Starting phenix.real_space_refine on Tue Feb 13 20:40:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c98_30308/02_2024/7c98_30308_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c98_30308/02_2024/7c98_30308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c98_30308/02_2024/7c98_30308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c98_30308/02_2024/7c98_30308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c98_30308/02_2024/7c98_30308_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c98_30308/02_2024/7c98_30308_updated.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 Ca 3 9.91 5 P 27 5.49 5 S 33 5.16 5 C 4755 2.51 5 N 1341 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.66, per 1000 atoms: 0.61 Number of scatterers: 7656 At special positions: 0 Unit cell: (81.48, 102.48, 114.24, 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) Ca 3 19.99 S 33 16.00 P 27 15.00 O 1497 8.00 N 1341 7.00 C 4755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.2 seconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 6 sheets defined 36.9% alpha, 10.4% beta 7 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.672A pdb=" N LYS A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 70 through 78 removed outlier: 4.197A pdb=" N ASN A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 97 removed outlier: 3.513A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N MET A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 132 through 144 removed outlier: 4.086A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 167 through 176 removed outlier: 3.724A pdb=" N ASP A 172 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 174 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.572A pdb=" N MET A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.106A pdb=" N LEU A 228 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A 229 " --> pdb=" O MET A 226 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG A 230 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 259 removed outlier: 3.574A pdb=" N GLN A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 37 through 43 removed outlier: 3.672A pdb=" N LYS B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 70 through 78 removed outlier: 4.196A pdb=" N ASN B 78 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 97 removed outlier: 3.514A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N MET B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 132 through 144 removed outlier: 4.087A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN B 144 " --> pdb=" O CYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 167 through 176 removed outlier: 3.724A pdb=" N ASP B 172 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 174 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.571A pdb=" N MET B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 4.107A pdb=" N LEU B 228 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 229 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG B 230 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 232 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 259 removed outlier: 3.574A pdb=" N GLN B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.673A pdb=" N LYS C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'C' and resid 70 through 78 removed outlier: 4.197A pdb=" N ASN C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 97 removed outlier: 3.513A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N MET C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 No H-bonds generated for 'chain 'C' and resid 107 through 110' Processing helix chain 'C' and resid 132 through 144 removed outlier: 4.088A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN C 144 " --> pdb=" O CYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 167 through 176 removed outlier: 3.724A pdb=" N ASP C 172 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA C 174 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.571A pdb=" N MET C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP C 204 " --> pdb=" O MET C 200 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 4.106A pdb=" N LEU C 228 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE C 229 " --> pdb=" O MET C 226 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG C 230 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP C 232 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 259 removed outlier: 3.575A pdb=" N GLN C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 Processing sheet with id= A, first strand: chain 'A' and resid 299 through 302 removed outlier: 6.843A pdb=" N VAL A 264 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ALA A 124 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 266 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A 267 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER A 224 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS A 155 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 220 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 157 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE A 222 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 159 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N SER A 224 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 303 through 305 Processing sheet with id= C, first strand: chain 'B' and resid 299 through 302 removed outlier: 6.843A pdb=" N VAL B 264 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ALA B 124 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 266 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 267 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER B 224 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS B 155 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU B 220 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 157 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE B 222 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B 159 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N SER B 224 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 303 through 305 Processing sheet with id= E, first strand: chain 'C' and resid 299 through 302 removed outlier: 6.843A pdb=" N VAL C 264 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ALA C 124 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 266 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR C 267 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER C 224 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS C 155 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU C 220 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE C 157 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE C 222 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 159 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER C 224 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 303 through 305 177 hydrogen bonds defined for protein. 414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1747 1.33 - 1.45: 1584 1.45 - 1.57: 4376 1.57 - 1.68: 47 1.68 - 1.80: 59 Bond restraints: 7813 Sorted by residual: bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 1.795 1.684 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.608 0.092 2.00e-02 2.50e+03 2.14e+01 ... (remaining 7808 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.67: 294 106.67 - 114.05: 4541 114.05 - 121.43: 3851 121.43 - 128.81: 1875 128.81 - 136.19: 39 Bond angle restraints: 10600 Sorted by residual: angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 105.78 21.17 3.00e+00 1.11e-01 4.98e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 107.30 19.65 3.00e+00 1.11e-01 4.29e+01 angle pdb=" O1B ANP C 401 " pdb=" PB ANP C 401 " pdb=" O2B ANP C 401 " ideal model delta sigma weight residual 120.08 109.23 10.85 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C PHE C 328 " pdb=" CA PHE C 328 " pdb=" CB PHE C 328 " ideal model delta sigma weight residual 113.33 105.31 8.02 2.26e+00 1.96e-01 1.26e+01 angle pdb=" C PHE B 328 " pdb=" CA PHE B 328 " pdb=" CB PHE B 328 " ideal model delta sigma weight residual 113.33 105.33 8.00 2.26e+00 1.96e-01 1.25e+01 ... (remaining 10595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.83: 4427 30.83 - 61.66: 289 61.66 - 92.48: 28 92.48 - 123.31: 2 123.31 - 154.14: 3 Dihedral angle restraints: 4749 sinusoidal: 2115 harmonic: 2634 Sorted by residual: dihedral pdb=" CA THR B 331 " pdb=" C THR B 331 " pdb=" N ALA B 332 " pdb=" CA ALA B 332 " ideal model delta harmonic sigma weight residual 180.00 144.78 35.22 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" CA THR C 331 " pdb=" C THR C 331 " pdb=" N ALA C 332 " pdb=" CA ALA C 332 " ideal model delta harmonic sigma weight residual 180.00 144.80 35.20 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" CA THR A 331 " pdb=" C THR A 331 " pdb=" N ALA A 332 " pdb=" CA ALA A 332 " ideal model delta harmonic sigma weight residual 180.00 144.82 35.18 0 5.00e+00 4.00e-02 4.95e+01 ... (remaining 4746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 977 0.068 - 0.136: 185 0.136 - 0.204: 26 0.204 - 0.272: 5 0.272 - 0.340: 1 Chirality restraints: 1194 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.70 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL A 62 " pdb=" CA VAL A 62 " pdb=" CG1 VAL A 62 " pdb=" CG2 VAL A 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1191 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP B 402 " -0.046 2.00e-02 2.50e+03 4.05e-02 4.50e+01 pdb=" C2 ANP B 402 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ANP B 402 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ANP B 402 " 0.078 2.00e-02 2.50e+03 pdb=" C6 ANP B 402 " -0.006 2.00e-02 2.50e+03 pdb=" C8 ANP B 402 " 0.053 2.00e-02 2.50e+03 pdb=" N1 ANP B 402 " -0.018 2.00e-02 2.50e+03 pdb=" N3 ANP B 402 " -0.005 2.00e-02 2.50e+03 pdb=" N6 ANP B 402 " -0.014 2.00e-02 2.50e+03 pdb=" N7 ANP B 402 " -0.076 2.00e-02 2.50e+03 pdb=" N9 ANP B 402 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 320 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C GLU C 320 " -0.078 2.00e-02 2.50e+03 pdb=" O GLU C 320 " 0.028 2.00e-02 2.50e+03 pdb=" N MET C 321 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 320 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C GLU A 320 " -0.077 2.00e-02 2.50e+03 pdb=" O GLU A 320 " 0.028 2.00e-02 2.50e+03 pdb=" N MET A 321 " 0.027 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 49 2.50 - 3.10: 4951 3.10 - 3.70: 11331 3.70 - 4.30: 16481 4.30 - 4.90: 26768 Nonbonded interactions: 59580 Sorted by model distance: nonbonded pdb="CA CA B 401 " pdb=" O3G ANP B 402 " model vdw 1.906 2.510 nonbonded pdb=" NZ LYS A 245 " pdb=" NH2 ARG B 57 " model vdw 1.966 3.200 nonbonded pdb=" O1B ANP C 401 " pdb="CA CA C 402 " model vdw 2.097 2.510 nonbonded pdb=" NZ LYS B 245 " pdb=" NH2 ARG C 57 " model vdw 2.142 3.200 nonbonded pdb="CA CA A 401 " pdb=" O1B ANP A 402 " model vdw 2.230 2.510 ... (remaining 59575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 337) selection = (chain 'B' and resid 22 through 337) selection = (chain 'C' and resid 22 through 337) } 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.490 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 26.360 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.008 0.159 7813 Z= 0.450 Angle : 1.015 21.173 10600 Z= 0.512 Chirality : 0.054 0.340 1194 Planarity : 0.005 0.060 1290 Dihedral : 18.649 154.140 3057 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -4.56 (0.22), residues: 915 helix: -4.21 (0.14), residues: 315 sheet: -1.90 (0.40), residues: 150 loop : -2.44 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 198 PHE 0.027 0.002 PHE A 128 TYR 0.014 0.001 TYR C 91 ARG 0.011 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7512 (m-80) cc_final: 0.6664 (t80) REVERT: A 118 SER cc_start: 0.7951 (p) cc_final: 0.7641 (m) REVERT: A 209 LYS cc_start: 0.9276 (tppt) cc_final: 0.8979 (tptt) REVERT: A 213 GLU cc_start: 0.8223 (mp0) cc_final: 0.7879 (mp0) REVERT: A 258 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 301 ILE cc_start: 0.9181 (mt) cc_final: 0.8899 (tp) REVERT: A 335 ILE cc_start: 0.8698 (mm) cc_final: 0.8437 (mm) REVERT: B 335 ILE cc_start: 0.8995 (mm) cc_final: 0.8599 (mm) REVERT: C 101 ILE cc_start: 0.9064 (mm) cc_final: 0.8755 (mt) REVERT: C 194 TYR cc_start: 0.8195 (m-80) cc_final: 0.7991 (m-80) REVERT: C 244 GLN cc_start: 0.8237 (mt0) cc_final: 0.7979 (mt0) REVERT: C 245 LYS cc_start: 0.8839 (mttp) cc_final: 0.8616 (mtpp) REVERT: C 248 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8492 (mp10) REVERT: C 249 MET cc_start: 0.8595 (ttm) cc_final: 0.8370 (ttm) REVERT: C 285 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8423 (mttm) REVERT: C 304 ARG cc_start: 0.7606 (ptt90) cc_final: 0.7259 (ptt90) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2296 time to fit residues: 77.2163 Evaluate side-chains 158 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 10.0000 chunk 68 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 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 30 HIS A 61 ASN A 144 GLN A 178 ASN A 254 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 163 ASN B 198 HIS C 30 HIS C 61 ASN C 106 GLN C 211 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7813 Z= 0.186 Angle : 0.588 7.741 10600 Z= 0.310 Chirality : 0.043 0.159 1194 Planarity : 0.004 0.049 1290 Dihedral : 18.160 162.971 1299 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.03 % Allowed : 18.45 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.24), residues: 915 helix: -2.44 (0.22), residues: 354 sheet: -1.78 (0.40), residues: 150 loop : -2.39 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 295 PHE 0.018 0.002 PHE C 128 TYR 0.022 0.001 TYR B 190 ARG 0.008 0.001 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7585 (m-80) cc_final: 0.6703 (t80) REVERT: A 95 ARG cc_start: 0.8559 (ttt90) cc_final: 0.8016 (mtm180) REVERT: A 118 SER cc_start: 0.8028 (p) cc_final: 0.7646 (p) REVERT: A 119 MET cc_start: 0.7870 (mmm) cc_final: 0.7611 (mmm) REVERT: A 268 ASN cc_start: 0.9226 (p0) cc_final: 0.8839 (p0) REVERT: A 335 ILE cc_start: 0.8662 (mm) cc_final: 0.8393 (mm) REVERT: B 254 GLN cc_start: 0.9273 (tp-100) cc_final: 0.9004 (tp-100) REVERT: C 244 GLN cc_start: 0.8374 (mt0) cc_final: 0.8131 (mt0) REVERT: C 245 LYS cc_start: 0.8825 (mttp) cc_final: 0.8489 (mtpp) REVERT: C 248 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8434 (mp10) REVERT: C 249 MET cc_start: 0.8556 (ttm) cc_final: 0.8350 (ttm) REVERT: C 285 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8302 (mttm) outliers start: 23 outliers final: 12 residues processed: 191 average time/residue: 0.1926 time to fit residues: 49.3528 Evaluate side-chains 160 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 chunk 55 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 163 ASN A 178 ASN A 198 HIS ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7813 Z= 0.209 Angle : 0.563 7.824 10600 Z= 0.297 Chirality : 0.042 0.149 1194 Planarity : 0.004 0.044 1290 Dihedral : 17.563 169.043 1299 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.69 % Allowed : 20.29 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.26), residues: 915 helix: -1.60 (0.26), residues: 369 sheet: -1.74 (0.40), residues: 153 loop : -2.38 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 198 PHE 0.022 0.002 PHE B 89 TYR 0.016 0.001 TYR C 190 ARG 0.008 0.001 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 85 PHE cc_start: 0.7733 (m-80) cc_final: 0.6695 (t80) REVERT: A 95 ARG cc_start: 0.8631 (ttt90) cc_final: 0.8132 (mtm180) REVERT: A 119 MET cc_start: 0.7701 (mmm) cc_final: 0.7449 (mmm) REVERT: A 224 SER cc_start: 0.8625 (m) cc_final: 0.8165 (p) REVERT: B 101 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8866 (mt) REVERT: B 260 TYR cc_start: 0.8556 (m-10) cc_final: 0.8333 (m-10) REVERT: B 335 ILE cc_start: 0.9134 (mm) cc_final: 0.8761 (mm) REVERT: C 101 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8804 (mt) REVERT: C 244 GLN cc_start: 0.8403 (mt0) cc_final: 0.8139 (mt0) REVERT: C 245 LYS cc_start: 0.8835 (mttp) cc_final: 0.8479 (mtpp) REVERT: C 252 ARG cc_start: 0.8065 (tpp80) cc_final: 0.7645 (ttm-80) REVERT: C 273 ASP cc_start: 0.8140 (t0) cc_final: 0.7884 (t0) REVERT: C 285 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8220 (mttm) REVERT: C 317 ASP cc_start: 0.6872 (t0) cc_final: 0.6449 (t0) outliers start: 28 outliers final: 18 residues processed: 178 average time/residue: 0.1986 time to fit residues: 47.3155 Evaluate side-chains 156 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.0170 chunk 42 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7813 Z= 0.145 Angle : 0.509 7.501 10600 Z= 0.268 Chirality : 0.041 0.138 1194 Planarity : 0.003 0.040 1290 Dihedral : 17.432 171.560 1299 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.43 % Allowed : 24.11 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.26), residues: 915 helix: -1.07 (0.28), residues: 366 sheet: -1.53 (0.40), residues: 150 loop : -2.17 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 198 PHE 0.018 0.001 PHE A 128 TYR 0.009 0.001 TYR B 190 ARG 0.008 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8560 (ttt90) cc_final: 0.8144 (mtt180) REVERT: A 119 MET cc_start: 0.7694 (mmm) cc_final: 0.7410 (mmm) REVERT: A 139 LEU cc_start: 0.9414 (mt) cc_final: 0.9175 (mm) REVERT: A 268 ASN cc_start: 0.9293 (p0) cc_final: 0.8838 (p0) REVERT: B 163 ASN cc_start: 0.7742 (t0) cc_final: 0.7488 (m-40) REVERT: C 101 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8666 (mt) REVERT: C 109 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7183 (p0) REVERT: C 245 LYS cc_start: 0.8851 (mttp) cc_final: 0.8508 (mtpp) REVERT: C 273 ASP cc_start: 0.8143 (t0) cc_final: 0.7893 (t0) REVERT: C 285 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8142 (mttm) REVERT: C 317 ASP cc_start: 0.6786 (t0) cc_final: 0.6343 (t0) outliers start: 26 outliers final: 18 residues processed: 170 average time/residue: 0.2022 time to fit residues: 45.9670 Evaluate side-chains 161 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.0060 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 261 ASN A 324 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7813 Z= 0.408 Angle : 0.680 8.811 10600 Z= 0.355 Chirality : 0.047 0.220 1194 Planarity : 0.004 0.040 1290 Dihedral : 17.652 167.020 1299 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 5.27 % Allowed : 23.32 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.48 (0.27), residues: 915 helix: -1.14 (0.27), residues: 375 sheet: -1.59 (0.39), residues: 150 loop : -2.06 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 137 PHE 0.030 0.003 PHE C 128 TYR 0.033 0.002 TYR B 260 ARG 0.007 0.001 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 0.867 Fit side-chains REVERT: A 67 GLU cc_start: 0.1972 (OUTLIER) cc_final: 0.1733 (mt-10) REVERT: A 85 PHE cc_start: 0.8038 (m-80) cc_final: 0.6785 (t80) REVERT: A 95 ARG cc_start: 0.8761 (ttt90) cc_final: 0.8224 (mtm180) REVERT: B 101 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8804 (mt) REVERT: C 101 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8801 (mt) REVERT: C 200 MET cc_start: 0.8314 (tpt) cc_final: 0.8001 (tpt) REVERT: C 245 LYS cc_start: 0.8889 (mttp) cc_final: 0.8580 (mtpp) REVERT: C 252 ARG cc_start: 0.8101 (tpp80) cc_final: 0.7817 (ttm-80) REVERT: C 273 ASP cc_start: 0.8282 (t0) cc_final: 0.8023 (t0) REVERT: C 317 ASP cc_start: 0.6782 (t0) cc_final: 0.6426 (t0) outliers start: 40 outliers final: 27 residues processed: 176 average time/residue: 0.1835 time to fit residues: 44.0346 Evaluate side-chains 167 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 331 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 28 optimal weight: 0.0000 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7813 Z= 0.146 Angle : 0.523 7.854 10600 Z= 0.277 Chirality : 0.042 0.151 1194 Planarity : 0.003 0.043 1290 Dihedral : 17.454 179.003 1299 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.08 % Allowed : 25.82 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.28), residues: 915 helix: -0.67 (0.29), residues: 366 sheet: -1.57 (0.39), residues: 153 loop : -1.96 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.018 0.001 PHE C 128 TYR 0.025 0.001 TYR B 190 ARG 0.009 0.001 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 0.876 Fit side-chains REVERT: A 95 ARG cc_start: 0.8662 (ttt90) cc_final: 0.8163 (mtt180) REVERT: A 224 SER cc_start: 0.8736 (m) cc_final: 0.8477 (p) REVERT: B 101 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8828 (mt) REVERT: B 163 ASN cc_start: 0.7800 (t0) cc_final: 0.7578 (m-40) REVERT: C 245 LYS cc_start: 0.8838 (mttp) cc_final: 0.8480 (mtpp) REVERT: C 260 TYR cc_start: 0.8981 (m-80) cc_final: 0.8748 (m-80) REVERT: C 273 ASP cc_start: 0.8208 (t0) cc_final: 0.7937 (t0) REVERT: C 285 LYS cc_start: 0.8724 (mtmm) cc_final: 0.8094 (mttm) REVERT: C 317 ASP cc_start: 0.6639 (t0) cc_final: 0.6157 (t0) outliers start: 31 outliers final: 25 residues processed: 164 average time/residue: 0.1929 time to fit residues: 42.4815 Evaluate side-chains 161 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 199 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7813 Z= 0.184 Angle : 0.540 6.690 10600 Z= 0.284 Chirality : 0.042 0.153 1194 Planarity : 0.004 0.046 1290 Dihedral : 17.336 177.552 1299 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.27 % Allowed : 24.11 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.28), residues: 915 helix: -0.54 (0.29), residues: 363 sheet: -1.41 (0.39), residues: 150 loop : -1.86 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.021 0.002 PHE C 128 TYR 0.026 0.001 TYR B 190 ARG 0.010 0.001 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.1980 (OUTLIER) cc_final: 0.1748 (mt-10) REVERT: A 95 ARG cc_start: 0.8694 (ttt90) cc_final: 0.8115 (mtm180) REVERT: A 139 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9194 (mp) REVERT: A 224 SER cc_start: 0.8735 (m) cc_final: 0.8496 (p) REVERT: B 101 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8831 (mt) REVERT: B 163 ASN cc_start: 0.7826 (t0) cc_final: 0.7623 (m-40) REVERT: C 245 LYS cc_start: 0.8850 (mttp) cc_final: 0.8492 (mtpp) REVERT: C 260 TYR cc_start: 0.8959 (m-80) cc_final: 0.8722 (m-80) REVERT: C 273 ASP cc_start: 0.8249 (t0) cc_final: 0.7981 (t0) REVERT: C 285 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8085 (mttm) REVERT: C 317 ASP cc_start: 0.6578 (t0) cc_final: 0.6120 (t0) outliers start: 40 outliers final: 31 residues processed: 171 average time/residue: 0.1858 time to fit residues: 43.0522 Evaluate side-chains 172 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 331 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7813 Z= 0.234 Angle : 0.582 7.352 10600 Z= 0.302 Chirality : 0.043 0.161 1194 Planarity : 0.004 0.051 1290 Dihedral : 17.322 175.482 1299 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.14 % Allowed : 24.64 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.28), residues: 915 helix: -0.52 (0.29), residues: 360 sheet: -1.41 (0.39), residues: 150 loop : -1.84 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 211 PHE 0.023 0.002 PHE C 128 TYR 0.029 0.001 TYR B 190 ARG 0.011 0.001 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 139 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.2245 (OUTLIER) cc_final: 0.2034 (mt-10) REVERT: A 95 ARG cc_start: 0.8691 (ttt90) cc_final: 0.8192 (mtm180) REVERT: A 139 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9242 (mp) REVERT: A 224 SER cc_start: 0.8747 (m) cc_final: 0.8530 (p) REVERT: B 101 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8777 (mt) REVERT: B 163 ASN cc_start: 0.7875 (t0) cc_final: 0.7655 (m-40) REVERT: C 245 LYS cc_start: 0.8872 (mttp) cc_final: 0.8527 (mtpp) REVERT: C 260 TYR cc_start: 0.8963 (m-80) cc_final: 0.8735 (m-80) REVERT: C 273 ASP cc_start: 0.8297 (t0) cc_final: 0.8036 (t0) REVERT: C 317 ASP cc_start: 0.6576 (t0) cc_final: 0.6101 (t0) outliers start: 39 outliers final: 31 residues processed: 163 average time/residue: 0.1895 time to fit residues: 41.9372 Evaluate side-chains 171 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 199 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 331 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 0.0870 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 199 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7813 Z= 0.142 Angle : 0.532 7.207 10600 Z= 0.277 Chirality : 0.042 0.153 1194 Planarity : 0.004 0.052 1290 Dihedral : 17.070 175.951 1299 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.69 % Allowed : 26.09 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.29), residues: 915 helix: 0.01 (0.31), residues: 339 sheet: -1.32 (0.39), residues: 150 loop : -1.52 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 30 PHE 0.019 0.001 PHE C 128 TYR 0.029 0.001 TYR B 190 ARG 0.012 0.001 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.2252 (OUTLIER) cc_final: 0.2033 (mt-10) REVERT: A 95 ARG cc_start: 0.8665 (ttt90) cc_final: 0.8153 (mtm180) REVERT: A 139 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9168 (mm) REVERT: A 224 SER cc_start: 0.8745 (m) cc_final: 0.8500 (p) REVERT: B 101 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8850 (mt) REVERT: B 254 GLN cc_start: 0.9312 (tp-100) cc_final: 0.9011 (tp-100) REVERT: C 245 LYS cc_start: 0.8836 (mttp) cc_final: 0.8465 (mtpp) REVERT: C 260 TYR cc_start: 0.8951 (m-80) cc_final: 0.8674 (m-80) REVERT: C 273 ASP cc_start: 0.8220 (t0) cc_final: 0.7977 (t0) REVERT: C 285 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8011 (mttm) REVERT: C 317 ASP cc_start: 0.6495 (t0) cc_final: 0.5986 (t0) outliers start: 28 outliers final: 21 residues processed: 167 average time/residue: 0.2039 time to fit residues: 46.3979 Evaluate side-chains 162 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7813 Z= 0.180 Angle : 0.559 6.867 10600 Z= 0.290 Chirality : 0.042 0.151 1194 Planarity : 0.004 0.061 1290 Dihedral : 16.991 174.525 1299 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.69 % Allowed : 26.48 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.28), residues: 915 helix: -0.06 (0.30), residues: 339 sheet: -1.33 (0.39), residues: 150 loop : -1.49 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.020 0.002 PHE C 128 TYR 0.029 0.002 TYR B 190 ARG 0.014 0.001 ARG C 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.6202 (mtt) REVERT: A 67 GLU cc_start: 0.2459 (OUTLIER) cc_final: 0.2229 (mt-10) REVERT: A 95 ARG cc_start: 0.8682 (ttt90) cc_final: 0.8083 (mtm180) REVERT: A 139 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9151 (mm) REVERT: A 224 SER cc_start: 0.8714 (m) cc_final: 0.8471 (p) REVERT: A 273 ASP cc_start: 0.8514 (t0) cc_final: 0.8240 (t0) REVERT: B 101 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8832 (mt) REVERT: C 109 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7507 (p0) REVERT: C 245 LYS cc_start: 0.8858 (mttp) cc_final: 0.8489 (mtpp) REVERT: C 260 TYR cc_start: 0.8973 (m-80) cc_final: 0.8743 (m-80) REVERT: C 273 ASP cc_start: 0.8273 (t0) cc_final: 0.8025 (t0) REVERT: C 285 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8060 (mttm) REVERT: C 317 ASP cc_start: 0.6434 (t0) cc_final: 0.5978 (t0) outliers start: 28 outliers final: 22 residues processed: 163 average time/residue: 0.1843 time to fit residues: 40.7799 Evaluate side-chains 166 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 199 GLN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 331 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 163 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.150122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117877 restraints weight = 13490.547| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.58 r_work: 0.3310 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7813 Z= 0.169 Angle : 0.553 6.745 10600 Z= 0.287 Chirality : 0.042 0.152 1194 Planarity : 0.004 0.063 1290 Dihedral : 16.858 172.100 1299 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.95 % Allowed : 26.35 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.29), residues: 915 helix: 0.02 (0.31), residues: 339 sheet: -1.32 (0.39), residues: 150 loop : -1.45 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.020 0.002 PHE C 128 TYR 0.035 0.002 TYR B 190 ARG 0.014 0.001 ARG C 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.12 seconds wall clock time: 38 minutes 34.93 seconds (2314.93 seconds total)