Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 23:09:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/04_2023/8ap7_15560_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/04_2023/8ap7_15560.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/04_2023/8ap7_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_15560/04_2023/8ap7_15560_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/04_2023/8ap7_15560_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/04_2023/8ap7_15560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/04_2023/8ap7_15560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/04_2023/8ap7_15560_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap7_15560/04_2023/8ap7_15560_trim_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 22.23, per 1000 atoms: 0.31 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: 45.89 Conformation dependent library (CDL) restraints added in 4.0 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: 2.24 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: 21.70 Time building geometry restraints manager: 48.28 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 - 29.28: 29646 29.28 - 58.56: 1297 58.56 - 87.84: 121 87.84 - 117.12: 8 117.12 - 146.40: 2 Dihedral angle restraints: 31074 sinusoidal: 15398 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=" C32 PEE R 101 " pdb=" C30 PEE R 101 " pdb=" C31 PEE R 101 " pdb=" O3 PEE R 101 " ideal model delta sinusoidal sigma weight residual 161.16 -52.44 -146.40 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C32 PEE r 101 " pdb=" C30 PEE r 101 " pdb=" C31 PEE r 101 " pdb=" O3 PEE r 101 " ideal model delta sinusoidal sigma weight residual 161.16 -52.48 -146.36 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 31071 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: 13.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.740 Extract box with map and model: 36.700 Check model and map are aligned: 0.950 Set scattering table: 0.470 Process input model: 164.750 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.660 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: 0.020 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 231.480 ------------------------------------------------------------------------------- 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 : 16.379 146.398 15666 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 % 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 *********************** 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 : 4.393 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 outliers start: 16 outliers final: 6 residues processed: 812 average time/residue: 2.9209 time to fit residues: 2827.8745 Evaluate side-chains 624 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 618 time to evaluate : 4.360 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 5.3940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 332 optimal weight: 0.1980 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: 0.5980 chunk 229 optimal weight: 1.9990 chunk 357 optimal weight: 0.9990 overall best weight: 0.4800 ------------------------------------------------------------------------------- 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 l 50 GLN m 40 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 38916 Z= 0.155 Angle : 0.490 7.648 52086 Z= 0.242 Chirality : 0.033 0.133 5036 Planarity : 0.004 0.063 6206 Dihedral : 18.423 137.483 7288 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.93 % 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: 2.72 (0.14), residues: 4010 helix: 2.48 (0.10), residues: 2604 sheet: -0.86 (1.00), residues: 20 loop : 0.61 (0.18), residues: 1386 *********************** 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 658 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 624 time to evaluate : 4.444 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 outliers start: 34 outliers final: 16 residues processed: 638 average time/residue: 3.0007 time to fit residues: 2304.1135 Evaluate side-chains 620 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 604 time to evaluate : 4.421 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 9 average time/residue: 1.3585 time to fit residues: 23.4507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 98 optimal weight: 0.9980 chunk 358 optimal weight: 1.9990 chunk 387 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 355 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 120 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 38916 Z= 0.257 Angle : 0.523 8.506 52086 Z= 0.263 Chirality : 0.036 0.130 5036 Planarity : 0.005 0.086 6206 Dihedral : 16.310 141.706 7288 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 1.39 % 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: 2.54 (0.14), residues: 4010 helix: 2.34 (0.10), residues: 2606 sheet: -0.65 (0.97), residues: 20 loop : 0.53 (0.18), residues: 1384 *********************** 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 670 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 619 time to evaluate : 4.348 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 outliers start: 51 outliers final: 27 residues processed: 644 average time/residue: 2.9026 time to fit residues: 2238.1374 Evaluate side-chains 628 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 601 time to evaluate : 4.304 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 14 residues processed: 13 average time/residue: 0.8779 time to fit residues: 23.7986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 39 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 240 optimal weight: 0.9980 chunk 359 optimal weight: 1.9990 chunk 380 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 340 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 L 50 GLN a 111 ASN e 24 GLN e 256 GLN f 42 ASN j 168 ASN m 40 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 38916 Z= 0.233 Angle : 0.498 8.331 52086 Z= 0.250 Chirality : 0.035 0.137 5036 Planarity : 0.004 0.068 6206 Dihedral : 15.397 144.258 7288 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 1.07 % 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 (0.14), residues: 4010 helix: 2.30 (0.10), residues: 2610 sheet: -0.53 (0.99), residues: 20 loop : 0.53 (0.18), residues: 1380 *********************** 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 653 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 614 time to evaluate : 4.411 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 outliers start: 39 outliers final: 23 residues processed: 635 average time/residue: 2.9741 time to fit residues: 2261.7295 Evaluate side-chains 625 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 602 time to evaluate : 4.368 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 8 average time/residue: 0.6475 time to fit residues: 15.0284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 157 optimal weight: 1.9990 chunk 324 optimal weight: 4.9990 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 L 50 GLN N 114 GLN a 111 ASN e 24 GLN f 42 ASN j 168 ASN m 40 GLN n 114 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 38916 Z= 0.371 Angle : 0.560 8.546 52086 Z= 0.282 Chirality : 0.039 0.136 5036 Planarity : 0.005 0.074 6206 Dihedral : 15.524 157.220 7288 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.56 % 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: 2.26 (0.13), residues: 4010 helix: 2.12 (0.10), residues: 2604 sheet: -0.54 (0.95), residues: 20 loop : 0.43 (0.18), residues: 1386 *********************** 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 668 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 611 time to evaluate : 4.505 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 outliers start: 57 outliers final: 30 residues processed: 641 average time/residue: 2.9136 time to fit residues: 2237.0425 Evaluate side-chains 628 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 598 time to evaluate : 4.360 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 17 residues processed: 13 average time/residue: 0.7887 time to fit residues: 22.8572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 94 optimal weight: 1.9990 chunk 381 optimal weight: 1.9990 chunk 316 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 L 50 GLN a 111 ASN e 24 GLN f 42 ASN j 168 ASN m 40 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 38916 Z= 0.289 Angle : 0.527 8.438 52086 Z= 0.267 Chirality : 0.037 0.139 5036 Planarity : 0.005 0.084 6206 Dihedral : 15.182 157.782 7288 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 1.23 % 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: 2.23 (0.13), residues: 4010 helix: 2.10 (0.10), residues: 2604 sheet: -0.55 (0.96), residues: 20 loop : 0.42 (0.18), residues: 1386 *********************** 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 649 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 604 time to evaluate : 4.444 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 outliers start: 45 outliers final: 27 residues processed: 626 average time/residue: 2.9533 time to fit residues: 2208.2592 Evaluate side-chains 618 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 591 time to evaluate : 4.386 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 17 residues processed: 10 average time/residue: 0.7766 time to fit residues: 18.7566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 367 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 379 optimal weight: 0.4980 chunk 237 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 L 50 GLN a 111 ASN e 24 GLN f 42 ASN j 168 ASN m 40 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 38916 Z= 0.272 Angle : 0.524 8.389 52086 Z= 0.264 Chirality : 0.036 0.135 5036 Planarity : 0.004 0.092 6206 Dihedral : 14.823 158.946 7288 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.18 % 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: 2.27 (0.13), residues: 4010 helix: 2.12 (0.10), residues: 2604 sheet: -0.60 (0.96), residues: 20 loop : 0.45 (0.18), residues: 1386 *********************** 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 646 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 603 time to evaluate : 4.351 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 outliers start: 43 outliers final: 23 residues processed: 628 average time/residue: 2.8975 time to fit residues: 2186.7436 Evaluate side-chains 618 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 595 time to evaluate : 4.350 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.7061 time to fit residues: 11.7172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 234 optimal weight: 5.9990 chunk 151 optimal weight: 0.0000 chunk 226 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 241 optimal weight: 0.2980 chunk 258 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 a 111 ASN e 24 GLN f 42 ASN j 168 ASN m 40 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 38916 Z= 0.161 Angle : 0.485 8.185 52086 Z= 0.243 Chirality : 0.034 0.144 5036 Planarity : 0.004 0.099 6206 Dihedral : 13.997 155.007 7288 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.15 % 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: 2.51 (0.14), residues: 4010 helix: 2.29 (0.10), residues: 2606 sheet: -0.51 (0.98), residues: 20 loop : 0.57 (0.18), residues: 1384 *********************** 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 645 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 603 time to evaluate : 4.683 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 outliers start: 42 outliers final: 24 residues processed: 626 average time/residue: 2.9116 time to fit residues: 2183.5552 Evaluate side-chains 612 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 588 time to evaluate : 4.372 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 6 average time/residue: 0.8808 time to fit residues: 13.9534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 353 optimal weight: 0.2980 chunk 212 optimal weight: 1.9990 chunk 154 optimal weight: 0.0980 chunk 277 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 319 optimal weight: 2.9990 chunk 334 optimal weight: 1.9990 chunk 352 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 e 256 GLN f 42 ASN i 96 GLN j 168 ASN m 40 GLN r 61 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2507 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= 0.164 Angle : 0.483 7.957 52086 Z= 0.241 Chirality : 0.034 0.138 5036 Planarity : 0.004 0.105 6206 Dihedral : 13.487 151.951 7288 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.85 % 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: 2.62 (0.14), residues: 4010 helix: 2.37 (0.10), residues: 2606 sheet: -0.45 (1.00), residues: 20 loop : 0.64 (0.18), residues: 1384 *********************** 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 624 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 593 time to evaluate : 4.385 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 outliers start: 31 outliers final: 21 residues processed: 616 average time/residue: 2.9148 time to fit residues: 2152.2234 Evaluate side-chains 609 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 588 time to evaluate : 4.391 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 2 average time/residue: 0.7407 time to fit residues: 8.0159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 232 optimal weight: 8.9990 chunk 374 optimal weight: 3.9990 chunk 228 optimal weight: 0.8980 chunk 177 optimal weight: 0.0980 chunk 260 optimal weight: 1.9990 chunk 392 optimal weight: 0.7980 chunk 361 optimal weight: 0.9980 chunk 312 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 241 optimal weight: 0.2980 chunk 191 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 38916 Z= 0.169 Angle : 0.484 7.774 52086 Z= 0.241 Chirality : 0.034 0.138 5036 Planarity : 0.004 0.098 6206 Dihedral : 13.103 148.888 7288 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 0.74 % 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: 2.67 (0.14), residues: 4010 helix: 2.41 (0.10), residues: 2608 sheet: -0.48 (1.01), residues: 20 loop : 0.65 (0.18), residues: 1382 ********************** 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 631 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 604 time to evaluate : 4.398 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 outliers start: 27 outliers final: 21 residues processed: 625 average time/residue: 2.8845 time to fit residues: 2159.6680 Evaluate side-chains 612 residues out of total 3656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 591 time to evaluate : 4.350 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.6869 time to fit residues: 7.8200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 248 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 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: 0.2980 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 m 40 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.087625 restraints weight = 128732.712| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.26 r_work: 0.2709 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 38916 Z= 0.229 Angle : 0.504 7.521 52086 Z= 0.253 Chirality : 0.035 0.136 5036 Planarity : 0.004 0.111 6206 Dihedral : 13.310 151.808 7288 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 0.71 % 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: 2.56 (0.14), residues: 4010 helix: 2.33 (0.10), residues: 2606 sheet: -0.43 (0.99), residues: 20 loop : 0.61 (0.18), residues: 1384 =============================================================================== Job complete usr+sys time: 29990.53 seconds wall clock time: 514 minutes 34.01 seconds (30874.01 seconds total)