Starting phenix.real_space_refine on Sun Aug 4 15:20:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt3_43517/08_2024/8vt3_43517_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt3_43517/08_2024/8vt3_43517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt3_43517/08_2024/8vt3_43517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt3_43517/08_2024/8vt3_43517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt3_43517/08_2024/8vt3_43517_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vt3_43517/08_2024/8vt3_43517_neut.cif" } resolution = 3.33 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= 0.037 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 63 5.16 5 C 6732 2.51 5 N 1818 2.21 5 O 2145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "G ASP 183": "OD1" <-> "OD2" Residue "G PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "G PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 305": "OE1" <-> "OE2" Residue "G ASP 331": "OD1" <-> "OD2" Residue "G TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 431": "OE1" <-> "OE2" Residue "G PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 468": "OE1" <-> "OE2" Residue "G GLU 479": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H ASP 167": "OD1" <-> "OD2" Residue "H PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 294": "OE1" <-> "OE2" Residue "H ASP 306": "OD1" <-> "OD2" Residue "H PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 345": "OE1" <-> "OE2" Residue "H TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 431": "OE1" <-> "OE2" Residue "H PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 468": "OE1" <-> "OE2" Residue "I PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 209": "OE1" <-> "OE2" Residue "I PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 280": "OD1" <-> "OD2" Residue "I GLU 345": "OE1" <-> "OE2" Residue "I TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 468": "OE1" <-> "OE2" Residue "I ASP 478": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10758 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2929 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 13, 'TRANS': 371} Chain: "H" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2929 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 13, 'TRANS': 371} Chain: "I" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2929 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 13, 'TRANS': 371} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.16, per 1000 atoms: 0.57 Number of scatterers: 10758 At special positions: 0 Unit cell: (89.18, 88.27, 141.05, 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 63 16.00 O 2145 8.00 N 1818 7.00 C 6732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG D 1 " - " ASN G 172 " " NAG E 1 " - " ASN A 57 " " NAG F 1 " - " ASN H 172 " " NAG J 1 " - " ASN B 57 " " NAG K 1 " - " ASN I 172 " " NAG L 1 " - " ASN C 57 " Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 2.0 seconds 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2574 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 21 sheets defined 33.9% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.901A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'C' and resid 54 through 58 removed outlier: 3.902A pdb=" N ASN C 57 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 58 " --> pdb=" O VAL C 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 54 through 58' Processing helix chain 'C' and resid 65 through 82 removed outlier: 3.882A pdb=" N THR C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 109 removed outlier: 3.819A pdb=" N ALA G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.547A pdb=" N ALA G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 138 removed outlier: 3.672A pdb=" N VAL G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 172 removed outlier: 3.663A pdb=" N PHE G 168 " --> pdb=" O GLU G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 197 removed outlier: 4.098A pdb=" N SER G 194 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN G 197 " --> pdb=" O PHE G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 210 removed outlier: 3.697A pdb=" N ARG G 205 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN G 206 " --> pdb=" O ASN G 202 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU G 209 " --> pdb=" O ARG G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 234 removed outlier: 3.524A pdb=" N MET G 234 " --> pdb=" O ILE G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 246 removed outlier: 3.719A pdb=" N LEU G 243 " --> pdb=" O GLY G 239 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 255 removed outlier: 4.171A pdb=" N ARG G 252 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG G 253 " --> pdb=" O MET G 250 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS G 254 " --> pdb=" O VAL G 251 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY G 255 " --> pdb=" O ARG G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 352 removed outlier: 3.981A pdb=" N LYS G 348 " --> pdb=" O GLU G 345 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS G 350 " --> pdb=" O SER G 347 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN G 351 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 446 removed outlier: 3.572A pdb=" N PHE G 446 " --> pdb=" O SER G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 486 removed outlier: 3.769A pdb=" N PHE G 464 " --> pdb=" O LEU G 460 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU G 465 " --> pdb=" O ASP G 461 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 470 " --> pdb=" O ASN G 466 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 474 " --> pdb=" O SER G 470 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 480 " --> pdb=" O LYS G 476 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 481 " --> pdb=" O PHE G 477 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU G 485 " --> pdb=" O LEU G 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 109 removed outlier: 3.833A pdb=" N ALA H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.581A pdb=" N ALA H 117 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA H 120 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 removed outlier: 3.724A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 172 removed outlier: 3.818A pdb=" N ASP H 167 " --> pdb=" O ARG H 163 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE H 168 " --> pdb=" O GLU H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 176 Processing helix chain 'H' and resid 188 through 197 removed outlier: 4.172A pdb=" N SER H 194 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 195 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN H 197 " --> pdb=" O PHE H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 210 removed outlier: 3.558A pdb=" N ARG H 205 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN H 206 " --> pdb=" O ASN H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 231 removed outlier: 3.725A pdb=" N ALA H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 231 " --> pdb=" O LEU H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 234 No H-bonds generated for 'chain 'H' and resid 232 through 234' Processing helix chain 'H' and resid 237 through 247 removed outlier: 3.616A pdb=" N ILE H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU H 243 " --> pdb=" O GLY H 239 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 247 " --> pdb=" O LEU H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 255 removed outlier: 4.233A pdb=" N ARG H 252 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG H 253 " --> pdb=" O MET H 250 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY H 255 " --> pdb=" O ARG H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 340 No H-bonds generated for 'chain 'H' and resid 338 through 340' Processing helix chain 'H' and resid 344 through 352 removed outlier: 3.939A pdb=" N LYS H 348 " --> pdb=" O GLU H 345 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS H 350 " --> pdb=" O SER H 347 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN H 351 " --> pdb=" O LYS H 348 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 352 " --> pdb=" O GLU H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 446 removed outlier: 3.585A pdb=" N PHE H 446 " --> pdb=" O SER H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 486 removed outlier: 3.652A pdb=" N PHE H 464 " --> pdb=" O LEU H 460 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER H 470 " --> pdb=" O ASN H 466 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP H 473 " --> pdb=" O ASN H 469 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL H 474 " --> pdb=" O SER H 470 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER H 482 " --> pdb=" O ASP H 478 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE H 484 " --> pdb=" O ILE H 480 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU H 485 " --> pdb=" O LEU H 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 109 removed outlier: 3.528A pdb=" N ILE I 108 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 104 through 109' Processing helix chain 'I' and resid 111 through 129 removed outlier: 3.515A pdb=" N ALA I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I 128 " --> pdb=" O ILE I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 138 removed outlier: 3.664A pdb=" N THR I 135 " --> pdb=" O GLU I 131 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA I 136 " --> pdb=" O SER I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 177 removed outlier: 3.648A pdb=" N ASP I 167 " --> pdb=" O ARG I 163 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU I 173 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR I 174 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG I 175 " --> pdb=" O LYS I 171 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA I 176 " --> pdb=" O ASN I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 197 removed outlier: 4.061A pdb=" N ASN I 197 " --> pdb=" O PHE I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 207 removed outlier: 3.891A pdb=" N ARG I 205 " --> pdb=" O LEU I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 234 removed outlier: 3.619A pdb=" N MET I 234 " --> pdb=" O ILE I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 246 removed outlier: 3.682A pdb=" N LEU I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU I 246 " --> pdb=" O LYS I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 255 removed outlier: 4.200A pdb=" N ARG I 252 " --> pdb=" O ALA I 249 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG I 253 " --> pdb=" O MET I 250 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS I 254 " --> pdb=" O VAL I 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY I 255 " --> pdb=" O ARG I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'I' and resid 344 through 349 removed outlier: 3.948A pdb=" N LYS I 348 " --> pdb=" O GLU I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 445 Processing helix chain 'I' and resid 460 through 486 removed outlier: 3.796A pdb=" N PHE I 464 " --> pdb=" O LEU I 460 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU I 465 " --> pdb=" O ASP I 461 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE I 467 " --> pdb=" O VAL I 463 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER I 470 " --> pdb=" O ASN I 466 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL I 474 " --> pdb=" O SER I 470 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU I 479 " --> pdb=" O ARG I 475 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU I 481 " --> pdb=" O PHE I 477 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER I 482 " --> pdb=" O ASP I 478 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE I 484 " --> pdb=" O ILE I 480 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU I 485 " --> pdb=" O LEU I 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 328 through 329 removed outlier: 3.659A pdb=" N HIS G 332 " --> pdb=" O ARG G 329 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL G 333 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 36 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER A 29 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA G 288 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE A 31 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL G 286 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU A 33 " --> pdb=" O TRP G 284 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TRP G 284 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR A 35 " --> pdb=" O PRO G 282 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER A 37 " --> pdb=" O ASP G 280 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL G 278 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP G 309 " --> pdb=" O TYR G 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 328 through 329 removed outlier: 3.659A pdb=" N HIS G 332 " --> pdb=" O ARG G 329 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL G 333 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 36 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU A 21 " --> pdb=" O HIS G 435 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE G 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR A 23 " --> pdb=" O ILE G 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 146 through 150 removed outlier: 5.330A pdb=" N THR A 45 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR G 269 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N MET G 270 " --> pdb=" O LEU G 259 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU G 259 " --> pdb=" O MET G 270 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLN G 272 " --> pdb=" O GLY G 257 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLY G 257 " --> pdb=" O GLN G 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 328 through 329 removed outlier: 3.668A pdb=" N HIS H 332 " --> pdb=" O ARG H 329 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 40 " --> pdb=" O CYS H 335 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER B 29 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA H 288 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE B 31 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL H 286 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU B 33 " --> pdb=" O TRP H 284 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TRP H 284 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR B 35 " --> pdb=" O PRO H 282 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER B 37 " --> pdb=" O ASP H 280 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL H 278 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY H 308 " --> pdb=" O VAL H 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 328 through 329 removed outlier: 3.668A pdb=" N HIS H 332 " --> pdb=" O ARG H 329 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 40 " --> pdb=" O CYS H 335 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU B 21 " --> pdb=" O HIS H 435 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE H 437 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR B 23 " --> pdb=" O ILE H 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 146 through 150 removed outlier: 8.526A pdb=" N ARG H 156 " --> pdb=" O TRP B 43 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR B 45 " --> pdb=" O ARG H 156 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER H 266 " --> pdb=" O VAL H 262 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL H 262 " --> pdb=" O SER H 266 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE H 268 " --> pdb=" O ILE H 260 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE H 256 " --> pdb=" O GLN H 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 318 through 320 removed outlier: 3.633A pdb=" N TRP I 309 " --> pdb=" O TYR I 320 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL I 278 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER C 37 " --> pdb=" O ASP I 280 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR C 35 " --> pdb=" O PRO I 282 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP I 284 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU C 33 " --> pdb=" O TRP I 284 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL I 286 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE C 31 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA I 288 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER C 29 " --> pdb=" O ALA I 288 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS I 332 " --> pdb=" O ARG I 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 318 through 320 removed outlier: 3.633A pdb=" N TRP I 309 " --> pdb=" O TYR I 320 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL I 278 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER C 37 " --> pdb=" O ASP I 280 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR C 35 " --> pdb=" O PRO I 282 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TRP I 284 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU C 33 " --> pdb=" O TRP I 284 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL I 286 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE C 31 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA I 288 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER C 29 " --> pdb=" O ALA I 288 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU C 21 " --> pdb=" O HIS I 435 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE I 437 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR C 23 " --> pdb=" O ILE I 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 146 through 150 removed outlier: 5.287A pdb=" N THR C 45 " --> pdb=" O ARG I 156 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR I 269 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET I 270 " --> pdb=" O LEU I 259 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU I 259 " --> pdb=" O MET I 270 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN I 272 " --> pdb=" O GLY I 257 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLY I 257 " --> pdb=" O GLN I 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 294 through 295 Processing sheet with id=AB2, first strand: chain 'G' and resid 362 through 363 Processing sheet with id=AB3, first strand: chain 'G' and resid 372 through 376 Processing sheet with id=AB4, first strand: chain 'G' and resid 398 through 402 removed outlier: 7.181A pdb=" N ILE G 392 " --> pdb=" O ILE G 400 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLN G 402 " --> pdb=" O CYS G 390 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N CYS G 390 " --> pdb=" O GLN G 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 294 through 295 Processing sheet with id=AB6, first strand: chain 'H' and resid 303 through 304 Processing sheet with id=AB7, first strand: chain 'H' and resid 372 through 376 Processing sheet with id=AB8, first strand: chain 'H' and resid 399 through 401 removed outlier: 7.195A pdb=" N ILE H 392 " --> pdb=" O ILE H 400 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 294 through 295 removed outlier: 3.705A pdb=" N ASN I 298 " --> pdb=" O LYS I 295 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 303 through 304 Processing sheet with id=AC2, first strand: chain 'I' and resid 372 through 376 removed outlier: 3.545A pdb=" N GLY I 379 " --> pdb=" O SER I 376 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS I 384 " --> pdb=" O GLY I 406 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 399 through 402 removed outlier: 7.006A pdb=" N ILE I 392 " --> pdb=" O ILE I 400 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLN I 402 " --> pdb=" O CYS I 390 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N CYS I 390 " --> pdb=" O GLN I 402 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR I 417 " --> pdb=" O GLY I 393 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1020 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: 3.65 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3237 1.33 - 1.45: 1420 1.45 - 1.57: 6167 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 10908 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.563 -0.044 2.00e-02 2.50e+03 4.73e+00 ... (remaining 10903 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.75: 152 105.75 - 112.85: 6102 112.85 - 119.96: 3709 119.96 - 127.06: 4742 127.06 - 134.16: 70 Bond angle restraints: 14775 Sorted by residual: angle pdb=" N THR H 174 " pdb=" CA THR H 174 " pdb=" C THR H 174 " ideal model delta sigma weight residual 113.20 108.56 4.64 1.36e+00 5.41e-01 1.17e+01 angle pdb=" C THR H 411 " pdb=" N ASN H 412 " pdb=" CA ASN H 412 " ideal model delta sigma weight residual 121.94 115.38 6.56 2.00e+00 2.50e-01 1.08e+01 angle pdb=" N ILE G 124 " pdb=" CA ILE G 124 " pdb=" C ILE G 124 " ideal model delta sigma weight residual 113.42 109.80 3.62 1.17e+00 7.31e-01 9.56e+00 angle pdb=" C ILE I 420 " pdb=" N ASP I 421 " pdb=" CA ASP I 421 " ideal model delta sigma weight residual 121.54 126.86 -5.32 1.91e+00 2.74e-01 7.76e+00 angle pdb=" CA LEU C 50 " pdb=" CB LEU C 50 " pdb=" CG LEU C 50 " ideal model delta sigma weight residual 116.30 126.00 -9.70 3.50e+00 8.16e-02 7.68e+00 ... (remaining 14770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 6437 23.98 - 47.96: 313 47.96 - 71.94: 55 71.94 - 95.92: 40 95.92 - 119.90: 31 Dihedral angle restraints: 6876 sinusoidal: 2892 harmonic: 3984 Sorted by residual: dihedral pdb=" CA TYR G 385 " pdb=" C TYR G 385 " pdb=" N LYS G 386 " pdb=" CA LYS G 386 " ideal model delta harmonic sigma weight residual 180.00 -153.38 -26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA TYR I 385 " pdb=" C TYR I 385 " pdb=" N LYS I 386 " pdb=" CA LYS I 386 " ideal model delta harmonic sigma weight residual -180.00 -155.98 -24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA TYR H 385 " pdb=" C TYR H 385 " pdb=" N LYS H 386 " pdb=" CA LYS H 386 " ideal model delta harmonic sigma weight residual 180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 6873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1246 0.059 - 0.117: 481 0.117 - 0.176: 65 0.176 - 0.235: 1 0.235 - 0.294: 4 Chirality restraints: 1797 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN G 172 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1794 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 193 " 0.017 2.00e-02 2.50e+03 2.08e-02 7.58e+00 pdb=" CG PHE I 193 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE I 193 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE I 193 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE I 193 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE I 193 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE I 193 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 193 " 0.018 2.00e-02 2.50e+03 1.84e-02 5.90e+00 pdb=" CG PHE G 193 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE G 193 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE G 193 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 193 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE G 193 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE G 193 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR G 359 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO G 360 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 360 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 360 " -0.028 5.00e-02 4.00e+02 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 409 2.70 - 3.25: 9815 3.25 - 3.80: 14320 3.80 - 4.35: 18965 4.35 - 4.90: 34740 Nonbonded interactions: 78249 Sorted by model distance: nonbonded pdb=" OD1 ASN H 353 " pdb=" OG1 THR H 356 " model vdw 2.153 3.040 nonbonded pdb=" O LEU H 141 " pdb=" NH2 ARG H 163 " model vdw 2.176 3.120 nonbonded pdb=" ND2 ASN I 353 " pdb=" OG1 THR I 356 " model vdw 2.212 3.120 nonbonded pdb=" OG1 THR B 45 " pdb=" OE1 GLN H 272 " model vdw 2.219 3.040 nonbonded pdb=" ND2 ASN I 412 " pdb=" O SER I 428 " model vdw 2.297 3.120 ... (remaining 78244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.360 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.920 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.011 0.084 10908 Z= 0.743 Angle : 0.872 9.698 14775 Z= 0.458 Chirality : 0.058 0.294 1797 Planarity : 0.005 0.052 1872 Dihedral : 18.193 119.897 4302 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.20), residues: 1365 helix: -2.93 (0.22), residues: 369 sheet: -1.51 (0.28), residues: 318 loop : -2.44 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 284 HIS 0.005 0.002 HIS I 332 PHE 0.047 0.003 PHE I 193 TYR 0.020 0.004 TYR I 310 ARG 0.016 0.001 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.292 Fit side-chains REVERT: A 54 ASP cc_start: 0.7255 (p0) cc_final: 0.6722 (p0) REVERT: H 325 ASP cc_start: 0.7314 (m-30) cc_final: 0.7006 (m-30) REVERT: H 353 ASN cc_start: 0.7862 (t0) cc_final: 0.7602 (t0) REVERT: I 325 ASP cc_start: 0.7698 (m-30) cc_final: 0.7452 (m-30) REVERT: I 471 GLN cc_start: 0.8105 (tp40) cc_final: 0.7414 (tm-30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2554 time to fit residues: 41.1085 Evaluate side-chains 90 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 353 ASN I 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10908 Z= 0.197 Angle : 0.646 11.182 14775 Z= 0.323 Chirality : 0.047 0.212 1797 Planarity : 0.005 0.043 1872 Dihedral : 14.090 95.365 1845 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.34 % Allowed : 6.07 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.72 (0.21), residues: 1365 helix: -1.94 (0.24), residues: 414 sheet: -1.06 (0.33), residues: 258 loop : -1.98 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 284 HIS 0.002 0.001 HIS I 332 PHE 0.014 0.001 PHE G 193 TYR 0.017 0.001 TYR I 385 ARG 0.006 0.000 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.292 Fit side-chains REVERT: A 54 ASP cc_start: 0.7205 (p0) cc_final: 0.6719 (p0) REVERT: G 478 ASP cc_start: 0.7911 (t0) cc_final: 0.7689 (t0) REVERT: I 471 GLN cc_start: 0.7782 (tp40) cc_final: 0.7229 (tm-30) outliers start: 4 outliers final: 3 residues processed: 104 average time/residue: 0.2376 time to fit residues: 35.9402 Evaluate side-chains 92 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 0.0170 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 121 optimal weight: 0.0670 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.3560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10908 Z= 0.280 Angle : 0.613 8.280 14775 Z= 0.308 Chirality : 0.046 0.236 1797 Planarity : 0.004 0.045 1872 Dihedral : 9.152 82.424 1845 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.68 % Allowed : 8.29 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.46 (0.22), residues: 1365 helix: -1.55 (0.25), residues: 414 sheet: -0.88 (0.33), residues: 258 loop : -1.95 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 284 HIS 0.002 0.001 HIS I 332 PHE 0.017 0.002 PHE G 193 TYR 0.012 0.002 TYR G 319 ARG 0.003 0.000 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.272 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 0.2335 time to fit residues: 32.3291 Evaluate side-chains 89 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain H residue 357 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 0.0670 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10908 Z= 0.172 Angle : 0.528 7.399 14775 Z= 0.272 Chirality : 0.044 0.258 1797 Planarity : 0.004 0.042 1872 Dihedral : 7.603 74.308 1845 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.68 % Allowed : 9.83 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.13 (0.22), residues: 1365 helix: -1.21 (0.26), residues: 411 sheet: -0.64 (0.33), residues: 258 loop : -1.82 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 284 HIS 0.001 0.000 HIS I 332 PHE 0.010 0.001 PHE G 193 TYR 0.014 0.001 TYR H 385 ARG 0.005 0.000 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.330 Fit side-chains REVERT: G 478 ASP cc_start: 0.8053 (t0) cc_final: 0.7817 (t0) outliers start: 8 outliers final: 6 residues processed: 102 average time/residue: 0.2452 time to fit residues: 35.5374 Evaluate side-chains 95 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.0870 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 overall best weight: 1.6564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10908 Z= 0.328 Angle : 0.592 7.920 14775 Z= 0.303 Chirality : 0.046 0.260 1797 Planarity : 0.004 0.045 1872 Dihedral : 7.246 69.166 1845 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.28 % Allowed : 10.43 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.20 (0.22), residues: 1365 helix: -1.29 (0.26), residues: 414 sheet: -0.61 (0.33), residues: 258 loop : -1.89 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 284 HIS 0.001 0.001 HIS G 435 PHE 0.014 0.002 PHE G 193 TYR 0.014 0.002 TYR G 319 ARG 0.007 0.000 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.243 Fit side-chains REVERT: G 478 ASP cc_start: 0.7999 (t0) cc_final: 0.7754 (t0) REVERT: H 475 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7457 (ttp-110) REVERT: I 246 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: I 471 GLN cc_start: 0.7680 (tp40) cc_final: 0.7408 (tp40) outliers start: 15 outliers final: 12 residues processed: 102 average time/residue: 0.2575 time to fit residues: 37.1252 Evaluate side-chains 105 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 420 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 108 optimal weight: 0.0170 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10908 Z= 0.235 Angle : 0.546 8.474 14775 Z= 0.281 Chirality : 0.045 0.263 1797 Planarity : 0.004 0.044 1872 Dihedral : 6.642 61.960 1845 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.62 % Allowed : 11.11 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.07 (0.22), residues: 1365 helix: -1.13 (0.26), residues: 414 sheet: -0.55 (0.33), residues: 258 loop : -1.84 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 284 HIS 0.001 0.000 HIS I 332 PHE 0.011 0.001 PHE G 193 TYR 0.012 0.002 TYR H 269 ARG 0.007 0.000 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.239 Fit side-chains REVERT: G 478 ASP cc_start: 0.8100 (t0) cc_final: 0.7828 (t0) REVERT: I 246 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: I 471 GLN cc_start: 0.7711 (tp40) cc_final: 0.7428 (tp40) outliers start: 19 outliers final: 13 residues processed: 106 average time/residue: 0.2459 time to fit residues: 36.8527 Evaluate side-chains 106 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 420 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10908 Z= 0.270 Angle : 0.566 9.080 14775 Z= 0.289 Chirality : 0.045 0.254 1797 Planarity : 0.004 0.044 1872 Dihedral : 6.315 55.841 1845 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.37 % Allowed : 11.62 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.06 (0.22), residues: 1365 helix: -1.10 (0.26), residues: 414 sheet: -0.54 (0.33), residues: 258 loop : -1.84 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 284 HIS 0.001 0.000 HIS G 435 PHE 0.012 0.001 PHE G 193 TYR 0.012 0.002 TYR H 269 ARG 0.007 0.000 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 1.183 Fit side-chains REVERT: G 478 ASP cc_start: 0.8116 (t0) cc_final: 0.7854 (t0) REVERT: I 246 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: I 471 GLN cc_start: 0.7742 (tp40) cc_final: 0.7509 (tp40) outliers start: 16 outliers final: 15 residues processed: 103 average time/residue: 0.2491 time to fit residues: 36.1267 Evaluate side-chains 105 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain H residue 475 ARG Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 420 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10908 Z= 0.188 Angle : 0.526 9.049 14775 Z= 0.270 Chirality : 0.044 0.233 1797 Planarity : 0.004 0.043 1872 Dihedral : 5.689 45.929 1845 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.20 % Allowed : 11.97 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.85 (0.23), residues: 1365 helix: -0.88 (0.27), residues: 411 sheet: -0.41 (0.33), residues: 258 loop : -1.75 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 284 HIS 0.001 0.000 HIS I 332 PHE 0.009 0.001 PHE G 193 TYR 0.012 0.001 TYR H 269 ARG 0.008 0.000 ARG I 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.105 Fit side-chains REVERT: G 478 ASP cc_start: 0.8123 (t0) cc_final: 0.7881 (t0) REVERT: I 246 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: I 471 GLN cc_start: 0.7705 (tp40) cc_final: 0.7476 (tp40) outliers start: 14 outliers final: 11 residues processed: 100 average time/residue: 0.2521 time to fit residues: 35.9838 Evaluate side-chains 100 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 420 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 72 optimal weight: 0.0040 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10908 Z= 0.202 Angle : 0.543 10.539 14775 Z= 0.274 Chirality : 0.044 0.211 1797 Planarity : 0.004 0.043 1872 Dihedral : 5.340 38.082 1845 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.28 % Allowed : 12.39 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.79 (0.23), residues: 1365 helix: -0.84 (0.27), residues: 414 sheet: -0.36 (0.33), residues: 258 loop : -1.72 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 284 HIS 0.001 0.000 HIS I 435 PHE 0.010 0.001 PHE G 193 TYR 0.013 0.001 TYR H 385 ARG 0.008 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.437 Fit side-chains REVERT: I 246 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: I 471 GLN cc_start: 0.7695 (tp40) cc_final: 0.7121 (tp40) outliers start: 15 outliers final: 12 residues processed: 102 average time/residue: 0.2409 time to fit residues: 34.9973 Evaluate side-chains 103 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 420 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 10908 Z= 0.298 Angle : 0.586 10.096 14775 Z= 0.296 Chirality : 0.045 0.186 1797 Planarity : 0.004 0.044 1872 Dihedral : 5.246 30.908 1845 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.20 % Allowed : 12.56 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.88 (0.23), residues: 1365 helix: -0.91 (0.26), residues: 414 sheet: -0.40 (0.33), residues: 258 loop : -1.79 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 284 HIS 0.001 0.000 HIS I 332 PHE 0.013 0.001 PHE G 193 TYR 0.013 0.002 TYR G 319 ARG 0.004 0.000 ARG B 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.219 Fit side-chains REVERT: I 246 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7362 (mt-10) REVERT: I 471 GLN cc_start: 0.7738 (tp40) cc_final: 0.7168 (tp40) outliers start: 14 outliers final: 13 residues processed: 103 average time/residue: 0.2630 time to fit residues: 38.0829 Evaluate side-chains 107 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 357 THR Chi-restraints excluded: chain H residue 399 ILE Chi-restraints excluded: chain I residue 246 GLU Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 294 GLU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 420 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119536 restraints weight = 12221.062| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.97 r_work: 0.3247 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10908 Z= 0.157 Angle : 0.519 10.477 14775 Z= 0.264 Chirality : 0.044 0.161 1797 Planarity : 0.004 0.041 1872 Dihedral : 4.728 22.766 1845 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.03 % Allowed : 12.74 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.23), residues: 1365 helix: -0.63 (0.27), residues: 411 sheet: -0.28 (0.33), residues: 258 loop : -1.64 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 284 HIS 0.001 0.000 HIS I 435 PHE 0.008 0.001 PHE G 193 TYR 0.012 0.001 TYR H 269 ARG 0.004 0.000 ARG B 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.43 seconds wall clock time: 39 minutes 8.69 seconds (2348.69 seconds total)