Starting phenix.real_space_refine on Mon Feb 19 01:24:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/02_2024/8ap7_15560_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/02_2024/8ap7_15560.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/02_2024/8ap7_15560_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/02_2024/8ap7_15560_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/02_2024/8ap7_15560_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/02_2024/8ap7_15560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/02_2024/8ap7_15560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/02_2024/8ap7_15560_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/02_2024/8ap7_15560_trim_updated.pdb" } resolution = 2.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 60 5.49 5 S 204 5.16 5 C 25258 2.51 5 N 5806 2.21 5 O 6530 1.98 5 H 33618 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 71476 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 4076 Classifications: {'peptide': 231} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 230} Chain: "C" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1115 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "D" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3212 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "E" Number of atoms: 6270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6270 Classifications: {'peptide': 383} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 366} Chain: "F" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2256 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "I" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1740 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "J" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2835 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 162} Chain: "K" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1749 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 11, 'TRANS': 93} Chain: "L" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1082 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "M" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2069 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2210 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 126} Chain: "O" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1556 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "P" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1335 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 72} Chain: "Q" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1486 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 7, 'TRANS': 77} Chain: "R" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1040 Classifications: {'peptide': 62} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "a" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 4076 Classifications: {'peptide': 231} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 230} Chain: "c" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1115 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "d" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3212 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "e" Number of atoms: 6270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6270 Classifications: {'peptide': 383} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 366} Chain: "f" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2256 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "i" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1740 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "j" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2835 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 162} Chain: "k" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1749 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 11, 'TRANS': 93} Chain: "l" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1082 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "m" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2069 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2210 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 126} Chain: "o" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1556 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "p" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1335 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 72} Chain: "q" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1486 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 7, 'TRANS': 77} Chain: "r" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1040 Classifications: {'peptide': 62} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 583 Unusual residues: {'CDL': 5, 'LMT': 1, 'Q7G': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 25 Chain: "F" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 259 Unusual residues: {'CDL': 1, 'PC1': 2, 'PEE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 289 Unusual residues: {'CDL': 2, 'LMT': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'Q7G': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 583 Unusual residues: {'CDL': 5, 'LMT': 1, 'Q7G': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 25 Chain: "f" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 259 Unusual residues: {'CDL': 1, 'PC1': 2, 'PEE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 289 Unusual residues: {'CDL': 2, 'LMT': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "l" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'Q7G': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "f" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 26.42, per 1000 atoms: 0.37 Number of scatterers: 71476 At special positions: 0 Unit cell: (234.89, 165.17, 153.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 204 16.00 P 60 15.00 O 6530 8.00 N 5806 7.00 C 25258 6.00 H 33618 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 45.35 Conformation dependent library (CDL) restraints added in 5.6 seconds 8012 Ramachandran restraints generated. 4006 Oldfield, 0 Emsley, 4006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 2 sheets defined 62.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.30 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 53 through 67 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 82 through 102 Processing helix chain 'A' and resid 106 through 112 removed outlier: 4.428A pdb=" N ASN A 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 177 removed outlier: 3.838A pdb=" N LEU A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TYR A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 224 removed outlier: 3.646A pdb=" N ILE A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 217 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 37 through 49 removed outlier: 4.222A pdb=" N VAL C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TRP C 44 " --> pdb=" O TRP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 58 Processing helix chain 'C' and resid 60 through 89 Proline residue: C 70 - end of helix Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 99 through 118 Processing helix chain 'D' and resid 123 through 129 removed outlier: 3.951A pdb=" N ARG D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 220 through 254 Proline residue: D 238 - end of helix Processing helix chain 'D' and resid 260 through 266 Processing helix chain 'D' and resid 268 through 279 Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 302 through 324 Processing helix chain 'E' and resid 5 through 13 Processing helix chain 'E' and resid 15 through 43 Processing helix chain 'E' and resid 46 through 50 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 82 through 120 removed outlier: 6.981A pdb=" N GLY E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR E 111 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA E 112 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 134 through 166 Proline residue: E 153 - end of helix Processing helix chain 'E' and resid 172 through 181 Processing helix chain 'E' and resid 191 through 202 Proline residue: E 196 - end of helix removed outlier: 4.152A pdb=" N GLU E 199 " --> pdb=" O ARG E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 232 through 256 removed outlier: 3.586A pdb=" N THR E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 No H-bonds generated for 'chain 'E' and resid 258 through 261' Processing helix chain 'E' and resid 264 through 274 Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 285 through 299 Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 312 through 323 removed outlier: 4.216A pdb=" N TYR E 322 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR E 323 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 351 through 360 Processing helix chain 'E' and resid 364 through 382 Processing helix chain 'F' and resid 19 through 33 removed outlier: 4.871A pdb=" N TYR F 32 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 70 Proline residue: F 57 - end of helix Processing helix chain 'F' and resid 72 through 83 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 96 through 112 Processing helix chain 'F' and resid 118 through 120 No H-bonds generated for 'chain 'F' and resid 118 through 120' Processing helix chain 'I' and resid 5 through 8 No H-bonds generated for 'chain 'I' and resid 5 through 8' Processing helix chain 'I' and resid 11 through 21 Processing helix chain 'I' and resid 24 through 40 Processing helix chain 'I' and resid 46 through 52 Processing helix chain 'I' and resid 64 through 80 Processing helix chain 'I' and resid 87 through 90 No H-bonds generated for 'chain 'I' and resid 87 through 90' Processing helix chain 'I' and resid 94 through 103 Processing helix chain 'J' and resid 4 through 17 removed outlier: 4.529A pdb=" N TYR J 10 " --> pdb=" O LEU J 6 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE J 11 " --> pdb=" O LYS J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 21 No H-bonds generated for 'chain 'J' and resid 19 through 21' Processing helix chain 'J' and resid 24 through 54 Processing helix chain 'J' and resid 58 through 64 Processing helix chain 'J' and resid 75 through 89 Processing helix chain 'J' and resid 98 through 128 Proline residue: J 107 - end of helix Processing helix chain 'J' and resid 133 through 144 Processing helix chain 'J' and resid 151 through 154 No H-bonds generated for 'chain 'J' and resid 151 through 154' Processing helix chain 'K' and resid 34 through 36 No H-bonds generated for 'chain 'K' and resid 34 through 36' Processing helix chain 'K' and resid 49 through 53 removed outlier: 3.626A pdb=" N LEU K 53 " --> pdb=" O PHE K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 65 Processing helix chain 'K' and resid 69 through 85 removed outlier: 4.857A pdb=" N THR K 74 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Proline residue: K 75 - end of helix removed outlier: 3.871A pdb=" N PHE K 78 " --> pdb=" O PRO K 75 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR K 85 " --> pdb=" O TRP K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 94 Processing helix chain 'L' and resid 11 through 66 Processing helix chain 'M' and resid 18 through 33 Processing helix chain 'M' and resid 37 through 49 Processing helix chain 'M' and resid 53 through 67 Processing helix chain 'M' and resid 69 through 84 Processing helix chain 'M' and resid 87 through 90 No H-bonds generated for 'chain 'M' and resid 87 through 90' Processing helix chain 'M' and resid 94 through 119 Processing helix chain 'M' and resid 131 through 137 removed outlier: 3.942A pdb=" N GLU M 134 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 85 through 87 No H-bonds generated for 'chain 'N' and resid 85 through 87' Processing helix chain 'N' and resid 100 through 127 Processing helix chain 'N' and resid 153 through 155 No H-bonds generated for 'chain 'N' and resid 153 through 155' Processing helix chain 'O' and resid 12 through 17 removed outlier: 4.240A pdb=" N GLY O 17 " --> pdb=" O ASP O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 45 Processing helix chain 'O' and resid 54 through 68 Processing helix chain 'O' and resid 77 through 86 Processing helix chain 'O' and resid 89 through 97 Processing helix chain 'P' and resid 42 through 47 removed outlier: 3.613A pdb=" N LYS P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 54 No H-bonds generated for 'chain 'P' and resid 52 through 54' Processing helix chain 'P' and resid 64 through 66 No H-bonds generated for 'chain 'P' and resid 64 through 66' Processing helix chain 'P' and resid 80 through 100 removed outlier: 5.466A pdb=" N GLU P 98 " --> pdb=" O TYR P 94 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL P 100 " --> pdb=" O PHE P 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 19 Processing helix chain 'Q' and resid 33 through 48 Processing helix chain 'Q' and resid 58 through 75 removed outlier: 4.872A pdb=" N TYR Q 66 " --> pdb=" O LEU Q 62 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER Q 67 " --> pdb=" O GLY Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 16 removed outlier: 4.160A pdb=" N ASN R 15 " --> pdb=" O SER R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 41 removed outlier: 4.210A pdb=" N TYR R 34 " --> pdb=" O TRP R 30 " (cutoff:3.500A) Proline residue: R 35 - end of helix Processing helix chain 'R' and resid 57 through 61 Processing helix chain 'a' and resid 10 through 19 Processing helix chain 'a' and resid 32 through 34 No H-bonds generated for 'chain 'a' and resid 32 through 34' Processing helix chain 'a' and resid 53 through 67 Processing helix chain 'a' and resid 69 through 71 No H-bonds generated for 'chain 'a' and resid 69 through 71' Processing helix chain 'a' and resid 82 through 102 Processing helix chain 'a' and resid 106 through 112 removed outlier: 4.429A pdb=" N ASN a 111 " --> pdb=" O LEU a 108 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 177 removed outlier: 3.838A pdb=" N LEU a 137 " --> pdb=" O CYS a 133 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU a 151 " --> pdb=" O LEU a 147 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE a 173 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR a 174 " --> pdb=" O VAL a 170 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY a 175 " --> pdb=" O PHE a 171 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL a 176 " --> pdb=" O PHE a 172 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE a 177 " --> pdb=" O PHE a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 224 removed outlier: 3.646A pdb=" N ILE a 207 " --> pdb=" O LEU a 203 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE a 217 " --> pdb=" O PHE a 213 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE a 224 " --> pdb=" O LEU a 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 37 through 49 removed outlier: 4.057A pdb=" N VAL c 43 " --> pdb=" O SER c 39 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP c 44 " --> pdb=" O TRP c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 51 through 58 Processing helix chain 'c' and resid 60 through 89 Proline residue: c 70 - end of helix Processing helix chain 'd' and resid 70 through 82 Processing helix chain 'd' and resid 99 through 118 Processing helix chain 'd' and resid 123 through 129 removed outlier: 3.951A pdb=" N ARG d 128 " --> pdb=" O ASP d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 134 through 143 Processing helix chain 'd' and resid 220 through 254 Proline residue: d 238 - end of helix Processing helix chain 'd' and resid 260 through 266 Processing helix chain 'd' and resid 268 through 279 Processing helix chain 'd' and resid 288 through 294 Processing helix chain 'd' and resid 302 through 324 Processing helix chain 'e' and resid 5 through 13 Processing helix chain 'e' and resid 15 through 43 Processing helix chain 'e' and resid 46 through 50 Processing helix chain 'e' and resid 76 through 78 No H-bonds generated for 'chain 'e' and resid 76 through 78' Processing helix chain 'e' and resid 82 through 120 removed outlier: 6.982A pdb=" N GLY e 110 " --> pdb=" O LEU e 106 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR e 111 " --> pdb=" O ALA e 107 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA e 112 " --> pdb=" O THR e 108 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) Proline residue: e 114 - end of helix Processing helix chain 'e' and resid 128 through 130 No H-bonds generated for 'chain 'e' and resid 128 through 130' Processing helix chain 'e' and resid 134 through 166 Proline residue: e 153 - end of helix Processing helix chain 'e' and resid 172 through 181 Processing helix chain 'e' and resid 191 through 202 Proline residue: e 196 - end of helix removed outlier: 4.152A pdb=" N GLU e 199 " --> pdb=" O ARG e 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 207 through 209 No H-bonds generated for 'chain 'e' and resid 207 through 209' Processing helix chain 'e' and resid 212 through 221 Processing helix chain 'e' and resid 232 through 256 removed outlier: 3.587A pdb=" N THR e 237 " --> pdb=" O LEU e 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 258 through 261 No H-bonds generated for 'chain 'e' and resid 258 through 261' Processing helix chain 'e' and resid 264 through 274 Processing helix chain 'e' and resid 279 through 281 No H-bonds generated for 'chain 'e' and resid 279 through 281' Processing helix chain 'e' and resid 285 through 299 Processing helix chain 'e' and resid 301 through 306 Processing helix chain 'e' and resid 312 through 323 removed outlier: 4.217A pdb=" N TYR e 322 " --> pdb=" O TYR e 318 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR e 323 " --> pdb=" O VAL e 319 " (cutoff:3.500A) Processing helix chain 'e' and resid 333 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 351 through 360 Processing helix chain 'e' and resid 364 through 382 Processing helix chain 'f' and resid 19 through 33 removed outlier: 4.871A pdb=" N TYR f 32 " --> pdb=" O LEU f 28 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE f 33 " --> pdb=" O GLY f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 49 through 70 Proline residue: f 57 - end of helix Processing helix chain 'f' and resid 72 through 83 Processing helix chain 'f' and resid 88 through 92 Processing helix chain 'f' and resid 96 through 112 Processing helix chain 'f' and resid 118 through 120 No H-bonds generated for 'chain 'f' and resid 118 through 120' Processing helix chain 'i' and resid 5 through 8 No H-bonds generated for 'chain 'i' and resid 5 through 8' Processing helix chain 'i' and resid 11 through 21 Processing helix chain 'i' and resid 24 through 40 Processing helix chain 'i' and resid 46 through 52 Processing helix chain 'i' and resid 64 through 80 Processing helix chain 'i' and resid 87 through 90 No H-bonds generated for 'chain 'i' and resid 87 through 90' Processing helix chain 'i' and resid 94 through 103 Processing helix chain 'j' and resid 4 through 17 removed outlier: 4.529A pdb=" N TYR j 10 " --> pdb=" O LEU j 6 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE j 11 " --> pdb=" O LYS j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 19 through 21 No H-bonds generated for 'chain 'j' and resid 19 through 21' Processing helix chain 'j' and resid 24 through 54 Processing helix chain 'j' and resid 58 through 64 Processing helix chain 'j' and resid 75 through 89 Processing helix chain 'j' and resid 98 through 128 Proline residue: j 107 - end of helix Processing helix chain 'j' and resid 133 through 144 Processing helix chain 'j' and resid 151 through 154 No H-bonds generated for 'chain 'j' and resid 151 through 154' Processing helix chain 'k' and resid 34 through 36 No H-bonds generated for 'chain 'k' and resid 34 through 36' Processing helix chain 'k' and resid 49 through 53 removed outlier: 3.626A pdb=" N LEU k 53 " --> pdb=" O PHE k 50 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 65 Processing helix chain 'k' and resid 69 through 85 removed outlier: 4.857A pdb=" N THR k 74 " --> pdb=" O LEU k 71 " (cutoff:3.500A) Proline residue: k 75 - end of helix removed outlier: 3.872A pdb=" N PHE k 78 " --> pdb=" O PRO k 75 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR k 85 " --> pdb=" O TRP k 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 94 Processing helix chain 'l' and resid 11 through 66 Processing helix chain 'm' and resid 18 through 33 Processing helix chain 'm' and resid 37 through 49 Processing helix chain 'm' and resid 53 through 67 Processing helix chain 'm' and resid 69 through 84 Processing helix chain 'm' and resid 87 through 90 No H-bonds generated for 'chain 'm' and resid 87 through 90' Processing helix chain 'm' and resid 94 through 119 Processing helix chain 'm' and resid 131 through 137 removed outlier: 3.943A pdb=" N GLU m 134 " --> pdb=" O PRO m 131 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 39 No H-bonds generated for 'chain 'n' and resid 37 through 39' Processing helix chain 'n' and resid 85 through 87 No H-bonds generated for 'chain 'n' and resid 85 through 87' Processing helix chain 'n' and resid 100 through 127 Processing helix chain 'n' and resid 153 through 155 No H-bonds generated for 'chain 'n' and resid 153 through 155' Processing helix chain 'o' and resid 12 through 17 removed outlier: 4.239A pdb=" N GLY o 17 " --> pdb=" O ASP o 13 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 45 Processing helix chain 'o' and resid 54 through 68 Processing helix chain 'o' and resid 77 through 86 Processing helix chain 'o' and resid 89 through 97 Processing helix chain 'p' and resid 42 through 47 removed outlier: 3.613A pdb=" N LYS p 47 " --> pdb=" O GLU p 43 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 54 No H-bonds generated for 'chain 'p' and resid 52 through 54' Processing helix chain 'p' and resid 64 through 66 No H-bonds generated for 'chain 'p' and resid 64 through 66' Processing helix chain 'p' and resid 80 through 100 removed outlier: 5.465A pdb=" N GLU p 98 " --> pdb=" O TYR p 94 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU p 99 " --> pdb=" O GLN p 95 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL p 100 " --> pdb=" O PHE p 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 16 through 19 Processing helix chain 'q' and resid 33 through 48 Processing helix chain 'q' and resid 58 through 75 removed outlier: 4.873A pdb=" N TYR q 66 " --> pdb=" O LEU q 62 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER q 67 " --> pdb=" O GLY q 63 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 16 removed outlier: 4.160A pdb=" N ASN r 15 " --> pdb=" O SER r 12 " (cutoff:3.500A) Processing helix chain 'r' and resid 18 through 41 removed outlier: 4.210A pdb=" N TYR r 34 " --> pdb=" O TRP r 30 " (cutoff:3.500A) Proline residue: r 35 - end of helix Processing helix chain 'r' and resid 57 through 61 Processing sheet with id= A, first strand: chain 'N' and resid 59 through 62 Processing sheet with id= B, first strand: chain 'n' and resid 59 through 62 1710 hydrogen bonds defined for protein. 5004 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: 21.69 Time building geometry restraints manager: 47.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.72 - 1.10: 33534 1.10 - 1.48: 21847 1.48 - 1.86: 17151 1.86 - 2.24: 0 2.24 - 2.62: 2 Bond restraints: 72534 Sorted by residual: bond pdb=" C GLU d 322 " pdb=" N ARG d 323 " ideal model delta sigma weight residual 1.335 2.625 -1.290 1.34e-02 5.57e+03 9.26e+03 bond pdb=" C GLU D 322 " pdb=" N ARG D 323 " ideal model delta sigma weight residual 1.335 2.625 -1.289 1.34e-02 5.57e+03 9.26e+03 bond pdb=" C08 Q7G e 407 " pdb=" C09 Q7G e 407 " ideal model delta sigma weight residual 0.930 1.535 -0.605 2.00e-02 2.50e+03 9.16e+02 bond pdb=" C08 Q7G E 407 " pdb=" C09 Q7G E 407 " ideal model delta sigma weight residual 0.930 1.535 -0.605 2.00e-02 2.50e+03 9.16e+02 bond pdb=" C08 Q7G n 201 " pdb=" C09 Q7G n 201 " ideal model delta sigma weight residual 0.930 1.534 -0.604 2.00e-02 2.50e+03 9.11e+02 ... (remaining 72529 not shown) Histogram of bond angle deviations from ideal: 72.58 - 85.52: 1 85.52 - 98.46: 2 98.46 - 111.40: 74423 111.40 - 124.34: 48513 124.34 - 137.27: 5337 Bond angle restraints: 128276 Sorted by residual: angle pdb=" CA GLU d 322 " pdb=" C GLU d 322 " pdb=" N ARG d 323 " ideal model delta sigma weight residual 117.30 86.63 30.67 1.16e+00 7.43e-01 6.99e+02 angle pdb=" CA GLU D 322 " pdb=" C GLU D 322 " pdb=" N ARG D 323 " ideal model delta sigma weight residual 117.30 86.63 30.67 1.16e+00 7.43e-01 6.99e+02 angle pdb=" O72 Q7G N 201 " pdb=" C73 Q7G N 201 " pdb=" O80 Q7G N 201 " ideal model delta sigma weight residual 62.42 110.05 -47.63 3.00e+00 1.11e-01 2.52e+02 angle pdb=" O72 Q7G n 201 " pdb=" C73 Q7G n 201 " pdb=" O80 Q7G n 201 " ideal model delta sigma weight residual 62.42 110.05 -47.63 3.00e+00 1.11e-01 2.52e+02 angle pdb=" CD2 TYR A 93 " pdb=" CE2 TYR A 93 " pdb=" HE2 TYR A 93 " ideal model delta sigma weight residual 120.20 72.58 47.62 3.00e+00 1.11e-01 2.52e+02 ... (remaining 128271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.05: 34410 32.05 - 64.09: 1808 64.09 - 96.14: 74 96.14 - 128.18: 14 128.18 - 160.23: 16 Dihedral angle restraints: 36322 sinusoidal: 20646 harmonic: 15676 Sorted by residual: dihedral pdb=" CG TYR A 93 " pdb=" CD2 TYR A 93 " pdb=" CE2 TYR A 93 " pdb=" HE2 TYR A 93 " ideal model delta harmonic sigma weight residual -180.00 -142.49 -37.51 0 5.00e+00 4.00e-02 5.63e+01 dihedral pdb=" C4 PEE F 202 " pdb=" O4P PEE F 202 " pdb=" P PEE F 202 " pdb=" O1P PEE F 202 " ideal model delta sinusoidal sigma weight residual 57.28 -102.95 160.23 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C4 PEE f 202 " pdb=" O4P PEE f 202 " pdb=" P PEE f 202 " pdb=" O1P PEE f 202 " ideal model delta sinusoidal sigma weight residual 57.28 -102.92 160.20 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 36319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 5024 0.230 - 0.459: 4 0.459 - 0.689: 0 0.689 - 0.918: 4 0.918 - 1.148: 4 Chirality restraints: 5036 Sorted by residual: chirality pdb=" C02 Q7G E 407 " pdb=" C03 Q7G E 407 " pdb=" C06 Q7G E 407 " pdb=" C10 Q7G E 407 " both_signs ideal model delta sigma weight residual True 1.85 3.00 -1.15 2.00e-01 2.50e+01 3.29e+01 chirality pdb=" C02 Q7G e 407 " pdb=" C03 Q7G e 407 " pdb=" C06 Q7G e 407 " pdb=" C10 Q7G e 407 " both_signs ideal model delta sigma weight residual True 1.85 2.99 -1.14 2.00e-01 2.50e+01 3.28e+01 chirality pdb=" C02 Q7G N 201 " pdb=" C03 Q7G N 201 " pdb=" C06 Q7G N 201 " pdb=" C10 Q7G N 201 " both_signs ideal model delta sigma weight residual True 1.85 2.98 -1.14 2.00e-01 2.50e+01 3.22e+01 ... (remaining 5033 not shown) Planarity restraints: 10052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU d 322 " 0.143 2.00e-02 2.50e+03 2.43e-01 5.89e+02 pdb=" C GLU d 322 " -0.406 2.00e-02 2.50e+03 pdb=" O GLU d 322 " 0.220 2.00e-02 2.50e+03 pdb=" N ARG d 323 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 322 " 0.143 2.00e-02 2.50e+03 2.43e-01 5.89e+02 pdb=" C GLU D 322 " -0.406 2.00e-02 2.50e+03 pdb=" O GLU D 322 " 0.220 2.00e-02 2.50e+03 pdb=" N ARG D 323 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 93 " 0.013 2.00e-02 2.50e+03 1.08e-01 3.50e+02 pdb=" CG TYR A 93 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 TYR A 93 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR A 93 " -0.076 2.00e-02 2.50e+03 pdb=" CE1 TYR A 93 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 93 " -0.194 2.00e-02 2.50e+03 pdb=" CZ TYR A 93 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 93 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 TYR A 93 " 0.087 2.00e-02 2.50e+03 pdb=" HD2 TYR A 93 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR A 93 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR A 93 " 0.275 2.00e-02 2.50e+03 ... (remaining 10049 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.69: 50 1.69 - 2.41: 30646 2.41 - 3.14: 209404 3.14 - 3.87: 290095 3.87 - 4.60: 474311 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1004506 Sorted by model distance: nonbonded pdb=" OXT AME e 1 " pdb=" H GLN e 2 " model vdw 0.958 1.960 nonbonded pdb=" OXT AME E 1 " pdb=" H GLN E 2 " model vdw 0.958 1.960 nonbonded pdb=" OXT AME e 1 " pdb=" CA GLN e 2 " model vdw 1.432 2.480 nonbonded pdb=" OXT AME E 1 " pdb=" CA GLN E 2 " model vdw 1.434 2.480 nonbonded pdb="HH21 ARG F 101 " pdb=" O PRO M 124 " model vdw 1.563 1.850 ... (remaining 1004501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } 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: 8.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.750 Extract box with map and model: 34.970 Check model and map are aligned: 0.840 Set scattering table: 0.510 Process input model: 178.290 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.680 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:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 237.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 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 : 0.015 1.290 38916 Z= 1.060 Angle : 0.873 47.631 52086 Z= 0.388 Chirality : 0.052 1.148 5036 Planarity : 0.006 0.243 6206 Dihedral : 18.008 160.226 16578 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.44 % Allowed : 1.64 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % 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: 2.70 (0.14), residues: 4006 helix: 2.49 (0.10), residues: 2602 sheet: -1.11 (0.98), residues: 20 loop : 0.56 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 56 HIS 0.007 0.001 HIS R 58 PHE 0.014 0.001 PHE A 144 TYR 0.080 0.002 TYR a 93 ARG 0.002 0.000 ARG e 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8012 Ramachandran restraints generated. 4006 Oldfield, 0 Emsley, 4006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8012 Ramachandran restraints generated. 4006 Oldfield, 0 Emsley, 4006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 800 time to evaluate : 4.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 MET cc_start: 0.8841 (mmp) cc_final: 0.8612 (mmp) REVERT: D 78 ASP cc_start: 0.7527 (m-30) cc_final: 0.6968 (m-30) REVERT: D 139 LYS cc_start: 0.8598 (mmtt) cc_final: 0.7579 (tttm) REVERT: E 290 GLU cc_start: 0.7399 (tt0) cc_final: 0.7099 (tp30) REVERT: F 55 MET cc_start: 0.8921 (mmt) cc_final: 0.8295 (mmt) REVERT: I 70 GLU cc_start: 0.8027 (tt0) cc_final: 0.7815 (tt0) REVERT: I 93 SER cc_start: 0.8315 (t) cc_final: 0.8077 (m) REVERT: M 66 ARG cc_start: 0.7984 (ttm110) cc_final: 0.7525 (ttp-170) REVERT: P 103 LYS cc_start: 0.7872 (mttt) cc_final: 0.7641 (mptp) REVERT: a 165 PHE cc_start: 0.8319 (t80) cc_final: 0.8099 (t80) REVERT: a 190 PHE cc_start: 0.7665 (t80) cc_final: 0.7393 (t80) REVERT: d 139 LYS cc_start: 0.8521 (mmtt) cc_final: 0.7434 (tttm) REVERT: f 55 MET cc_start: 0.8917 (mmt) cc_final: 0.8346 (mmt) REVERT: i 70 GLU cc_start: 0.8032 (tt0) cc_final: 0.7804 (tt0) REVERT: i 74 LYS cc_start: 0.8655 (mttt) cc_final: 0.8406 (mtmm) REVERT: i 93 SER cc_start: 0.8344 (t) cc_final: 0.8049 (p) REVERT: m 66 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7561 (ttp-170) REVERT: n 132 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8163 (pp20) REVERT: p 103 LYS cc_start: 0.7942 (mttt) cc_final: 0.7689 (mptp) outliers start: 16 outliers final: 6 residues processed: 812 average time/residue: 2.8885 time to fit residues: 2789.0968 Evaluate side-chains 625 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 618 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain a residue 144 PHE Chi-restraints excluded: chain e residue 226 THR Chi-restraints excluded: chain j residue 147 ILE Chi-restraints excluded: chain n residue 132 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 332 optimal weight: 0.0000 chunk 298 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 119 optimal weight: 0.0070 chunk 187 optimal weight: 0.3980 chunk 229 optimal weight: 4.9990 chunk 357 optimal weight: 0.9980 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 209 GLN E 24 GLN E 69 ASN E 256 GLN F 42 ASN J 131 ASN J 168 ASN K 36 GLN L 44 GLN L 50 GLN M 40 GLN N 54 GLN a 111 ASN a 209 GLN c 76 GLN d 72 GLN e 24 GLN e 256 GLN f 42 ASN j 131 ASN j 168 ASN l 44 GLN m 40 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 38916 Z= 0.148 Angle : 0.495 8.060 52086 Z= 0.240 Chirality : 0.033 0.133 5036 Planarity : 0.004 0.061 6206 Dihedral : 20.200 146.895 8213 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.90 % Allowed : 9.76 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % 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: 2.75 (0.14), residues: 4010 helix: 2.51 (0.10), residues: 2604 sheet: -0.82 (1.00), residues: 20 loop : 0.63 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 56 HIS 0.009 0.001 HIS r 61 PHE 0.011 0.001 PHE A 144 TYR 0.019 0.001 TYR f 62 ARG 0.010 0.000 ARG J 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 629 time to evaluate : 4.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 128 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.8051 (ttm110) REVERT: D 139 LYS cc_start: 0.8577 (mmtt) cc_final: 0.7478 (pttm) REVERT: E 290 GLU cc_start: 0.7392 (tt0) cc_final: 0.7110 (tp30) REVERT: F 55 MET cc_start: 0.8912 (mmt) cc_final: 0.8443 (mmt) REVERT: I 70 GLU cc_start: 0.8022 (tt0) cc_final: 0.7811 (tt0) REVERT: I 74 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8533 (mtmm) REVERT: K 66 MET cc_start: 0.8648 (mtp) cc_final: 0.8431 (mtp) REVERT: L 8 LYS cc_start: 0.8880 (mttm) cc_final: 0.8540 (mttp) REVERT: M 56 SER cc_start: 0.8575 (m) cc_final: 0.8346 (p) REVERT: M 66 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7578 (ttp-170) REVERT: M 67 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8378 (mt0) REVERT: O 59 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: P 103 LYS cc_start: 0.7878 (mttt) cc_final: 0.7650 (mptp) REVERT: Q 45 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: a 165 PHE cc_start: 0.8331 (t80) cc_final: 0.8117 (t80) REVERT: a 190 PHE cc_start: 0.7684 (t80) cc_final: 0.7414 (t80) REVERT: d 139 LYS cc_start: 0.8512 (mmtt) cc_final: 0.7434 (tttm) REVERT: e 186 ASP cc_start: 0.8281 (p0) cc_final: 0.8075 (p0) REVERT: f 55 MET cc_start: 0.8916 (mmt) cc_final: 0.8459 (mmt) REVERT: i 70 GLU cc_start: 0.8030 (tt0) cc_final: 0.7793 (tt0) REVERT: i 74 LYS cc_start: 0.8628 (mttt) cc_final: 0.8379 (mtmm) REVERT: i 93 SER cc_start: 0.8420 (t) cc_final: 0.8125 (p) REVERT: j 62 LYS cc_start: 0.8548 (mttt) cc_final: 0.8343 (mttp) REVERT: m 66 ARG cc_start: 0.7989 (ttm110) cc_final: 0.7578 (ttp-170) REVERT: n 132 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8228 (pp20) REVERT: o 59 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: p 103 LYS cc_start: 0.7959 (mttt) cc_final: 0.7704 (mptp) REVERT: q 32 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7929 (mt-10) REVERT: q 45 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7740 (tt0) outliers start: 33 outliers final: 13 residues processed: 645 average time/residue: 2.8990 time to fit residues: 2227.1999 Evaluate side-chains 619 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 600 time to evaluate : 4.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 132 GLU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain a residue 144 PHE Chi-restraints excluded: chain d residue 75 LYS Chi-restraints excluded: chain e residue 226 THR Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain m residue 109 VAL Chi-restraints excluded: chain n residue 132 GLU Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 77 SER Chi-restraints excluded: chain q residue 45 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 198 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 297 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 358 optimal weight: 1.9990 chunk 387 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 209 GLN E 24 GLN E 38 ASN F 38 ASN F 42 ASN F 66 HIS J 168 ASN M 120 GLN O 92 GLN a 111 ASN e 24 GLN e 38 ASN e 69 ASN f 38 ASN f 42 ASN f 66 HIS j 168 ASN m 40 GLN m 120 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 38916 Z= 0.291 Angle : 0.537 8.432 52086 Z= 0.270 Chirality : 0.037 0.133 5036 Planarity : 0.005 0.073 6206 Dihedral : 18.358 154.210 8209 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.48 % Allowed : 9.82 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % 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: 2.50 (0.13), residues: 4010 helix: 2.30 (0.10), residues: 2608 sheet: -0.61 (0.98), residues: 20 loop : 0.52 (0.18), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP o 67 HIS 0.008 0.001 HIS r 61 PHE 0.020 0.001 PHE A 58 TYR 0.022 0.002 TYR Q 36 ARG 0.006 0.001 ARG J 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 615 time to evaluate : 4.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7515 (ttt) REVERT: D 139 LYS cc_start: 0.8568 (mmtt) cc_final: 0.7547 (tttm) REVERT: F 55 MET cc_start: 0.9073 (mmt) cc_final: 0.8549 (mmt) REVERT: I 70 GLU cc_start: 0.8072 (tt0) cc_final: 0.7861 (tt0) REVERT: J 24 GLU cc_start: 0.7541 (tt0) cc_final: 0.7322 (tt0) REVERT: K 27 LYS cc_start: 0.8316 (mttt) cc_final: 0.8092 (mmmm) REVERT: K 108 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7624 (mt-10) REVERT: M 66 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7518 (ttp-170) REVERT: M 67 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8349 (mt0) REVERT: M 84 ILE cc_start: 0.9157 (mm) cc_final: 0.8872 (pt) REVERT: O 59 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: P 32 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7879 (ttp-170) REVERT: P 103 LYS cc_start: 0.7970 (mttt) cc_final: 0.7710 (mptp) REVERT: a 1 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7517 (ttt) REVERT: a 190 PHE cc_start: 0.7713 (t80) cc_final: 0.7404 (t80) REVERT: d 139 LYS cc_start: 0.8525 (mmtt) cc_final: 0.7420 (tttm) REVERT: e 195 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7636 (ttt-90) REVERT: f 55 MET cc_start: 0.9083 (mmt) cc_final: 0.8553 (mmt) REVERT: i 70 GLU cc_start: 0.8091 (tt0) cc_final: 0.7867 (tt0) REVERT: i 93 SER cc_start: 0.8476 (t) cc_final: 0.8223 (p) REVERT: j 62 LYS cc_start: 0.8607 (mttt) cc_final: 0.8395 (mttp) REVERT: k 108 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7616 (mt-10) REVERT: m 66 ARG cc_start: 0.7990 (ttm110) cc_final: 0.7525 (ttp-170) REVERT: m 84 ILE cc_start: 0.9158 (mm) cc_final: 0.8913 (pt) REVERT: n 132 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8081 (pt0) REVERT: n 150 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8062 (mtpp) REVERT: o 59 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: p 103 LYS cc_start: 0.8015 (mttt) cc_final: 0.7740 (mptp) REVERT: r 33 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8383 (tt0) outliers start: 54 outliers final: 27 residues processed: 642 average time/residue: 2.8410 time to fit residues: 2183.1657 Evaluate side-chains 626 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 590 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 144 PHE Chi-restraints excluded: chain e residue 77 CYS Chi-restraints excluded: chain e residue 195 ARG Chi-restraints excluded: chain e residue 226 THR Chi-restraints excluded: chain e residue 261 SER Chi-restraints excluded: chain e residue 346 SER Chi-restraints excluded: chain e residue 378 ARG Chi-restraints excluded: chain j residue 143 SER Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain m residue 138 THR Chi-restraints excluded: chain n residue 105 GLU Chi-restraints excluded: chain n residue 132 GLU Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 77 SER Chi-restraints excluded: chain o residue 80 GLN Chi-restraints excluded: chain p residue 71 SER Chi-restraints excluded: chain r residue 33 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 354 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 186 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 359 optimal weight: 1.9990 chunk 380 optimal weight: 1.9990 chunk 187 optimal weight: 0.0060 chunk 340 optimal weight: 3.9990 chunk 102 optimal weight: 0.0970 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 209 GLN E 24 GLN E 256 GLN F 42 ASN J 168 ASN a 111 ASN e 24 GLN e 256 GLN f 42 ASN j 168 ASN l 50 GLN m 40 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 38916 Z= 0.133 Angle : 0.459 8.390 52086 Z= 0.230 Chirality : 0.033 0.141 5036 Planarity : 0.004 0.071 6206 Dihedral : 16.952 154.740 8209 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.82 % Allowed : 10.86 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % 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: 2.75 (0.14), residues: 4010 helix: 2.48 (0.10), residues: 2612 sheet: -0.58 (1.01), residues: 20 loop : 0.66 (0.18), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 56 HIS 0.009 0.001 HIS R 61 PHE 0.012 0.001 PHE A 144 TYR 0.019 0.001 TYR f 62 ARG 0.012 0.000 ARG J 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 614 time to evaluate : 4.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7539 (ttt) REVERT: D 139 LYS cc_start: 0.8581 (mmtt) cc_final: 0.7577 (tttm) REVERT: F 55 MET cc_start: 0.8972 (mmt) cc_final: 0.8386 (mmt) REVERT: I 70 GLU cc_start: 0.8033 (tt0) cc_final: 0.7815 (tt0) REVERT: I 74 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8482 (mtmm) REVERT: M 66 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7545 (ttp-170) REVERT: M 67 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: M 84 ILE cc_start: 0.9169 (mm) cc_final: 0.8881 (pt) REVERT: O 59 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: P 32 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7612 (ttt180) REVERT: P 103 LYS cc_start: 0.7919 (mttt) cc_final: 0.7660 (mptp) REVERT: a 1 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7534 (ttt) REVERT: a 190 PHE cc_start: 0.7698 (t80) cc_final: 0.7419 (t80) REVERT: d 74 GLU cc_start: 0.8212 (tt0) cc_final: 0.7744 (tm-30) REVERT: d 139 LYS cc_start: 0.8532 (mmtt) cc_final: 0.7440 (tttm) REVERT: e 195 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7572 (ttt-90) REVERT: e 378 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8263 (mtt90) REVERT: f 55 MET cc_start: 0.8977 (mmt) cc_final: 0.8388 (mmt) REVERT: i 70 GLU cc_start: 0.8057 (tt0) cc_final: 0.7836 (tt0) REVERT: m 66 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7556 (ttp-170) REVERT: m 84 ILE cc_start: 0.9161 (mm) cc_final: 0.8916 (pt) REVERT: n 132 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7965 (pt0) REVERT: n 150 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8033 (mtpp) REVERT: o 59 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: p 103 LYS cc_start: 0.7965 (mttt) cc_final: 0.7700 (mptp) REVERT: r 33 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8265 (tt0) outliers start: 30 outliers final: 15 residues processed: 628 average time/residue: 2.9086 time to fit residues: 2191.3191 Evaluate side-chains 623 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 599 time to evaluate : 4.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 132 GLU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 144 PHE Chi-restraints excluded: chain e residue 77 CYS Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 195 ARG Chi-restraints excluded: chain e residue 226 THR Chi-restraints excluded: chain e residue 261 SER Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain n residue 132 GLU Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 77 SER Chi-restraints excluded: chain o residue 80 GLN Chi-restraints excluded: chain r residue 33 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 317 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 341 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 209 GLN E 24 GLN F 42 ASN J 168 ASN K 36 GLN N 114 GLN a 111 ASN e 24 GLN f 42 ASN j 168 ASN l 50 GLN m 40 GLN n 114 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 38916 Z= 0.381 Angle : 0.566 8.438 52086 Z= 0.285 Chirality : 0.039 0.141 5036 Planarity : 0.005 0.074 6206 Dihedral : 17.318 158.667 8209 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.53 % Allowed : 10.42 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % 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: 2.36 (0.13), residues: 4010 helix: 2.19 (0.10), residues: 2604 sheet: -0.51 (0.97), residues: 20 loop : 0.48 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 67 HIS 0.007 0.001 HIS E 162 PHE 0.021 0.002 PHE a 58 TYR 0.023 0.002 TYR Q 36 ARG 0.011 0.001 ARG j 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 596 time to evaluate : 4.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7556 (ttt) REVERT: D 139 LYS cc_start: 0.8601 (mmtt) cc_final: 0.7457 (pttt) REVERT: F 55 MET cc_start: 0.9096 (mmt) cc_final: 0.8470 (mmt) REVERT: F 110 LYS cc_start: 0.8604 (tttt) cc_final: 0.8358 (tttm) REVERT: I 70 GLU cc_start: 0.8095 (tt0) cc_final: 0.7893 (tt0) REVERT: M 66 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7637 (ttp-170) REVERT: M 67 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8264 (mt0) REVERT: O 59 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: P 32 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7858 (ttp-170) REVERT: P 103 LYS cc_start: 0.8021 (mttt) cc_final: 0.7737 (mptp) REVERT: a 1 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7565 (ttt) REVERT: a 190 PHE cc_start: 0.7734 (t80) cc_final: 0.7435 (t80) REVERT: d 139 LYS cc_start: 0.8549 (mmtt) cc_final: 0.7441 (tttm) REVERT: e 195 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7679 (ttt-90) REVERT: f 55 MET cc_start: 0.9104 (mmt) cc_final: 0.8544 (mmt) REVERT: i 70 GLU cc_start: 0.8104 (tt0) cc_final: 0.7895 (tt0) REVERT: m 66 ARG cc_start: 0.7997 (ttm110) cc_final: 0.7638 (ttp-170) REVERT: n 132 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: n 150 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8077 (mtpp) REVERT: o 59 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: p 103 LYS cc_start: 0.8070 (mttt) cc_final: 0.7777 (mptp) outliers start: 56 outliers final: 31 residues processed: 625 average time/residue: 3.0525 time to fit residues: 2294.7325 Evaluate side-chains 626 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 587 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 138 THR Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 144 PHE Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain e residue 77 CYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 195 ARG Chi-restraints excluded: chain e residue 226 THR Chi-restraints excluded: chain e residue 346 SER Chi-restraints excluded: chain j residue 25 SER Chi-restraints excluded: chain j residue 143 SER Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain m residue 138 THR Chi-restraints excluded: chain n residue 105 GLU Chi-restraints excluded: chain n residue 132 GLU Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 77 SER Chi-restraints excluded: chain o residue 80 GLN Chi-restraints excluded: chain p residue 71 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 128 optimal weight: 2.9990 chunk 342 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 223 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 381 optimal weight: 1.9990 chunk 316 optimal weight: 0.2980 chunk 176 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 209 GLN F 42 ASN J 168 ASN a 111 ASN e 24 GLN f 42 ASN j 168 ASN l 50 GLN m 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 38916 Z= 0.245 Angle : 0.506 8.464 52086 Z= 0.256 Chirality : 0.036 0.138 5036 Planarity : 0.005 0.082 6206 Dihedral : 16.762 159.838 8209 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.42 % Allowed : 11.02 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % 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: 2.39 (0.13), residues: 4010 helix: 2.21 (0.10), residues: 2604 sheet: -0.44 (1.00), residues: 20 loop : 0.52 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 56 HIS 0.008 0.001 HIS R 61 PHE 0.017 0.001 PHE a 58 TYR 0.019 0.001 TYR Q 36 ARG 0.009 0.000 ARG j 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 593 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7547 (ttt) REVERT: D 74 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7831 (tm-30) REVERT: D 139 LYS cc_start: 0.8570 (mmtt) cc_final: 0.7568 (tttm) REVERT: F 55 MET cc_start: 0.9069 (mmt) cc_final: 0.8502 (mmt) REVERT: I 70 GLU cc_start: 0.8070 (tt0) cc_final: 0.7869 (tt0) REVERT: I 74 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8530 (mtmm) REVERT: M 66 ARG cc_start: 0.7999 (ttm110) cc_final: 0.7646 (ttp-170) REVERT: M 84 ILE cc_start: 0.9145 (mm) cc_final: 0.8882 (pt) REVERT: O 59 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: P 32 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7570 (ttp-170) REVERT: P 103 LYS cc_start: 0.8005 (mttt) cc_final: 0.7701 (mptp) REVERT: a 1 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7550 (ttt) REVERT: a 190 PHE cc_start: 0.7720 (t80) cc_final: 0.7443 (t80) REVERT: d 128 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.8065 (ttm110) REVERT: d 139 LYS cc_start: 0.8543 (mmtt) cc_final: 0.7438 (tttm) REVERT: e 195 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7690 (ttt-90) REVERT: f 55 MET cc_start: 0.9081 (mmt) cc_final: 0.8523 (mmt) REVERT: i 70 GLU cc_start: 0.8095 (tt0) cc_final: 0.7883 (tt0) REVERT: m 66 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7654 (ttp-170) REVERT: m 67 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8283 (mt0) REVERT: m 84 ILE cc_start: 0.9136 (mm) cc_final: 0.8912 (pt) REVERT: n 132 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: n 150 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8069 (mtpp) REVERT: o 59 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: p 103 LYS cc_start: 0.8056 (mttt) cc_final: 0.7764 (mptp) outliers start: 52 outliers final: 25 residues processed: 617 average time/residue: 2.8916 time to fit residues: 2123.3790 Evaluate side-chains 618 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 585 time to evaluate : 4.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 144 PHE Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain e residue 77 CYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 195 ARG Chi-restraints excluded: chain e residue 226 THR Chi-restraints excluded: chain e residue 346 SER Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain n residue 105 GLU Chi-restraints excluded: chain n residue 132 GLU Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 77 SER Chi-restraints excluded: chain p residue 71 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 367 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 320 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 379 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 209 GLN E 24 GLN F 42 ASN J 168 ASN K 36 GLN a 111 ASN e 24 GLN f 42 ASN j 168 ASN l 50 GLN m 40 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 38916 Z= 0.384 Angle : 0.565 8.424 52086 Z= 0.285 Chirality : 0.039 0.137 5036 Planarity : 0.005 0.093 6206 Dihedral : 17.127 163.029 8209 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.42 % Allowed : 11.08 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % 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: 2.17 (0.13), residues: 4010 helix: 2.04 (0.10), residues: 2604 sheet: -0.47 (0.97), residues: 20 loop : 0.41 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 67 HIS 0.007 0.001 HIS r 61 PHE 0.021 0.002 PHE A 58 TYR 0.022 0.002 TYR Q 36 ARG 0.014 0.001 ARG j 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 602 time to evaluate : 4.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7537 (ttt) REVERT: D 74 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7905 (tm-30) REVERT: D 78 ASP cc_start: 0.7694 (m-30) cc_final: 0.7309 (m-30) REVERT: D 139 LYS cc_start: 0.8584 (mmtt) cc_final: 0.7596 (tttm) REVERT: F 55 MET cc_start: 0.9101 (mmt) cc_final: 0.8484 (mmt) REVERT: M 67 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: M 84 ILE cc_start: 0.9150 (mm) cc_final: 0.8879 (pt) REVERT: O 59 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: P 32 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7770 (ttt180) REVERT: P 69 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8472 (pttm) REVERT: P 103 LYS cc_start: 0.8040 (mttt) cc_final: 0.7749 (mptp) REVERT: a 1 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7539 (ttt) REVERT: a 190 PHE cc_start: 0.7755 (t80) cc_final: 0.7445 (t80) REVERT: d 128 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.8109 (ttm110) REVERT: d 139 LYS cc_start: 0.8556 (mmtt) cc_final: 0.7448 (tttm) REVERT: e 195 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7688 (ttt-90) REVERT: f 55 MET cc_start: 0.9112 (mmt) cc_final: 0.8503 (mmt) REVERT: i 70 GLU cc_start: 0.8125 (tt0) cc_final: 0.7919 (tt0) REVERT: m 66 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7820 (ttp-110) REVERT: m 67 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: m 84 ILE cc_start: 0.9142 (mm) cc_final: 0.8910 (pt) REVERT: n 132 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: n 150 LYS cc_start: 0.8583 (ttmt) cc_final: 0.8080 (mtpp) REVERT: o 59 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: p 69 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8485 (pttm) REVERT: p 103 LYS cc_start: 0.8083 (mttt) cc_final: 0.7784 (mptp) outliers start: 52 outliers final: 31 residues processed: 628 average time/residue: 2.8912 time to fit residues: 2163.4124 Evaluate side-chains 633 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 591 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 144 PHE Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain e residue 77 CYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 195 ARG Chi-restraints excluded: chain e residue 226 THR Chi-restraints excluded: chain e residue 346 SER Chi-restraints excluded: chain j residue 25 SER Chi-restraints excluded: chain j residue 143 SER Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain n residue 105 GLU Chi-restraints excluded: chain n residue 132 GLU Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 77 SER Chi-restraints excluded: chain p residue 69 LYS Chi-restraints excluded: chain p residue 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 234 optimal weight: 4.9990 chunk 151 optimal weight: 0.0020 chunk 226 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 209 GLN E 24 GLN F 42 ASN J 168 ASN a 111 ASN e 24 GLN f 42 ASN i 96 GLN j 168 ASN l 50 GLN m 40 GLN o 80 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 38916 Z= 0.182 Angle : 0.492 8.298 52086 Z= 0.248 Chirality : 0.035 0.139 5036 Planarity : 0.005 0.098 6206 Dihedral : 16.327 163.027 8209 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.15 % Allowed : 11.79 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % 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: 2.42 (0.14), residues: 4010 helix: 2.22 (0.10), residues: 2606 sheet: -0.51 (1.00), residues: 20 loop : 0.56 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 56 HIS 0.009 0.001 HIS R 61 PHE 0.014 0.001 PHE i 14 TYR 0.018 0.001 TYR F 62 ARG 0.014 0.000 ARG J 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 602 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7532 (ttt) REVERT: D 74 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7814 (tm-30) REVERT: D 139 LYS cc_start: 0.8580 (mmtt) cc_final: 0.7586 (tttm) REVERT: F 55 MET cc_start: 0.9056 (mmt) cc_final: 0.8421 (mmt) REVERT: I 74 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8500 (mtmm) REVERT: M 30 LYS cc_start: 0.8547 (mmmt) cc_final: 0.8256 (mtmt) REVERT: M 84 ILE cc_start: 0.9139 (mm) cc_final: 0.8881 (pt) REVERT: O 59 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: P 32 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7602 (ttp-170) REVERT: P 69 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8456 (pttm) REVERT: P 103 LYS cc_start: 0.7983 (mttt) cc_final: 0.7688 (mptp) REVERT: a 1 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7522 (ttt) REVERT: a 190 PHE cc_start: 0.7726 (t80) cc_final: 0.7427 (t80) REVERT: d 128 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.8105 (ttm110) REVERT: d 139 LYS cc_start: 0.8517 (mmtt) cc_final: 0.7297 (pttm) REVERT: e 195 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7642 (ttt-90) REVERT: f 55 MET cc_start: 0.9068 (mmt) cc_final: 0.8443 (mmt) REVERT: i 70 GLU cc_start: 0.8087 (tt0) cc_final: 0.7873 (tt0) REVERT: m 66 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7814 (ttp-110) REVERT: m 84 ILE cc_start: 0.9148 (mm) cc_final: 0.8918 (pt) REVERT: n 132 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8074 (pt0) REVERT: n 150 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8079 (mtpp) REVERT: o 59 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: p 103 LYS cc_start: 0.8026 (mttt) cc_final: 0.7729 (mptp) outliers start: 42 outliers final: 24 residues processed: 622 average time/residue: 2.9107 time to fit residues: 2157.8785 Evaluate side-chains 625 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 593 time to evaluate : 4.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 144 PHE Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 233 LEU Chi-restraints excluded: chain e residue 77 CYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 195 ARG Chi-restraints excluded: chain e residue 226 THR Chi-restraints excluded: chain e residue 346 SER Chi-restraints excluded: chain j residue 143 SER Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain n residue 105 GLU Chi-restraints excluded: chain n residue 132 GLU Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 345 optimal weight: 2.9990 chunk 363 optimal weight: 4.9990 chunk 331 optimal weight: 0.5980 chunk 353 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 319 optimal weight: 2.9990 chunk 334 optimal weight: 1.9990 chunk 352 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 209 GLN E 24 GLN F 42 ASN J 125 GLN J 168 ASN K 36 GLN O 80 GLN R 61 HIS a 111 ASN e 24 GLN f 42 ASN j 168 ASN l 50 GLN m 40 GLN o 80 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38916 Z= 0.284 Angle : 0.526 8.223 52086 Z= 0.265 Chirality : 0.036 0.135 5036 Planarity : 0.005 0.104 6206 Dihedral : 16.349 164.597 8209 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.23 % Allowed : 11.79 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % 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: 2.34 (0.14), residues: 4010 helix: 2.16 (0.10), residues: 2606 sheet: -0.49 (0.99), residues: 20 loop : 0.53 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 67 HIS 0.008 0.001 HIS R 61 PHE 0.018 0.001 PHE A 58 TYR 0.020 0.002 TYR Q 36 ARG 0.016 0.000 ARG J 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 596 time to evaluate : 4.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7545 (ttt) REVERT: D 74 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7897 (tm-30) REVERT: D 139 LYS cc_start: 0.8590 (mmtt) cc_final: 0.7615 (tttm) REVERT: F 55 MET cc_start: 0.9075 (mmt) cc_final: 0.8510 (mmt) REVERT: M 30 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8201 (mtmt) REVERT: M 84 ILE cc_start: 0.9147 (mm) cc_final: 0.8880 (pt) REVERT: N 132 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7461 (pp20) REVERT: O 59 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: P 32 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7807 (ttt180) REVERT: P 69 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8461 (pttm) REVERT: P 103 LYS cc_start: 0.8020 (mttt) cc_final: 0.7734 (mptp) REVERT: a 1 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7551 (ttt) REVERT: a 190 PHE cc_start: 0.7730 (t80) cc_final: 0.7453 (t80) REVERT: d 139 LYS cc_start: 0.8529 (mmtt) cc_final: 0.7434 (tttm) REVERT: e 138 ARG cc_start: 0.7419 (tpt90) cc_final: 0.7169 (tpt90) REVERT: e 195 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7678 (ttt-90) REVERT: f 55 MET cc_start: 0.9089 (mmt) cc_final: 0.8539 (mmt) REVERT: i 70 GLU cc_start: 0.8120 (tt0) cc_final: 0.7910 (tt0) REVERT: m 66 ARG cc_start: 0.8026 (ttm110) cc_final: 0.7816 (ttp-110) REVERT: m 84 ILE cc_start: 0.9151 (mm) cc_final: 0.8914 (pt) REVERT: n 132 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8115 (pt0) REVERT: n 150 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8090 (mtpp) REVERT: o 59 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: p 69 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8470 (pttm) REVERT: p 103 LYS cc_start: 0.8077 (mttt) cc_final: 0.7760 (mptp) outliers start: 45 outliers final: 27 residues processed: 622 average time/residue: 2.9279 time to fit residues: 2170.8636 Evaluate side-chains 627 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 590 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain N residue 132 GLU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 144 PHE Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain e residue 77 CYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 195 ARG Chi-restraints excluded: chain e residue 226 THR Chi-restraints excluded: chain e residue 346 SER Chi-restraints excluded: chain j residue 143 SER Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain n residue 105 GLU Chi-restraints excluded: chain n residue 132 GLU Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 77 SER Chi-restraints excluded: chain p residue 69 LYS Chi-restraints excluded: chain p residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 232 optimal weight: 6.9990 chunk 374 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 260 optimal weight: 0.9990 chunk 392 optimal weight: 1.9990 chunk 361 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 209 GLN F 42 ASN J 125 GLN J 168 ASN a 111 ASN e 24 GLN f 42 ASN j 168 ASN m 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 38916 Z= 0.289 Angle : 0.530 7.997 52086 Z= 0.267 Chirality : 0.037 0.137 5036 Planarity : 0.005 0.109 6206 Dihedral : 16.356 166.000 8209 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.18 % Allowed : 11.79 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % 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: 2.29 (0.13), residues: 4010 helix: 2.12 (0.10), residues: 2606 sheet: -0.57 (1.00), residues: 20 loop : 0.50 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 67 HIS 0.008 0.001 HIS r 61 PHE 0.018 0.001 PHE A 58 TYR 0.020 0.002 TYR Q 36 ARG 0.016 0.000 ARG J 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8020 Ramachandran restraints generated. 4010 Oldfield, 0 Emsley, 4010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 591 time to evaluate : 5.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7526 (ttt) REVERT: D 74 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7897 (tm-30) REVERT: D 78 ASP cc_start: 0.7739 (m-30) cc_final: 0.7381 (m-30) REVERT: D 139 LYS cc_start: 0.8584 (mmtt) cc_final: 0.7604 (tttm) REVERT: F 55 MET cc_start: 0.9079 (mmt) cc_final: 0.8515 (mmt) REVERT: I 41 MET cc_start: 0.8614 (mmt) cc_final: 0.8088 (mmt) REVERT: I 74 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8530 (mtmm) REVERT: M 30 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8210 (mtmt) REVERT: M 84 ILE cc_start: 0.9165 (mm) cc_final: 0.8888 (pt) REVERT: N 132 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7417 (pp20) REVERT: O 59 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: P 32 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7775 (ttt180) REVERT: P 69 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8467 (pttm) REVERT: P 103 LYS cc_start: 0.8019 (mttt) cc_final: 0.7732 (mptp) REVERT: a 1 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7525 (ttt) REVERT: a 190 PHE cc_start: 0.7749 (t80) cc_final: 0.7467 (t80) REVERT: d 139 LYS cc_start: 0.8531 (mmtt) cc_final: 0.7462 (tttm) REVERT: e 9 LYS cc_start: 0.8392 (mtpp) cc_final: 0.7751 (mptt) REVERT: e 138 ARG cc_start: 0.7414 (tpt90) cc_final: 0.7163 (tpt90) REVERT: e 195 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7686 (ttt-90) REVERT: f 55 MET cc_start: 0.9094 (mmt) cc_final: 0.8544 (mmt) REVERT: i 70 GLU cc_start: 0.8116 (tt0) cc_final: 0.7906 (tt0) REVERT: m 66 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7816 (ttp-110) REVERT: m 84 ILE cc_start: 0.9155 (mm) cc_final: 0.8913 (pt) REVERT: n 132 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8129 (pt0) REVERT: n 150 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8093 (mtpp) REVERT: o 59 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: p 69 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8475 (pttm) REVERT: p 103 LYS cc_start: 0.8082 (mttt) cc_final: 0.7785 (mptp) outliers start: 43 outliers final: 27 residues processed: 615 average time/residue: 2.9606 time to fit residues: 2187.3275 Evaluate side-chains 627 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 590 time to evaluate : 4.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain N residue 132 GLU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 32 ARG Chi-restraints excluded: chain P residue 69 LYS Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 144 PHE Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain e residue 77 CYS Chi-restraints excluded: chain e residue 187 VAL Chi-restraints excluded: chain e residue 195 ARG Chi-restraints excluded: chain e residue 226 THR Chi-restraints excluded: chain e residue 346 SER Chi-restraints excluded: chain j residue 143 SER Chi-restraints excluded: chain m residue 104 LEU Chi-restraints excluded: chain n residue 105 GLU Chi-restraints excluded: chain n residue 132 GLU Chi-restraints excluded: chain o residue 43 LEU Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 77 SER Chi-restraints excluded: chain p residue 69 LYS Chi-restraints excluded: chain p residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 248 optimal weight: 0.9980 chunk 332 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 321 optimal weight: 0.0980 chunk 39 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 209 GLN E 24 GLN F 42 ASN J 125 GLN J 168 ASN K 36 GLN a 111 ASN e 24 GLN f 42 ASN j 168 ASN l 50 GLN m 40 GLN r 61 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.087681 restraints weight = 128585.412| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.24 r_work: 0.2768 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38916 Z= 0.180 Angle : 0.490 7.736 52086 Z= 0.246 Chirality : 0.034 0.138 5036 Planarity : 0.004 0.111 6206 Dihedral : 15.644 165.875 8209 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.98 % Allowed : 11.93 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % 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: 2.52 (0.14), residues: 4010 helix: 2.29 (0.10), residues: 2606 sheet: -0.49 (1.01), residues: 20 loop : 0.61 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 56 HIS 0.008 0.001 HIS r 61 PHE 0.014 0.001 PHE i 14 TYR 0.018 0.001 TYR Q 36 ARG 0.017 0.000 ARG J 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30376.90 seconds wall clock time: 520 minutes 49.16 seconds (31249.16 seconds total)