Starting phenix.real_space_refine on Fri Sep 11 05:19:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6sni_10258/09_2026/6sni_10258.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sni_10258/09_2026/6sni_10258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6sni_10258/09_2026/6sni_10258.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6sni_10258/09_2026/6sni_10258.cif" model { file = "/net/cci-nas-00/data/ceres_data/6sni_10258/09_2026/6sni_10258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sni_10258/09_2026/6sni_10258.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sni_10258/09_2026/6sni_10258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sni_10258/09_2026/6sni_10258.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 4967 2.51 5 N 1156 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7510 Number of models: 1 Model: "" Number of chains: 7 Chain: "X" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3924 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 25, 'TRANS': 453} Chain breaks: 1 Chain: "H" Number of atoms: 1687 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Conformer: "B" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} bond proxies already assigned to first conformer: 1725 Chain: "L" Number of atoms: 1659 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1654 Chain: "X" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 163 Unusual residues: {'PTY': 5, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 3} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.08, per 1000 atoms: 0.28 Number of scatterers: 7510 At special positions: 0 Unit cell: (115.92, 86.52, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 1 15.00 O 1355 8.00 N 1156 7.00 C 4967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS X 314 " - pdb=" SG CYS X 515 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.54 Conformation dependent library (CDL) restraints added in 630.2 milliseconds 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 42.7% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'X' and resid 41 through 53 removed outlier: 3.886A pdb=" N VAL X 47 " --> pdb=" O PHE X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 56 No H-bonds generated for 'chain 'X' and resid 54 through 56' Processing helix chain 'X' and resid 68 through 81 removed outlier: 3.749A pdb=" N ALA X 72 " --> pdb=" O GLY X 68 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN X 73 " --> pdb=" O ASP X 69 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN X 81 " --> pdb=" O MET X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 119 removed outlier: 3.674A pdb=" N ALA X 105 " --> pdb=" O PRO X 101 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE X 118 " --> pdb=" O ILE X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 154 removed outlier: 3.541A pdb=" N ILE X 147 " --> pdb=" O ARG X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 170 Processing helix chain 'X' and resid 172 through 185 removed outlier: 3.593A pdb=" N ALA X 179 " --> pdb=" O GLY X 175 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE X 183 " --> pdb=" O ALA X 179 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 194 Processing helix chain 'X' and resid 199 through 217 removed outlier: 4.425A pdb=" N MET X 203 " --> pdb=" O TYR X 199 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR X 207 " --> pdb=" O MET X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 218 through 231 removed outlier: 3.921A pdb=" N VAL X 224 " --> pdb=" O ALA X 220 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 237 removed outlier: 6.959A pdb=" N MET X 235 " --> pdb=" O PHE X 232 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 253 removed outlier: 4.127A pdb=" N ALA X 245 " --> pdb=" O PRO X 241 " (cutoff:3.500A) Processing helix chain 'X' and resid 258 through 282 removed outlier: 3.904A pdb=" N LEU X 262 " --> pdb=" O ASN X 258 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU X 270 " --> pdb=" O ALA X 266 " (cutoff:3.500A) Proline residue: X 279 - end of helix Processing helix chain 'X' and resid 286 through 298 removed outlier: 3.596A pdb=" N ILE X 290 " --> pdb=" O GLY X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 317 removed outlier: 3.729A pdb=" N THR X 316 " --> pdb=" O PHE X 312 " (cutoff:3.500A) Processing helix chain 'X' and resid 321 through 325 Processing helix chain 'X' and resid 327 through 352 removed outlier: 3.647A pdb=" N LEU X 336 " --> pdb=" O GLN X 332 " (cutoff:3.500A) Proline residue: X 345 - end of helix Processing helix chain 'X' and resid 358 through 374 removed outlier: 3.666A pdb=" N SER X 369 " --> pdb=" O ALA X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 382 through 392 Proline residue: X 388 - end of helix Processing helix chain 'X' and resid 393 through 395 No H-bonds generated for 'chain 'X' and resid 393 through 395' Processing helix chain 'X' and resid 398 through 414 Processing helix chain 'X' and resid 415 through 421 removed outlier: 3.846A pdb=" N LYS X 421 " --> pdb=" O PRO X 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 424 through 440 removed outlier: 3.508A pdb=" N ALA X 429 " --> pdb=" O HIS X 425 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN X 436 " --> pdb=" O PHE X 432 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY X 440 " --> pdb=" O ASN X 436 " (cutoff:3.500A) Processing helix chain 'X' and resid 476 through 491 removed outlier: 3.845A pdb=" N LYS X 480 " --> pdb=" O ASN X 476 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER X 481 " --> pdb=" O VAL X 477 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE X 482 " --> pdb=" O VAL X 478 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 497 removed outlier: 3.623A pdb=" N LEU X 496 " --> pdb=" O PHE X 492 " (cutoff:3.500A) Processing helix chain 'X' and resid 509 through 536 removed outlier: 3.554A pdb=" N GLY X 518 " --> pdb=" O ASN X 514 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE X 519 " --> pdb=" O CYS X 515 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE X 520 " --> pdb=" O ALA X 516 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS X 521 " --> pdb=" O VAL X 517 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU X 527 " --> pdb=" O SER X 523 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE X 534 " --> pdb=" O TYR X 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.674A pdb=" N SER H 31 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 101 through 105 removed outlier: 3.624A pdb=" N SER H 104 " --> pdb=" O SER H 101 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR H 105 " --> pdb=" O TRP H 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 101 through 105' Processing helix chain 'H' and resid 194 through 198 removed outlier: 4.024A pdb=" N LEU H 198 " --> pdb=" O SER H 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.299A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 removed outlier: 3.584A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 191 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.985A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER H 58 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.912A pdb=" N TYR H 111 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 129 through 133 removed outlier: 6.186A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 160 through 162 removed outlier: 4.386A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.800A pdb=" N LEU L 11 " --> pdb=" O LYS L 105 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 89 through 91 Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.898A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 147 through 152 341 hydrogen bonds defined for protein. 947 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: 1.03 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1122 1.30 - 1.44: 2314 1.44 - 1.58: 4221 1.58 - 1.72: 33 1.72 - 1.86: 47 Bond restraints: 7737 Sorted by residual: bond pdb=" CAK Y01 H2202 " pdb=" CBD Y01 H2202 " ideal model delta sigma weight residual 1.525 1.160 0.365 2.00e-02 2.50e+03 3.33e+02 bond pdb=" CAU Y01 H2202 " pdb=" CBI Y01 H2202 " ideal model delta sigma weight residual 1.530 1.166 0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" CAK Y01 X1606 " pdb=" CBD Y01 X1606 " ideal model delta sigma weight residual 1.525 1.162 0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" CAU Y01 X1606 " pdb=" CBI Y01 X1606 " ideal model delta sigma weight residual 1.530 1.172 0.358 2.00e-02 2.50e+03 3.20e+02 bond pdb=" CAK Y01 H2201 " pdb=" CBD Y01 H2201 " ideal model delta sigma weight residual 1.525 1.168 0.357 2.00e-02 2.50e+03 3.18e+02 ... (remaining 7732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 10323 3.27 - 6.55: 175 6.55 - 9.82: 26 9.82 - 13.09: 5 13.09 - 16.37: 5 Bond angle restraints: 10534 Sorted by residual: angle pdb=" CA PRO H 156 " pdb=" N PRO H 156 " pdb=" CD PRO H 156 " ideal model delta sigma weight residual 111.50 98.22 13.28 1.40e+00 5.10e-01 9.00e+01 angle pdb=" O SER L 10 " pdb=" C SER L 10 " pdb=" CA ASER L 10 " ideal model delta sigma weight residual 119.98 130.90 -10.92 1.22e+00 6.72e-01 8.00e+01 angle pdb=" O SER L 10 " pdb=" C SER L 10 " pdb=" CA BSER L 10 " ideal model delta sigma weight residual 119.98 130.90 -10.92 1.22e+00 6.72e-01 8.00e+01 angle pdb=" N SER L 10 " pdb=" CA ASER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 107.93 121.33 -13.40 1.65e+00 3.67e-01 6.59e+01 angle pdb=" N SER L 10 " pdb=" CA BSER L 10 " pdb=" C SER L 10 " ideal model delta sigma weight residual 107.93 121.33 -13.40 1.65e+00 3.67e-01 6.59e+01 ... (remaining 10529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4097 17.99 - 35.98: 282 35.98 - 53.97: 92 53.97 - 71.96: 20 71.96 - 89.94: 2 Dihedral angle restraints: 4493 sinusoidal: 1774 harmonic: 2719 Sorted by residual: dihedral pdb=" CA MET X 541 " pdb=" C MET X 541 " pdb=" N LYS X 542 " pdb=" CA LYS X 542 " ideal model delta harmonic sigma weight residual -180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CB CYS X 314 " pdb=" SG CYS X 314 " pdb=" SG CYS X 515 " pdb=" CB CYS X 515 " ideal model delta sinusoidal sigma weight residual -86.00 -126.33 40.33 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA TRP X 90 " pdb=" C TRP X 90 " pdb=" N TYR X 91 " pdb=" CA TYR X 91 " ideal model delta harmonic sigma weight residual 180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 1144 0.315 - 0.631: 12 0.631 - 0.946: 3 0.946 - 1.262: 0 1.262 - 1.577: 3 Chirality restraints: 1162 Sorted by residual: chirality pdb=" CBD Y01 H2201 " pdb=" CAK Y01 H2201 " pdb=" CBF Y01 H2201 " pdb=" CBG Y01 H2201 " both_signs ideal model delta sigma weight residual False 2.70 1.12 1.58 2.00e-01 2.50e+01 6.22e+01 chirality pdb=" CBD Y01 X1606 " pdb=" CAK Y01 X1606 " pdb=" CBF Y01 X1606 " pdb=" CBG Y01 X1606 " both_signs ideal model delta sigma weight residual False 2.70 1.12 1.57 2.00e-01 2.50e+01 6.19e+01 chirality pdb=" CBD Y01 H2202 " pdb=" CAK Y01 H2202 " pdb=" CBF Y01 H2202 " pdb=" CBG Y01 H2202 " both_signs ideal model delta sigma weight residual False 2.70 1.13 1.56 2.00e-01 2.50e+01 6.11e+01 ... (remaining 1159 not shown) Planarity restraints: 1275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA X 278 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO X 279 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO X 279 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO X 279 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 193 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO H 194 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO H 194 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 194 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE X 384 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO X 385 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO X 385 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO X 385 " 0.020 5.00e-02 4.00e+02 ... (remaining 1272 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 102 2.62 - 3.19: 6680 3.19 - 3.76: 10613 3.76 - 4.33: 16211 4.33 - 4.90: 27373 Nonbonded interactions: 60979 Sorted by model distance: nonbonded pdb=" O LYS X 380 " pdb=" OG1 THR X 381 " model vdw 2.044 3.040 nonbonded pdb=" CE1 TYR H 154 " pdb=" OE2 GLU H 157 " model vdw 2.057 3.340 nonbonded pdb=" O THR H 140 " pdb=" OG SER H 195 " model vdw 2.201 3.040 nonbonded pdb=" O GLN L 126 " pdb=" OG SER L 129 " model vdw 2.201 3.040 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.206 3.120 ... (remaining 60974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.30 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: 1.750 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.610 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.020 0.365 7742 Z= 1.016 Angle : 1.039 16.368 10544 Z= 0.550 Chirality : 0.106 1.577 1162 Planarity : 0.004 0.039 1275 Dihedral : 14.149 89.944 2744 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.23 % Favored : 90.55 % Rotamer: Outliers : 8.07 % Allowed : 8.20 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.23), residues: 917 helix: -2.35 (0.22), residues: 343 sheet: -1.68 (0.35), residues: 193 loop : -3.79 (0.25), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 213 TYR 0.016 0.002 TYR L 175 PHE 0.019 0.001 PHE X 197 TRP 0.012 0.001 TRP X 90 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.02007 / 1.02 ( 7737) covalent geometry : angle 1.03816 / 0.55 (10534) SS BOND : bond 0.00777 / 0.50 ( 5) SS BOND : angle 1.81194 / 1.12 ( 10) hydrogen bonds : bond 0.15630 / 9.94 ( 336) hydrogen bonds : angle 7.22983 / 5.13 ( 947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 111 time to evaluate : 0.186 Fit side-chains REVERT: X 98 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8136 (tt) REVERT: X 142 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7852 (mmt) REVERT: X 167 ARG cc_start: 0.7684 (tmm160) cc_final: 0.6745 (mtm110) REVERT: X 473 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8018 (mt) REVERT: H 46 GLU cc_start: 0.7778 (tt0) cc_final: 0.7541 (tt0) REVERT: H 157 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5519 (mp0) outliers start: 65 outliers final: 33 residues processed: 167 average time/residue: 0.3621 time to fit residues: 65.4382 Evaluate side-chains 118 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 81 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 78 GLU Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 142 MET Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 264 VAL Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 343 PHE Chi-restraints excluded: chain X residue 367 SER Chi-restraints excluded: chain X residue 387 LEU Chi-restraints excluded: chain X residue 397 ASP Chi-restraints excluded: chain X residue 430 VAL Chi-restraints excluded: chain X residue 473 LEU Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 199 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 40.0000 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 171 GLN X 213 ASN X 317 ASN H 13 GLN H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS L 201 GLN L 212 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.171184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128834 restraints weight = 27641.216| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 5.31 r_work: 0.3232 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7742 Z= 0.137 Angle : 0.647 9.187 10544 Z= 0.327 Chirality : 0.043 0.151 1162 Planarity : 0.006 0.082 1275 Dihedral : 11.935 59.386 1190 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.84 % Allowed : 12.92 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.27), residues: 917 helix: -0.22 (0.28), residues: 342 sheet: -0.80 (0.36), residues: 201 loop : -3.04 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.011 0.001 TYR X 141 PHE 0.025 0.001 PHE X 343 TRP 0.008 0.001 TRP H 112 HIS 0.004 0.001 HIS X 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 7737) covalent geometry : angle 0.64515 / 0.33 (10534) SS BOND : bond 0.00590 / 0.37 ( 5) SS BOND : angle 1.61492 / 1.02 ( 10) hydrogen bonds : bond 0.03988 / 2.64 ( 336) hydrogen bonds : angle 5.40891 / 3.83 ( 947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.313 Fit side-chains REVERT: X 98 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.7980 (tt) REVERT: X 167 ARG cc_start: 0.7700 (tmm160) cc_final: 0.6846 (ttp-110) REVERT: X 473 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8010 (mt) REVERT: X 530 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8565 (m-80) REVERT: H 46 GLU cc_start: 0.8702 (tt0) cc_final: 0.8476 (tt0) REVERT: H 205 CYS cc_start: 0.2981 (OUTLIER) cc_final: 0.2612 (t) REVERT: L 59 PRO cc_start: 0.8177 (Cg_exo) cc_final: 0.7865 (Cg_endo) outliers start: 39 outliers final: 17 residues processed: 122 average time/residue: 0.4665 time to fit residues: 61.0085 Evaluate side-chains 104 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 264 VAL Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 393 TYR Chi-restraints excluded: chain X residue 473 LEU Chi-restraints excluded: chain X residue 477 VAL Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 60 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 0.0050 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 75 HIS X 213 ASN H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.172526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131138 restraints weight = 24175.736| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 4.76 r_work: 0.3290 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7742 Z= 0.119 Angle : 0.585 9.527 10544 Z= 0.295 Chirality : 0.042 0.148 1162 Planarity : 0.005 0.076 1275 Dihedral : 10.251 58.497 1158 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.35 % Allowed : 15.16 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.28), residues: 917 helix: 0.48 (0.29), residues: 342 sheet: -0.25 (0.37), residues: 200 loop : -2.63 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.014 0.001 TYR X 281 PHE 0.023 0.001 PHE X 343 TRP 0.008 0.001 TRP X 90 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7737) covalent geometry : angle 0.58353 / 0.29 (10534) SS BOND : bond 0.00587 / 0.35 ( 5) SS BOND : angle 1.28875 / 0.83 ( 10) hydrogen bonds : bond 0.03482 / 2.28 ( 336) hydrogen bonds : angle 4.93377 / 3.50 ( 947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.282 Fit side-chains REVERT: X 98 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.7880 (tt) REVERT: X 117 PHE cc_start: 0.8130 (t80) cc_final: 0.7899 (t80) REVERT: X 132 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: H 46 GLU cc_start: 0.8553 (tt0) cc_final: 0.8329 (tt0) REVERT: H 205 CYS cc_start: 0.2925 (OUTLIER) cc_final: 0.2566 (t) REVERT: L 59 PRO cc_start: 0.8179 (Cg_exo) cc_final: 0.7877 (Cg_endo) outliers start: 27 outliers final: 15 residues processed: 106 average time/residue: 0.4650 time to fit residues: 52.8684 Evaluate side-chains 97 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 393 TYR Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 9 optimal weight: 0.0970 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN L 102 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.172682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130860 restraints weight = 22379.739| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 4.36 r_work: 0.3303 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 7742 Z= 0.120 Angle : 0.565 8.385 10544 Z= 0.286 Chirality : 0.041 0.145 1162 Planarity : 0.005 0.076 1275 Dihedral : 9.458 58.681 1152 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.23 % Allowed : 16.52 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.28), residues: 917 helix: 0.76 (0.29), residues: 344 sheet: 0.10 (0.38), residues: 200 loop : -2.35 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 24 TYR 0.019 0.001 TYR H 154 PHE 0.023 0.001 PHE X 343 TRP 0.009 0.001 TRP X 90 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7737) covalent geometry : angle 0.56319 / 0.29 (10534) SS BOND : bond 0.00579 / 0.36 ( 5) SS BOND : angle 1.41084 / 0.86 ( 10) hydrogen bonds : bond 0.03443 / 2.25 ( 336) hydrogen bonds : angle 4.74596 / 3.37 ( 947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.275 Fit side-chains REVERT: X 98 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.7823 (tt) REVERT: X 117 PHE cc_start: 0.8044 (t80) cc_final: 0.7772 (t80) REVERT: X 132 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: X 167 ARG cc_start: 0.7768 (tmm160) cc_final: 0.7012 (ttp-110) REVERT: H 46 GLU cc_start: 0.8498 (tt0) cc_final: 0.8266 (tt0) REVERT: L 24 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7441 (ttm110) outliers start: 26 outliers final: 16 residues processed: 100 average time/residue: 0.4458 time to fit residues: 47.9378 Evaluate side-chains 90 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 393 TYR Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 291 HIS ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.174011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132625 restraints weight = 27686.775| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 5.36 r_work: 0.3261 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7742 Z= 0.108 Angle : 0.534 7.750 10544 Z= 0.271 Chirality : 0.041 0.140 1162 Planarity : 0.005 0.078 1275 Dihedral : 8.918 58.239 1149 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.11 % Allowed : 18.26 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.29), residues: 917 helix: 0.96 (0.29), residues: 345 sheet: 0.20 (0.38), residues: 200 loop : -2.08 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.010 0.001 TYR H 94 PHE 0.022 0.001 PHE X 343 TRP 0.009 0.001 TRP X 90 HIS 0.003 0.001 HIS X 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7737) covalent geometry : angle 0.53266 / 0.27 (10534) SS BOND : bond 0.00513 / 0.32 ( 5) SS BOND : angle 1.28559 / 0.80 ( 10) hydrogen bonds : bond 0.03263 / 2.13 ( 336) hydrogen bonds : angle 4.58342 / 3.26 ( 947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.262 Fit side-chains REVERT: X 117 PHE cc_start: 0.7956 (t80) cc_final: 0.7702 (t80) REVERT: X 132 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: X 167 ARG cc_start: 0.7829 (tmm160) cc_final: 0.6833 (ttp-110) REVERT: H 46 GLU cc_start: 0.8556 (tt0) cc_final: 0.8320 (tt0) REVERT: H 114 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7245 (pt0) REVERT: L 29 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8526 (t) outliers start: 25 outliers final: 19 residues processed: 99 average time/residue: 0.4389 time to fit residues: 46.7143 Evaluate side-chains 93 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 211 ILE Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 393 TYR Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 186 GLN X 289 ASN ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.171539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130135 restraints weight = 29024.917| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 5.72 r_work: 0.3216 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7742 Z= 0.136 Angle : 0.560 7.592 10544 Z= 0.283 Chirality : 0.042 0.138 1162 Planarity : 0.005 0.078 1275 Dihedral : 8.800 59.197 1147 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.60 % Allowed : 17.89 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.29), residues: 917 helix: 0.89 (0.28), residues: 352 sheet: 0.26 (0.38), residues: 200 loop : -2.01 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 24 TYR 0.017 0.001 TYR H 154 PHE 0.023 0.001 PHE X 343 TRP 0.010 0.001 TRP X 437 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 7737) covalent geometry : angle 0.55773 / 0.28 (10534) SS BOND : bond 0.00660 / 0.42 ( 5) SS BOND : angle 1.58440 / 0.95 ( 10) hydrogen bonds : bond 0.03647 / 2.39 ( 336) hydrogen bonds : angle 4.64820 / 3.32 ( 947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.295 Fit side-chains REVERT: X 98 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.7888 (tt) REVERT: X 117 PHE cc_start: 0.7981 (t80) cc_final: 0.7688 (t80) REVERT: X 132 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: X 167 ARG cc_start: 0.7842 (tmm160) cc_final: 0.6801 (ttp-110) REVERT: X 178 ILE cc_start: 0.7768 (mt) cc_final: 0.7551 (mm) REVERT: H 114 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7207 (pt0) REVERT: L 24 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7239 (ttm110) REVERT: L 29 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8527 (t) outliers start: 29 outliers final: 19 residues processed: 101 average time/residue: 0.4707 time to fit residues: 50.9792 Evaluate side-chains 96 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 98 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 369 SER Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 4 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 157 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 = 0.4014 r_free = 0.4014 target = 0.173196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130839 restraints weight = 28428.078| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 5.65 r_work: 0.3235 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7742 Z= 0.115 Angle : 0.539 7.134 10544 Z= 0.273 Chirality : 0.041 0.138 1162 Planarity : 0.005 0.079 1275 Dihedral : 8.654 59.089 1145 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.48 % Allowed : 18.26 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.29), residues: 917 helix: 1.06 (0.28), residues: 350 sheet: 0.36 (0.38), residues: 200 loop : -1.94 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.010 0.001 TYR H 94 PHE 0.022 0.001 PHE X 343 TRP 0.009 0.001 TRP X 90 HIS 0.005 0.001 HIS X 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 7737) covalent geometry : angle 0.53760 / 0.27 (10534) SS BOND : bond 0.00580 / 0.37 ( 5) SS BOND : angle 1.48427 / 0.88 ( 10) hydrogen bonds : bond 0.03422 / 2.23 ( 336) hydrogen bonds : angle 4.61193 / 3.29 ( 947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.273 Fit side-chains REVERT: X 117 PHE cc_start: 0.7928 (t80) cc_final: 0.7656 (t80) REVERT: X 132 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: X 167 ARG cc_start: 0.7875 (tmm160) cc_final: 0.6843 (ttp-110) REVERT: X 178 ILE cc_start: 0.7809 (mt) cc_final: 0.7593 (mm) REVERT: H 114 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7121 (pt0) REVERT: L 29 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8532 (t) outliers start: 28 outliers final: 18 residues processed: 100 average time/residue: 0.4270 time to fit residues: 46.0165 Evaluate side-chains 94 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 132 GLU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 369 SER Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 157 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 = 0.4022 r_free = 0.4022 target = 0.174056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131411 restraints weight = 25161.737| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 5.26 r_work: 0.3274 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7742 Z= 0.104 Angle : 0.521 6.765 10544 Z= 0.263 Chirality : 0.040 0.147 1162 Planarity : 0.005 0.080 1275 Dihedral : 8.454 59.751 1145 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.86 % Allowed : 18.39 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.29), residues: 917 helix: 1.39 (0.29), residues: 341 sheet: 0.48 (0.38), residues: 200 loop : -1.82 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.017 0.001 TYR H 154 PHE 0.022 0.001 PHE X 343 TRP 0.009 0.001 TRP X 90 HIS 0.005 0.001 HIS X 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 7737) covalent geometry : angle 0.51969 / 0.26 (10534) SS BOND : bond 0.00523 / 0.32 ( 5) SS BOND : angle 1.23886 / 0.79 ( 10) hydrogen bonds : bond 0.03205 / 2.09 ( 336) hydrogen bonds : angle 4.48754 / 3.19 ( 947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.282 Fit side-chains REVERT: X 41 ILE cc_start: 0.8046 (pt) cc_final: 0.7557 (mm) REVERT: X 117 PHE cc_start: 0.7918 (t80) cc_final: 0.7707 (t80) REVERT: X 167 ARG cc_start: 0.7891 (tmm160) cc_final: 0.6961 (ttp-110) REVERT: X 178 ILE cc_start: 0.7876 (mt) cc_final: 0.7663 (mm) REVERT: X 368 MET cc_start: 0.8673 (tpp) cc_final: 0.8456 (mmt) REVERT: H 114 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7123 (pt0) REVERT: L 24 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7379 (ttm110) REVERT: L 29 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8481 (t) outliers start: 23 outliers final: 18 residues processed: 100 average time/residue: 0.4523 time to fit residues: 48.6393 Evaluate side-chains 91 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 211 ILE Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 369 SER Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 157 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 = 0.4031 r_free = 0.4031 target = 0.174905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132107 restraints weight = 27958.218| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 5.52 r_work: 0.3269 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7742 Z= 0.097 Angle : 0.516 6.608 10544 Z= 0.261 Chirality : 0.040 0.148 1162 Planarity : 0.005 0.079 1275 Dihedral : 8.363 59.174 1145 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.86 % Allowed : 18.63 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.29), residues: 917 helix: 1.51 (0.29), residues: 344 sheet: 0.63 (0.39), residues: 189 loop : -1.73 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 110 TYR 0.009 0.001 TYR H 94 PHE 0.022 0.001 PHE X 343 TRP 0.009 0.001 TRP X 437 HIS 0.004 0.001 HIS X 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 7737) covalent geometry : angle 0.51514 / 0.26 (10534) SS BOND : bond 0.00502 / 0.31 ( 5) SS BOND : angle 1.25702 / 0.77 ( 10) hydrogen bonds : bond 0.03116 / 2.03 ( 336) hydrogen bonds : angle 4.44044 / 3.15 ( 947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.267 Fit side-chains REVERT: X 41 ILE cc_start: 0.7984 (pt) cc_final: 0.7542 (mm) REVERT: X 117 PHE cc_start: 0.7878 (t80) cc_final: 0.7657 (t80) REVERT: X 167 ARG cc_start: 0.7870 (tmm160) cc_final: 0.6916 (ttp-110) REVERT: X 178 ILE cc_start: 0.7807 (mt) cc_final: 0.7601 (mm) REVERT: X 368 MET cc_start: 0.8643 (tpp) cc_final: 0.8423 (mmt) REVERT: H 114 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7073 (pt0) REVERT: L 29 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8477 (t) outliers start: 23 outliers final: 17 residues processed: 92 average time/residue: 0.4351 time to fit residues: 43.1286 Evaluate side-chains 85 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 211 ILE Chi-restraints excluded: chain X residue 273 PHE Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 369 SER Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 515 CYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 76 ASN ** L 157 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 = 0.4014 r_free = 0.4014 target = 0.173269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130101 restraints weight = 26204.672| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 5.07 r_work: 0.3249 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7742 Z= 0.115 Angle : 0.534 6.706 10544 Z= 0.270 Chirality : 0.041 0.153 1162 Planarity : 0.005 0.079 1275 Dihedral : 8.402 58.271 1145 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.36 % Allowed : 18.76 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 917 helix: 1.37 (0.28), residues: 353 sheet: 0.69 (0.39), residues: 189 loop : -1.70 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 110 TYR 0.011 0.001 TYR H 94 PHE 0.024 0.001 PHE X 343 TRP 0.009 0.001 TRP X 90 HIS 0.005 0.001 HIS X 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 7737) covalent geometry : angle 0.53207 / 0.27 (10534) SS BOND : bond 0.00606 / 0.38 ( 5) SS BOND : angle 1.45507 / 0.87 ( 10) hydrogen bonds : bond 0.03382 / 2.21 ( 336) hydrogen bonds : angle 4.45705 / 3.17 ( 947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.258 Fit side-chains REVERT: X 41 ILE cc_start: 0.8041 (pt) cc_final: 0.7606 (mm) REVERT: X 117 PHE cc_start: 0.7912 (t80) cc_final: 0.7693 (t80) REVERT: X 167 ARG cc_start: 0.7872 (tmm160) cc_final: 0.6935 (ttp-110) REVERT: X 178 ILE cc_start: 0.7857 (mt) cc_final: 0.7652 (mm) REVERT: X 368 MET cc_start: 0.8700 (tpp) cc_final: 0.8484 (mmt) REVERT: H 114 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7250 (mm110) REVERT: L 29 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8492 (t) outliers start: 19 outliers final: 13 residues processed: 92 average time/residue: 0.4540 time to fit residues: 44.9603 Evaluate side-chains 84 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 289 ASN Chi-restraints excluded: chain X residue 309 VAL Chi-restraints excluded: chain X residue 369 SER Chi-restraints excluded: chain X residue 500 VAL Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 530 TYR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 203 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 378 HIS H 76 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132453 restraints weight = 28718.672| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 5.54 r_work: 0.3266 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7742 Z= 0.103 Angle : 0.524 6.520 10544 Z= 0.265 Chirality : 0.040 0.151 1162 Planarity : 0.005 0.078 1275 Dihedral : 8.137 58.287 1144 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.11 % Allowed : 19.13 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.29), residues: 917 helix: 1.58 (0.29), residues: 344 sheet: 0.77 (0.39), residues: 189 loop : -1.57 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 24 TYR 0.015 0.001 TYR H 154 PHE 0.023 0.001 PHE X 343 TRP 0.008 0.001 TRP X 90 HIS 0.004 0.001 HIS X 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 7737) covalent geometry : angle 0.52023 / 0.26 (10534) SS BOND : bond 0.00599 / 0.38 ( 5) SS BOND : angle 2.22491 / 1.52 ( 10) hydrogen bonds : bond 0.03173 / 2.07 ( 336) hydrogen bonds : angle 4.40402 / 3.12 ( 947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2829.13 seconds wall clock time: 48 minutes 59.57 seconds (2939.57 seconds total)