Starting phenix.real_space_refine on Fri Dec 8 13:09:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/12_2023/6k41_9911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/12_2023/6k41_9911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/12_2023/6k41_9911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/12_2023/6k41_9911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/12_2023/6k41_9911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k41_9911/12_2023/6k41_9911_updated.pdb" } resolution = 2.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5384 2.51 5 N 1435 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "R ARG 116": "NH1" <-> "NH2" Residue "R ARG 127": "NH1" <-> "NH2" Residue "R ARG 201": "NH1" <-> "NH2" Residue "R PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 439": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8430 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain breaks: 3 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2559 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "R" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1952 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain breaks: 5 Chain: "H" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1793 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CZX': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 5.06, per 1000 atoms: 0.60 Number of scatterers: 8430 At special positions: 0 Unit cell: (109.1, 110.191, 119.464, 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 55 16.00 O 1556 8.00 N 1435 7.00 C 5384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " 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: 3.01 Conformation dependent library (CDL) restraints added in 1.4 seconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 12 sheets defined 33.3% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 7 through 30 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.817A pdb=" N TYR A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 297 through 311 removed outlier: 4.937A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.632A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 24 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.872A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 12 through 38 Processing helix chain 'R' and resid 49 through 73 removed outlier: 3.734A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) Proline residue: R 67 - end of helix Processing helix chain 'R' and resid 86 through 115 Processing helix chain 'R' and resid 117 through 121 Processing helix chain 'R' and resid 126 through 147 Proline residue: R 146 - end of helix Processing helix chain 'R' and resid 171 through 180 removed outlier: 3.630A pdb=" N ALA R 175 " --> pdb=" O TRP R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 202 Processing helix chain 'R' and resid 363 through 392 removed outlier: 3.538A pdb=" N LYS R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE R 380 " --> pdb=" O VAL R 376 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL R 381 " --> pdb=" O ILE R 377 " (cutoff:3.500A) Proline residue: R 386 - end of helix Processing helix chain 'R' and resid 407 through 427 removed outlier: 3.802A pdb=" N TYR R 416 " --> pdb=" O PHE R 412 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN R 418 " --> pdb=" O ILE R 414 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 431 through 441 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.810A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.814A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.785A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.617A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.845A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.549A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.643A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.632A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'H' and resid 115 through 117 removed outlier: 5.824A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 134 through 137 removed outlier: 6.278A pdb=" N LYS H 232 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL H 137 " --> pdb=" O LYS H 232 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU H 234 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY H 213 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE H 177 " --> pdb=" O TRP H 164 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU H 166 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU H 175 " --> pdb=" O LEU H 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 143 through 148 removed outlier: 3.765A pdb=" N ALA H 199 " --> pdb=" O SER H 196 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1086 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: 2.55 Time building geometry restraints manager: 3.29 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: 2170 1.33 - 1.45: 1760 1.45 - 1.57: 4598 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 8603 Sorted by residual: bond pdb=" C09 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.385 1.523 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C11 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.386 1.522 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C08 CZX R 501 " pdb=" C11 CZX R 501 " ideal model delta sigma weight residual 1.392 1.526 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C04 CZX R 501 " pdb=" C09 CZX R 501 " ideal model delta sigma weight residual 1.393 1.521 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C04 CZX R 501 " pdb=" C05 CZX R 501 " ideal model delta sigma weight residual 1.403 1.531 -0.128 2.00e-02 2.50e+03 4.08e+01 ... (remaining 8598 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.55: 193 106.55 - 113.84: 4729 113.84 - 121.13: 4302 121.13 - 128.42: 2351 128.42 - 135.70: 75 Bond angle restraints: 11650 Sorted by residual: angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.71 107.35 6.36 9.50e-01 1.11e+00 4.49e+01 angle pdb=" N LEU R 145 " pdb=" CA LEU R 145 " pdb=" C LEU R 145 " ideal model delta sigma weight residual 109.81 122.76 -12.95 2.21e+00 2.05e-01 3.44e+01 angle pdb=" N PRO R 146 " pdb=" CA PRO R 146 " pdb=" C PRO R 146 " ideal model delta sigma weight residual 110.70 116.69 -5.99 1.22e+00 6.72e-01 2.41e+01 angle pdb=" C ARG H 179 " pdb=" N MET H 180 " pdb=" CA MET H 180 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C THR A 296 " pdb=" N TYR A 297 " pdb=" CA TYR A 297 " ideal model delta sigma weight residual 120.54 126.25 -5.71 1.35e+00 5.49e-01 1.79e+01 ... (remaining 11645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 4822 16.48 - 32.95: 219 32.95 - 49.43: 41 49.43 - 65.90: 2 65.90 - 82.38: 6 Dihedral angle restraints: 5090 sinusoidal: 1972 harmonic: 3118 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CA SER B 281 " pdb=" C SER B 281 " pdb=" N GLY B 282 " pdb=" CA GLY B 282 " ideal model delta harmonic sigma weight residual 180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ARG R 116 " pdb=" C ARG R 116 " pdb=" N ALA R 117 " pdb=" CA ALA R 117 " ideal model delta harmonic sigma weight residual -180.00 -154.16 -25.84 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 5087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1142 0.087 - 0.174: 169 0.174 - 0.260: 13 0.260 - 0.347: 3 0.347 - 0.434: 1 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CG LEU G 50 " pdb=" CB LEU G 50 " pdb=" CD1 LEU G 50 " pdb=" CD2 LEU G 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB VAL A 219 " pdb=" CA VAL A 219 " pdb=" CG1 VAL A 219 " pdb=" CG2 VAL A 219 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1325 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 62 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ALA R 62 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA R 62 " -0.018 2.00e-02 2.50e+03 pdb=" N THR R 63 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 111 " 0.019 2.00e-02 2.50e+03 1.72e-02 7.43e+00 pdb=" CG TRP H 111 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP H 111 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP H 111 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP H 111 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 111 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 111 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 111 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 50 " -0.019 2.00e-02 2.50e+03 1.94e-02 6.60e+00 pdb=" CG PHE R 50 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE R 50 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE R 50 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE R 50 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE R 50 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE R 50 " -0.001 2.00e-02 2.50e+03 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 302 2.71 - 3.26: 7578 3.26 - 3.81: 13462 3.81 - 4.35: 17801 4.35 - 4.90: 29883 Nonbonded interactions: 69026 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.166 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.189 2.440 nonbonded pdb=" OG SER R 69 " pdb=" OH TYR R 88 " model vdw 2.220 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.243 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR H 163 " model vdw 2.244 2.440 ... (remaining 69021 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=0.00 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: 5.650 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: 12.980 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 26.530 Find NCS groups from input model: 0.270 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.009 0.138 8603 Z= 0.562 Angle : 1.065 15.404 11650 Z= 0.571 Chirality : 0.062 0.434 1328 Planarity : 0.007 0.062 1467 Dihedral : 10.212 74.612 3065 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.44 % Allowed : 3.40 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.22), residues: 1049 helix: -1.40 (0.22), residues: 365 sheet: -0.89 (0.30), residues: 277 loop : -2.54 (0.25), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP H 111 HIS 0.014 0.004 HIS B 62 PHE 0.044 0.004 PHE R 50 TYR 0.030 0.004 TYR B 59 ARG 0.019 0.002 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 0.961 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 212 average time/residue: 1.2896 time to fit residues: 289.1584 Evaluate side-chains 134 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.3131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 205 GLN A 214 HIS A 257 ASN B 32 GLN B 239 ASN B 293 ASN R 30 ASN H 167 GLN H 171 GLN H 219 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8603 Z= 0.250 Angle : 0.626 10.018 11650 Z= 0.330 Chirality : 0.045 0.156 1328 Planarity : 0.005 0.048 1467 Dihedral : 5.185 22.903 1170 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.49 % Allowed : 11.06 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: -1.03 (0.25), residues: 1049 helix: 0.63 (0.27), residues: 358 sheet: -0.46 (0.30), residues: 289 loop : -2.04 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.007 0.002 HIS B 62 PHE 0.038 0.002 PHE R 369 TYR 0.024 0.002 TYR B 105 ARG 0.008 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 0.978 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 12 residues processed: 166 average time/residue: 1.3840 time to fit residues: 243.1534 Evaluate side-chains 143 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 1.0128 time to fit residues: 7.9228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 0.0570 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 256 ASN B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN H 130 GLN H 167 GLN H 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8603 Z= 0.248 Angle : 0.602 9.122 11650 Z= 0.318 Chirality : 0.045 0.158 1328 Planarity : 0.005 0.041 1467 Dihedral : 5.011 22.675 1170 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.16 % Allowed : 14.13 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: -0.29 (0.25), residues: 1049 helix: 1.38 (0.28), residues: 350 sheet: -0.10 (0.30), residues: 289 loop : -1.64 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.002 HIS B 54 PHE 0.035 0.002 PHE R 369 TYR 0.015 0.002 TYR R 391 ARG 0.006 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 0.816 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 158 average time/residue: 1.4398 time to fit residues: 239.7415 Evaluate side-chains 145 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.8908 time to fit residues: 6.1219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN R 72 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8603 Z= 0.166 Angle : 0.537 9.019 11650 Z= 0.281 Chirality : 0.042 0.146 1328 Planarity : 0.004 0.040 1467 Dihedral : 4.594 22.585 1170 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 5.26 % Allowed : 13.80 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.09 (0.26), residues: 1049 helix: 1.74 (0.28), residues: 355 sheet: 0.09 (0.30), residues: 281 loop : -1.47 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.003 0.001 HIS B 62 PHE 0.033 0.001 PHE R 369 TYR 0.013 0.001 TYR R 391 ARG 0.008 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 134 time to evaluate : 1.029 Fit side-chains outliers start: 48 outliers final: 20 residues processed: 164 average time/residue: 1.3271 time to fit residues: 230.9882 Evaluate side-chains 147 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.1582 time to fit residues: 2.1072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN H 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8603 Z= 0.148 Angle : 0.521 8.642 11650 Z= 0.270 Chirality : 0.041 0.144 1328 Planarity : 0.004 0.041 1467 Dihedral : 4.366 22.235 1170 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.38 % Allowed : 15.22 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.36 (0.26), residues: 1049 helix: 2.02 (0.28), residues: 357 sheet: 0.14 (0.30), residues: 287 loop : -1.34 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS B 62 PHE 0.031 0.001 PHE R 369 TYR 0.014 0.001 TYR H 59 ARG 0.008 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 1.066 Fit side-chains outliers start: 40 outliers final: 23 residues processed: 156 average time/residue: 1.3594 time to fit residues: 224.6604 Evaluate side-chains 146 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.3400 time to fit residues: 3.3680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.0770 chunk 102 optimal weight: 4.9990 chunk 85 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN H 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8603 Z= 0.134 Angle : 0.504 9.372 11650 Z= 0.262 Chirality : 0.041 0.141 1328 Planarity : 0.004 0.041 1467 Dihedral : 4.222 21.994 1170 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.38 % Allowed : 15.33 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.50 (0.26), residues: 1049 helix: 2.16 (0.28), residues: 358 sheet: 0.27 (0.30), residues: 279 loop : -1.31 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.002 0.001 HIS H 35 PHE 0.030 0.001 PHE R 369 TYR 0.011 0.001 TYR R 391 ARG 0.009 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 0.855 Fit side-chains outliers start: 40 outliers final: 23 residues processed: 156 average time/residue: 1.3008 time to fit residues: 215.0472 Evaluate side-chains 148 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.4616 time to fit residues: 3.9328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 245 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8603 Z= 0.168 Angle : 0.531 9.504 11650 Z= 0.276 Chirality : 0.042 0.146 1328 Planarity : 0.004 0.043 1467 Dihedral : 4.354 21.999 1170 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.27 % Allowed : 15.77 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.52 (0.26), residues: 1049 helix: 2.18 (0.28), residues: 356 sheet: 0.28 (0.30), residues: 281 loop : -1.29 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.030 0.001 PHE R 369 TYR 0.014 0.001 TYR H 59 ARG 0.009 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 1.003 Fit side-chains outliers start: 39 outliers final: 24 residues processed: 154 average time/residue: 1.4063 time to fit residues: 228.8116 Evaluate side-chains 149 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 6 average time/residue: 0.5391 time to fit residues: 4.8387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8603 Z= 0.239 Angle : 0.597 9.823 11650 Z= 0.310 Chirality : 0.044 0.154 1328 Planarity : 0.004 0.045 1467 Dihedral : 4.697 21.888 1170 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.05 % Allowed : 16.54 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.39 (0.26), residues: 1049 helix: 1.96 (0.28), residues: 356 sheet: 0.27 (0.30), residues: 289 loop : -1.33 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.031 0.002 PHE R 369 TYR 0.014 0.002 TYR R 391 ARG 0.010 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 0.902 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 147 average time/residue: 1.3683 time to fit residues: 212.9889 Evaluate side-chains 144 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 7 average time/residue: 0.4310 time to fit residues: 4.7108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 0.0470 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8603 Z= 0.184 Angle : 0.555 10.120 11650 Z= 0.287 Chirality : 0.043 0.149 1328 Planarity : 0.004 0.046 1467 Dihedral : 4.509 21.743 1170 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.50 % Allowed : 17.74 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.44 (0.26), residues: 1049 helix: 2.07 (0.28), residues: 356 sheet: 0.28 (0.30), residues: 294 loop : -1.37 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.030 0.001 PHE R 369 TYR 0.015 0.002 TYR H 59 ARG 0.010 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 0.971 Fit side-chains outliers start: 32 outliers final: 21 residues processed: 146 average time/residue: 1.3216 time to fit residues: 204.3187 Evaluate side-chains 140 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.1550 time to fit residues: 1.8814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8603 Z= 0.169 Angle : 0.557 10.487 11650 Z= 0.285 Chirality : 0.042 0.147 1328 Planarity : 0.004 0.046 1467 Dihedral : 4.388 21.526 1170 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.63 % Allowed : 18.95 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.55 (0.26), residues: 1049 helix: 2.17 (0.28), residues: 356 sheet: 0.38 (0.30), residues: 287 loop : -1.31 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.030 0.001 PHE R 369 TYR 0.012 0.001 TYR R 391 ARG 0.011 0.001 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.269 Fit side-chains outliers start: 24 outliers final: 21 residues processed: 143 average time/residue: 1.5282 time to fit residues: 230.8788 Evaluate side-chains 145 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.1722 time to fit residues: 1.6739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.160634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.148716 restraints weight = 8793.355| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 0.73 r_work: 0.3421 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8603 Z= 0.199 Angle : 0.572 10.589 11650 Z= 0.295 Chirality : 0.043 0.150 1328 Planarity : 0.004 0.046 1467 Dihedral : 4.542 21.669 1170 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.07 % Allowed : 18.51 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.10 % 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: 0.53 (0.26), residues: 1049 helix: 2.08 (0.28), residues: 356 sheet: 0.39 (0.30), residues: 287 loop : -1.29 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.030 0.002 PHE R 369 TYR 0.016 0.002 TYR H 59 ARG 0.011 0.001 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4185.52 seconds wall clock time: 75 minutes 12.77 seconds (4512.77 seconds total)