 0.7417 (m-10) REVERT: A 762 ARG cc_start: 0.7477 (mmt-90) cc_final: 0.6877 (mmp80) outliers start: 49 outliers final: 14 residues processed: 318 average time/residue: 1.1567 time to fit residues: 429.9284 Evaluate side-chains 291 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 272 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 746 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 0.0050 chunk 231 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 258 GLN A 210 ASN A 442 ASN A 499 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 22976 Z= 0.245 Angle : 0.499 11.513 31202 Z= 0.262 Chirality : 0.038 0.202 3711 Planarity : 0.004 0.045 3879 Dihedral : 8.877 113.069 3627 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.33 % Rotamer: Outliers : 2.60 % Allowed : 14.09 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.15), residues: 2881 helix: 1.29 (0.11), residues: 2128 sheet: -0.49 (0.81), residues: 36 loop : -0.08 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 737 HIS 0.005 0.001 HIS A 801 PHE 0.025 0.002 PHE C 80 TYR 0.012 0.001 TYR A 300 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 277 time to evaluate : 2.415 Fit side-chains REVERT: D 23 CYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8094 (m) REVERT: C 53 ARG cc_start: 0.8689 (mtp180) cc_final: 0.8460 (mtt-85) REVERT: C 134 TYR cc_start: 0.9035 (m-80) cc_final: 0.8800 (m-80) REVERT: G 131 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7454 (mp) REVERT: H 131 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7376 (tp) REVERT: J 3 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6806 (tt0) REVERT: K 52 LYS cc_start: 0.8486 (ptmt) cc_final: 0.8281 (ptpt) REVERT: K 127 VAL cc_start: 0.8419 (t) cc_final: 0.8166 (p) REVERT: L 46 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.7974 (mtp180) REVERT: B 145 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7494 (tp) REVERT: B 194 ASN cc_start: 0.7430 (m-40) cc_final: 0.6801 (m-40) REVERT: B 313 MET cc_start: 0.7923 (mmm) cc_final: 0.7569 (tpt) REVERT: A 27 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7828 (ttp80) REVERT: A 195 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.6971 (mtpp) REVERT: A 746 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8477 (mp) outliers start: 61 outliers final: 23 residues processed: 316 average time/residue: 1.1523 time to fit residues: 427.0608 Evaluate side-chains 297 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 266 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 748 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 271 optimal weight: 0.7980 chunk 225 optimal weight: 8.9990 chunk 125 optimal weight: 0.5980 chunk 22 optimal weight: 0.0470 chunk 89 optimal weight: 2.9990 chunk 142 optimal weight: 0.0050 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN B 244 ASN B 258 GLN A 210 ASN A 442 ASN A 499 HIS A 634 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22976 Z= 0.161 Angle : 0.454 9.532 31202 Z= 0.241 Chirality : 0.037 0.146 3711 Planarity : 0.004 0.044 3879 Dihedral : 8.463 110.625 3627 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.18 % Favored : 98.79 % Rotamer: Outliers : 2.22 % Allowed : 14.90 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.15), residues: 2881 helix: 1.44 (0.11), residues: 2137 sheet: -0.45 (0.78), residues: 42 loop : 0.00 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 204 HIS 0.003 0.000 HIS A 801 PHE 0.023 0.001 PHE B 254 TYR 0.020 0.001 TYR L 66 ARG 0.007 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 292 time to evaluate : 2.566 Fit side-chains REVERT: D 23 CYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8028 (m) REVERT: C 53 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8359 (mtt-85) REVERT: C 134 TYR cc_start: 0.8919 (m-80) cc_final: 0.8587 (m-80) REVERT: J 3 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: K 127 VAL cc_start: 0.8280 (t) cc_final: 0.8076 (p) REVERT: L 46 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.7992 (mtp180) REVERT: B 50 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7606 (t0) REVERT: B 112 THR cc_start: 0.8383 (m) cc_final: 0.7996 (m) REVERT: B 145 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7470 (tp) REVERT: B 194 ASN cc_start: 0.7432 (m-40) cc_final: 0.6811 (m-40) REVERT: B 313 MET cc_start: 0.7911 (mmm) cc_final: 0.7564 (tpt) REVERT: A 27 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7761 (ttp80) REVERT: A 369 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7378 (tm-30) REVERT: A 499 HIS cc_start: 0.6833 (t70) cc_final: 0.6329 (t-90) REVERT: A 746 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8435 (mp) outliers start: 52 outliers final: 22 residues processed: 325 average time/residue: 1.0812 time to fit residues: 415.4394 Evaluate side-chains 310 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 282 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 746 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 165 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN B 258 GLN A 210 ASN A 442 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22976 Z= 0.204 Angle : 0.480 7.801 31202 Z= 0.252 Chirality : 0.037 0.210 3711 Planarity : 0.004 0.043 3879 Dihedral : 8.399 112.286 3627 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.28 % Favored : 98.68 % Rotamer: Outliers : 2.35 % Allowed : 15.50 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.15), residues: 2881 helix: 1.46 (0.11), residues: 2134 sheet: -0.39 (0.82), residues: 36 loop : 0.02 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 204 HIS 0.004 0.000 HIS A 801 PHE 0.032 0.001 PHE A 774 TYR 0.021 0.001 TYR L 66 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 288 time to evaluate : 2.511 Fit side-chains REVERT: D 23 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8055 (m) REVERT: C 53 ARG cc_start: 0.8622 (mtp180) cc_final: 0.8393 (mtt-85) REVERT: C 134 TYR cc_start: 0.8969 (m-80) cc_final: 0.8708 (m-80) REVERT: J 3 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: K 127 VAL cc_start: 0.8318 (t) cc_final: 0.8093 (p) REVERT: L 46 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.8161 (mtp180) REVERT: B 50 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7658 (t0) REVERT: B 145 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7482 (tp) REVERT: B 194 ASN cc_start: 0.7418 (m-40) cc_final: 0.6836 (m-40) REVERT: B 313 MET cc_start: 0.7919 (mmm) cc_final: 0.7517 (tpt) REVERT: A 27 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7784 (ttp80) REVERT: A 126 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7402 (p0) REVERT: A 195 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7041 (mtpp) REVERT: A 201 GLN cc_start: 0.7393 (tp40) cc_final: 0.6846 (mt0) REVERT: A 369 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7319 (tm-30) REVERT: A 499 HIS cc_start: 0.6848 (t70) cc_final: 0.6318 (t-90) REVERT: A 753 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7240 (mmm) outliers start: 55 outliers final: 26 residues processed: 316 average time/residue: 1.1422 time to fit residues: 421.6505 Evaluate side-chains 314 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 280 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 753 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 3.9990 chunk 108 optimal weight: 0.0370 chunk 161 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 258 GLN A 210 ASN A 442 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22976 Z= 0.175 Angle : 0.465 7.058 31202 Z= 0.245 Chirality : 0.037 0.175 3711 Planarity : 0.004 0.042 3879 Dihedral : 8.172 111.563 3627 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.18 % Favored : 98.79 % Rotamer: Outliers : 1.96 % Allowed : 16.01 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.15), residues: 2881 helix: 1.52 (0.11), residues: 2132 sheet: -0.66 (0.78), residues: 38 loop : 0.06 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 204 HIS 0.003 0.000 HIS A 801 PHE 0.025 0.001 PHE B 254 TYR 0.027 0.001 TYR L 66 ARG 0.008 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 295 time to evaluate : 2.423 Fit side-chains REVERT: D 23 CYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8035 (m) REVERT: C 53 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8364 (mtt-85) REVERT: C 134 TYR cc_start: 0.8945 (m-80) cc_final: 0.8618 (m-80) REVERT: E 50 LEU cc_start: 0.7989 (tt) cc_final: 0.7697 (tp) REVERT: K 44 VAL cc_start: 0.8765 (t) cc_final: 0.8511 (m) REVERT: K 127 VAL cc_start: 0.8343 (t) cc_final: 0.8116 (p) REVERT: L 46 ARG cc_start: 0.8545 (mmm-85) cc_final: 0.8196 (mtp180) REVERT: B 50 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7640 (t0) REVERT: B 145 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7455 (tp) REVERT: B 181 ARG cc_start: 0.7482 (tmm-80) cc_final: 0.6857 (ttm-80) REVERT: B 194 ASN cc_start: 0.7432 (m-40) cc_final: 0.6856 (m-40) REVERT: B 313 MET cc_start: 0.7931 (mmm) cc_final: 0.7527 (tpt) REVERT: A 27 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7768 (ttp80) REVERT: A 126 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7411 (p0) REVERT: A 201 GLN cc_start: 0.7349 (tp40) cc_final: 0.6759 (mt0) REVERT: A 369 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 761 PHE cc_start: 0.7358 (m-10) cc_final: 0.7100 (m-10) REVERT: A 762 ARG cc_start: 0.7496 (mmt-90) cc_final: 0.6862 (mmp80) outliers start: 46 outliers final: 28 residues processed: 321 average time/residue: 1.1970 time to fit residues: 460.5768 Evaluate side-chains 320 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 287 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 1.9990 chunk 259 optimal weight: 0.0970 chunk 236 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 258 GLN A 210 ASN A 442 ASN A 499 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22976 Z= 0.238 Angle : 0.500 7.332 31202 Z= 0.261 Chirality : 0.038 0.188 3711 Planarity : 0.004 0.043 3879 Dihedral : 8.259 112.757 3627 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.49 % Favored : 98.47 % Rotamer: Outliers : 1.79 % Allowed : 16.35 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.15), residues: 2881 helix: 1.44 (0.11), residues: 2134 sheet: -0.53 (0.81), residues: 36 loop : 0.08 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 204 HIS 0.008 0.001 HIS A 79 PHE 0.026 0.001 PHE C 80 TYR 0.033 0.001 TYR L 66 ARG 0.011 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 286 time to evaluate : 2.496 Fit side-chains revert: symmetry clash REVERT: D 23 CYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8076 (m) REVERT: C 53 ARG cc_start: 0.8616 (mtp180) cc_final: 0.8382 (mtt-85) REVERT: C 108 GLU cc_start: 0.8312 (tt0) cc_final: 0.7961 (tt0) REVERT: C 134 TYR cc_start: 0.9001 (m-80) cc_final: 0.8759 (m-80) REVERT: K 127 VAL cc_start: 0.8391 (t) cc_final: 0.8157 (p) REVERT: L 46 ARG cc_start: 0.8595 (mmm-85) cc_final: 0.8242 (mtp180) REVERT: B 145 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7452 (tp) REVERT: B 181 ARG cc_start: 0.7488 (tmm-80) cc_final: 0.6905 (ttm-80) REVERT: B 194 ASN cc_start: 0.7436 (m-40) cc_final: 0.6861 (m-40) REVERT: B 313 MET cc_start: 0.7950 (mmm) cc_final: 0.7584 (tpt) REVERT: A 27 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7798 (ttp80) REVERT: A 126 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7410 (p0) REVERT: A 195 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7053 (mtpp) REVERT: A 201 GLN cc_start: 0.7390 (tp40) cc_final: 0.6777 (mt0) REVERT: A 369 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7305 (tm-30) REVERT: A 787 LEU cc_start: 0.8098 (mp) cc_final: 0.7862 (mt) outliers start: 42 outliers final: 27 residues processed: 312 average time/residue: 1.1591 time to fit residues: 421.5823 Evaluate side-chains 311 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 279 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 258 GLN Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 257 optimal weight: 0.5980 chunk 222 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 258 GLN A 210 ASN A 442 ASN A 499 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22976 Z= 0.210 Angle : 0.491 11.315 31202 Z= 0.256 Chirality : 0.038 0.171 3711 Planarity : 0.004 0.042 3879 Dihedral : 8.195 112.143 3627 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.15 % Favored : 98.82 % Rotamer: Outliers : 1.79 % Allowed : 16.48 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.15), residues: 2881 helix: 1.47 (0.11), residues: 2126 sheet: -0.56 (0.80), residues: 36 loop : 0.07 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 204 HIS 0.005 0.001 HIS A 79 PHE 0.039 0.001 PHE B 254 TYR 0.035 0.001 TYR L 66 ARG 0.010 0.000 ARG B 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 280 time to evaluate : 2.249 Fit side-chains REVERT: D 23 CYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8050 (m) REVERT: C 53 ARG cc_start: 0.8621 (mtp180) cc_final: 0.8384 (mtt-85) REVERT: C 134 TYR cc_start: 0.8988 (m-80) cc_final: 0.8746 (m-80) REVERT: G 131 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7453 (mp) REVERT: J 3 GLU cc_start: 0.7525 (tt0) cc_final: 0.7270 (tt0) REVERT: K 127 VAL cc_start: 0.8351 (t) cc_final: 0.8124 (p) REVERT: L 46 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8134 (mtp180) REVERT: B 40 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6769 (mm-30) REVERT: B 145 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7495 (tp) REVERT: B 181 ARG cc_start: 0.7492 (tmm-80) cc_final: 0.6913 (ttm-80) REVERT: B 194 ASN cc_start: 0.7429 (m-40) cc_final: 0.6863 (m-40) REVERT: B 313 MET cc_start: 0.7942 (mmm) cc_final: 0.7580 (tpt) REVERT: A 27 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7748 (ttp80) REVERT: A 126 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7428 (p0) REVERT: A 195 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7050 (mtpp) REVERT: A 201 GLN cc_start: 0.7358 (tp40) cc_final: 0.6765 (mt0) REVERT: A 762 ARG cc_start: 0.7488 (mmt-90) cc_final: 0.6853 (mmp80) REVERT: A 787 LEU cc_start: 0.8002 (mp) cc_final: 0.7782 (mt) outliers start: 42 outliers final: 30 residues processed: 310 average time/residue: 1.1727 time to fit residues: 423.0932 Evaluate side-chains 311 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 275 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 0.7980 chunk 237 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 258 GLN B 302 GLN A 210 ASN A 442 ASN A 499 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117185 restraints weight = 21636.466| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.30 r_work: 0.3068 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22976 Z= 0.243 Angle : 0.510 10.455 31202 Z= 0.265 Chirality : 0.038 0.186 3711 Planarity : 0.004 0.043 3879 Dihedral : 8.238 112.319 3627 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.51 % Rotamer: Outliers : 1.67 % Allowed : 16.78 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.15), residues: 2881 helix: 1.30 (0.11), residues: 2167 sheet: -0.58 (0.80), residues: 36 loop : 0.09 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 204 HIS 0.007 0.001 HIS A 79 PHE 0.027 0.001 PHE C 80 TYR 0.037 0.001 TYR L 66 ARG 0.011 0.000 ARG B 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7267.46 seconds wall clock time: 130 minutes 13.82 seconds (7813.82 seconds total)