Starting phenix.real_space_refine on Thu Mar 14 17:50:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkn_24501/03_2024/7rkn_24501_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkn_24501/03_2024/7rkn_24501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkn_24501/03_2024/7rkn_24501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkn_24501/03_2024/7rkn_24501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkn_24501/03_2024/7rkn_24501_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkn_24501/03_2024/7rkn_24501_updated.pdb" } resolution = 3.6 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 5993 2.51 5 N 1586 2.21 5 O 1743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ASP 73": "OD1" <-> "OD2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 69": "OD1" <-> "OD2" Residue "R PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 170": "OD1" <-> "OD2" Residue "R GLU 266": "OE1" <-> "OE2" Residue "R PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9393 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1736 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2575 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1761 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "L" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 520 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 65} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PCA:plan-2': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2397 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.41, per 1000 atoms: 0.58 Number of scatterers: 9393 At special positions: 0 Unit cell: (99.22, 122.18, 128.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 1743 8.00 N 1586 7.00 C 5993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 34 " distance=2.03 Simple disulfide: pdb=" SG CYS L 12 " - pdb=" SG CYS L 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 173 " distance=2.03 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: 3.50 Conformation dependent library (CDL) restraints added in 1.9 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2262 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 33.1% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.933A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.955A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.713A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.986A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.702A pdb=" N CYS A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 23 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 43 removed outlier: 4.148A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'L' and resid 56 through 67 removed outlier: 3.805A pdb=" N ARG L 67 " --> pdb=" O HIS L 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 59 Proline residue: R 34 - end of helix removed outlier: 4.742A pdb=" N LEU R 53 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 92 removed outlier: 3.608A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Proline residue: R 87 - end of helix Processing helix chain 'R' and resid 104 through 134 removed outlier: 3.618A pdb=" N ILE R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 163 Proline residue: R 161 - end of helix Processing helix chain 'R' and resid 184 through 194 Processing helix chain 'R' and resid 198 through 217 removed outlier: 4.252A pdb=" N VAL R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 239 removed outlier: 3.658A pdb=" N ARG R 225 " --> pdb=" O HIS R 222 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE R 226 " --> pdb=" O LYS R 223 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL R 227 " --> pdb=" O GLY R 224 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE R 239 " --> pdb=" O VAL R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 256 Processing helix chain 'R' and resid 263 through 291 removed outlier: 3.979A pdb=" N CYS R 284 " --> pdb=" O ALA R 280 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS R 285 " --> pdb=" O PHE R 281 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU R 286 " --> pdb=" O CYS R 282 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.795A pdb=" N TYR R 291 " --> pdb=" O ASN R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 305 removed outlier: 3.802A pdb=" N GLU R 301 " --> pdb=" O LYS R 297 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 263 through 265 removed outlier: 4.029A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.056A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.207A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.755A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.399A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.367A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.556A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.572A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 17 through 23 Processing sheet with id= J, first strand: chain 'D' and resid 143 through 148 Processing sheet with id= K, first strand: chain 'L' and resid 26 through 29 removed outlier: 3.951A pdb=" N HIS L 26 " --> pdb=" O GLU L 42 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 915 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: 2.48 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2996 1.34 - 1.46: 2237 1.46 - 1.58: 4265 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 9596 Sorted by residual: bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" C ILE R 160 " pdb=" N PRO R 161 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.28e-02 6.10e+03 2.53e+00 bond pdb=" N GLU R 308 " pdb=" CA GLU R 308 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.10e+00 bond pdb=" C ILE R 199 " pdb=" N PRO R 200 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.30e-02 5.92e+03 2.00e+00 bond pdb=" CA THR B 87 " pdb=" C THR B 87 " ideal model delta sigma weight residual 1.522 1.543 -0.021 1.51e-02 4.39e+03 1.93e+00 ... (remaining 9591 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.06: 173 106.06 - 113.05: 5010 113.05 - 120.05: 3541 120.05 - 127.04: 4175 127.04 - 134.03: 110 Bond angle restraints: 13009 Sorted by residual: angle pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " ideal model delta sigma weight residual 114.40 128.13 -13.73 2.30e+00 1.89e-01 3.56e+01 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C ALA R 307 " pdb=" N GLU R 308 " pdb=" CA GLU R 308 " ideal model delta sigma weight residual 121.70 129.70 -8.00 1.80e+00 3.09e-01 1.98e+01 angle pdb=" C GLN L 63 " pdb=" N HIS L 64 " pdb=" CA HIS L 64 " ideal model delta sigma weight residual 121.58 113.88 7.70 1.95e+00 2.63e-01 1.56e+01 angle pdb=" CB MET R 174 " pdb=" CG MET R 174 " pdb=" SD MET R 174 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 ... (remaining 13004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5256 17.61 - 35.22: 353 35.22 - 52.84: 67 52.84 - 70.45: 13 70.45 - 88.06: 7 Dihedral angle restraints: 5696 sinusoidal: 2195 harmonic: 3501 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual -86.00 -133.83 47.83 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CA TYR A 296 " pdb=" C TYR A 296 " pdb=" N GLU A 297 " pdb=" CA GLU A 297 " ideal model delta harmonic sigma weight residual -180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CB CYS R 104 " pdb=" SG CYS R 104 " pdb=" SG CYS R 173 " pdb=" CB CYS R 173 " ideal model delta sinusoidal sigma weight residual -86.00 -52.96 -33.04 1 1.00e+01 1.00e-02 1.55e+01 ... (remaining 5693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1304 0.086 - 0.171: 164 0.171 - 0.257: 10 0.257 - 0.342: 1 0.342 - 0.428: 1 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CB ILE A 222 " pdb=" CA ILE A 222 " pdb=" CG1 ILE A 222 " pdb=" CG2 ILE A 222 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA LYS R 33 " pdb=" N LYS R 33 " pdb=" C LYS R 33 " pdb=" CB LYS R 33 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1477 not shown) Planarity restraints: 1641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " -0.038 2.00e-02 2.50e+03 4.38e-02 4.80e+01 pdb=" CG TRP B 82 " 0.110 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 52 " 0.029 2.00e-02 2.50e+03 5.77e-02 3.33e+01 pdb=" C PHE R 52 " -0.100 2.00e-02 2.50e+03 pdb=" O PHE R 52 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU R 53 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 320 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C TYR A 320 " -0.060 2.00e-02 2.50e+03 pdb=" O TYR A 320 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 321 " 0.020 2.00e-02 2.50e+03 ... (remaining 1638 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 837 2.75 - 3.28: 9674 3.28 - 3.82: 15413 3.82 - 4.36: 18668 4.36 - 4.90: 31868 Nonbonded interactions: 76460 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.206 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.220 2.440 nonbonded pdb=" O LYS A 35 " pdb=" OG1 THR A 219 " model vdw 2.237 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.252 2.440 nonbonded pdb=" O GLY D 33 " pdb=" OG SER D 99 " model vdw 2.283 2.440 ... (remaining 76455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.000 Extract box with map and model: 7.470 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 28.310 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.004 0.118 9596 Z= 0.291 Angle : 0.974 13.731 13009 Z= 0.521 Chirality : 0.058 0.428 1480 Planarity : 0.007 0.086 1641 Dihedral : 12.675 88.061 3413 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.24), residues: 1182 helix: -0.08 (0.26), residues: 377 sheet: -2.46 (0.31), residues: 249 loop : -1.85 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.003 TRP B 82 HIS 0.014 0.001 HIS L 64 PHE 0.058 0.003 PHE R 52 TYR 0.016 0.002 TYR D 178 ARG 0.010 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.133 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2122 time to fit residues: 46.1566 Evaluate side-chains 114 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN L 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9596 Z= 0.208 Angle : 0.573 10.399 13009 Z= 0.306 Chirality : 0.042 0.149 1480 Planarity : 0.004 0.053 1641 Dihedral : 4.765 51.882 1300 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.28 % Allowed : 9.82 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.93 (0.24), residues: 1182 helix: 0.19 (0.26), residues: 382 sheet: -2.19 (0.31), residues: 262 loop : -1.83 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 82 HIS 0.013 0.001 HIS L 64 PHE 0.013 0.001 PHE A 334 TYR 0.013 0.001 TYR B 264 ARG 0.006 0.000 ARG L 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: B 262 MET cc_start: 0.7719 (mmp) cc_final: 0.7490 (mmp) REVERT: D 218 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7619 (ttt) REVERT: R 27 ASP cc_start: 0.7049 (p0) cc_final: 0.6773 (p0) REVERT: R 302 LEU cc_start: 0.7964 (mm) cc_final: 0.7677 (pp) outliers start: 13 outliers final: 8 residues processed: 127 average time/residue: 0.1944 time to fit residues: 35.9712 Evaluate side-chains 117 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain R residue 36 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 72 optimal weight: 0.0370 chunk 29 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9596 Z= 0.175 Angle : 0.545 10.619 13009 Z= 0.287 Chirality : 0.041 0.145 1480 Planarity : 0.004 0.042 1641 Dihedral : 4.594 50.112 1300 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.16 % Allowed : 11.30 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.71 (0.25), residues: 1182 helix: 0.34 (0.26), residues: 382 sheet: -2.02 (0.31), residues: 254 loop : -1.71 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 89 HIS 0.010 0.001 HIS L 64 PHE 0.013 0.001 PHE A 334 TYR 0.013 0.001 TYR D 178 ARG 0.009 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 1.222 Fit side-chains REVERT: D 76 LYS cc_start: 0.7928 (mttt) cc_final: 0.7270 (tptp) REVERT: D 218 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7571 (ttt) outliers start: 22 outliers final: 14 residues processed: 142 average time/residue: 0.1979 time to fit residues: 40.2972 Evaluate side-chains 127 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 282 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 50 optimal weight: 0.0970 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 0.0070 chunk 113 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9596 Z= 0.141 Angle : 0.533 10.133 13009 Z= 0.280 Chirality : 0.041 0.145 1480 Planarity : 0.004 0.039 1641 Dihedral : 4.393 48.151 1300 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.18 % Allowed : 14.44 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.25), residues: 1182 helix: 0.47 (0.27), residues: 381 sheet: -1.86 (0.32), residues: 255 loop : -1.64 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 89 HIS 0.009 0.001 HIS L 64 PHE 0.013 0.001 PHE R 111 TYR 0.012 0.001 TYR D 178 ARG 0.009 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: D 76 LYS cc_start: 0.7870 (mttt) cc_final: 0.7244 (tptp) REVERT: D 218 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7377 (ttt) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 0.1867 time to fit residues: 35.9198 Evaluate side-chains 121 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 78 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 overall best weight: 2.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 259 GLN B 340 ASN R 51 ASN R 283 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9596 Z= 0.342 Angle : 0.614 11.443 13009 Z= 0.324 Chirality : 0.044 0.183 1480 Planarity : 0.004 0.042 1641 Dihedral : 4.795 50.146 1300 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.65 % Allowed : 15.62 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.25), residues: 1182 helix: 0.16 (0.26), residues: 385 sheet: -2.03 (0.31), residues: 268 loop : -1.66 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.009 0.001 HIS L 64 PHE 0.017 0.002 PHE D 27 TYR 0.014 0.002 TYR D 178 ARG 0.009 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.144 Fit side-chains REVERT: A 324 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8103 (p) REVERT: D 218 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7917 (ttt) REVERT: L 56 GLN cc_start: 0.7733 (mp10) cc_final: 0.7192 (pm20) REVERT: R 168 LYS cc_start: 0.7364 (tptp) cc_final: 0.7130 (tptp) outliers start: 27 outliers final: 17 residues processed: 136 average time/residue: 0.1831 time to fit residues: 36.4947 Evaluate side-chains 128 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.0870 chunk 109 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9596 Z= 0.162 Angle : 0.551 10.499 13009 Z= 0.287 Chirality : 0.041 0.156 1480 Planarity : 0.004 0.041 1641 Dihedral : 4.535 49.882 1300 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.96 % Allowed : 17.58 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.57 (0.25), residues: 1182 helix: 0.40 (0.27), residues: 383 sheet: -2.02 (0.31), residues: 260 loop : -1.51 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 82 HIS 0.009 0.001 HIS L 64 PHE 0.013 0.001 PHE R 111 TYR 0.013 0.001 TYR D 178 ARG 0.003 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.116 Fit side-chains REVERT: A 324 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7746 (p) REVERT: D 218 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7586 (ttt) REVERT: L 56 GLN cc_start: 0.7590 (mp10) cc_final: 0.7204 (pm20) REVERT: R 158 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7523 (tt) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 0.1992 time to fit residues: 39.4853 Evaluate side-chains 125 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 158 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9596 Z= 0.300 Angle : 0.598 11.016 13009 Z= 0.314 Chirality : 0.043 0.165 1480 Planarity : 0.004 0.045 1641 Dihedral : 4.676 49.150 1300 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.14 % Allowed : 17.19 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.71 (0.25), residues: 1182 helix: 0.24 (0.26), residues: 382 sheet: -2.04 (0.31), residues: 272 loop : -1.57 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 82 HIS 0.009 0.001 HIS L 64 PHE 0.015 0.001 PHE B 234 TYR 0.014 0.001 TYR D 178 ARG 0.003 0.000 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 1.049 Fit side-chains REVERT: A 324 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8089 (p) REVERT: B 59 TYR cc_start: 0.8223 (m-80) cc_final: 0.7994 (m-80) REVERT: D 34 MET cc_start: 0.7551 (mmm) cc_final: 0.7031 (mtm) REVERT: D 218 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7864 (ttt) REVERT: L 56 GLN cc_start: 0.7668 (mp10) cc_final: 0.7241 (pm20) REVERT: R 158 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7606 (tt) outliers start: 32 outliers final: 24 residues processed: 143 average time/residue: 0.1887 time to fit residues: 38.7431 Evaluate side-chains 138 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9596 Z= 0.187 Angle : 0.561 10.403 13009 Z= 0.293 Chirality : 0.041 0.158 1480 Planarity : 0.004 0.043 1641 Dihedral : 4.526 48.912 1300 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.46 % Allowed : 18.76 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.53 (0.25), residues: 1182 helix: 0.41 (0.27), residues: 380 sheet: -1.99 (0.31), residues: 265 loop : -1.46 (0.29), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 82 HIS 0.009 0.001 HIS L 64 PHE 0.020 0.001 PHE R 111 TYR 0.013 0.001 TYR D 178 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 324 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7916 (p) REVERT: B 59 TYR cc_start: 0.8073 (m-80) cc_final: 0.7814 (m-80) REVERT: D 34 MET cc_start: 0.7411 (mmm) cc_final: 0.6889 (mtm) REVERT: D 218 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7713 (ttt) REVERT: L 25 ILE cc_start: 0.7455 (mm) cc_final: 0.7013 (mm) REVERT: L 56 GLN cc_start: 0.7620 (mp10) cc_final: 0.7256 (pm20) REVERT: R 158 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7522 (tt) REVERT: R 168 LYS cc_start: 0.7174 (tptp) cc_final: 0.6474 (tptt) outliers start: 25 outliers final: 19 residues processed: 138 average time/residue: 0.2021 time to fit residues: 39.9821 Evaluate side-chains 130 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 227 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 108 optimal weight: 0.0030 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN B 340 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9596 Z= 0.161 Angle : 0.573 10.949 13009 Z= 0.293 Chirality : 0.042 0.256 1480 Planarity : 0.004 0.042 1641 Dihedral : 4.436 47.055 1300 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.06 % Allowed : 19.45 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.47 (0.25), residues: 1182 helix: 0.47 (0.27), residues: 379 sheet: -1.86 (0.32), residues: 256 loop : -1.51 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 82 HIS 0.009 0.001 HIS L 64 PHE 0.019 0.001 PHE R 111 TYR 0.013 0.001 TYR D 178 ARG 0.002 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 324 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7813 (p) REVERT: D 34 MET cc_start: 0.7388 (mmm) cc_final: 0.6840 (mtm) REVERT: D 218 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7542 (ttt) REVERT: L 25 ILE cc_start: 0.7463 (mm) cc_final: 0.7032 (mm) REVERT: L 56 GLN cc_start: 0.7590 (mp10) cc_final: 0.7222 (pm20) REVERT: R 158 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7507 (tt) REVERT: R 168 LYS cc_start: 0.7177 (tptp) cc_final: 0.6453 (tptt) outliers start: 21 outliers final: 16 residues processed: 136 average time/residue: 0.1890 time to fit residues: 37.4220 Evaluate side-chains 129 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 9 optimal weight: 6.9990 chunk 71 optimal weight: 0.0060 chunk 56 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9596 Z= 0.205 Angle : 0.598 12.018 13009 Z= 0.305 Chirality : 0.042 0.205 1480 Planarity : 0.004 0.043 1641 Dihedral : 4.467 47.144 1300 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.06 % Allowed : 19.65 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.49 (0.25), residues: 1182 helix: 0.37 (0.27), residues: 380 sheet: -1.81 (0.32), residues: 263 loop : -1.48 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 82 HIS 0.009 0.001 HIS L 64 PHE 0.015 0.001 PHE R 111 TYR 0.016 0.001 TYR D 60 ARG 0.002 0.000 ARG D 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 324 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7861 (p) REVERT: B 59 TYR cc_start: 0.8032 (m-80) cc_final: 0.7737 (m-80) REVERT: C 52 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7843 (t) REVERT: D 34 MET cc_start: 0.7430 (mmm) cc_final: 0.6902 (mtm) REVERT: D 218 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7600 (ttt) REVERT: L 25 ILE cc_start: 0.7474 (mm) cc_final: 0.7062 (mm) REVERT: L 56 GLN cc_start: 0.7576 (mp10) cc_final: 0.7195 (pm20) REVERT: R 158 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7521 (tt) REVERT: R 168 LYS cc_start: 0.7167 (tptp) cc_final: 0.6436 (tptt) outliers start: 21 outliers final: 16 residues processed: 131 average time/residue: 0.1897 time to fit residues: 36.3879 Evaluate side-chains 127 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.071185 restraints weight = 24469.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.073417 restraints weight = 13519.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073881 restraints weight = 8533.645| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9596 Z= 0.236 Angle : 0.606 11.709 13009 Z= 0.311 Chirality : 0.043 0.221 1480 Planarity : 0.004 0.044 1641 Dihedral : 4.556 47.246 1300 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.46 % Allowed : 19.84 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.53 (0.25), residues: 1182 helix: 0.28 (0.26), residues: 380 sheet: -1.82 (0.31), residues: 274 loop : -1.44 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 82 HIS 0.009 0.001 HIS L 64 PHE 0.013 0.001 PHE R 111 TYR 0.014 0.001 TYR D 60 ARG 0.003 0.000 ARG D 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2087.66 seconds wall clock time: 38 minutes 35.80 seconds (2315.80 seconds total)