Starting phenix.real_space_refine on Fri Jul 19 08:09:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/07_2024/7xn6_33312.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/07_2024/7xn6_33312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/07_2024/7xn6_33312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/07_2024/7xn6_33312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/07_2024/7xn6_33312.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn6_33312/07_2024/7xn6_33312.cif" } resolution = 3.45 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= 1.000 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 2 5.49 5 S 38 5.16 5 C 4346 2.51 5 N 1211 2.21 5 O 1277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 190": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6874 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1714 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3256 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1394 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain breaks: 5 Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'APR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.13, per 1000 atoms: 0.75 Number of scatterers: 6874 At special positions: 0 Unit cell: (107.776, 96.83, 76.622, 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 38 16.00 P 2 15.00 O 1277 8.00 N 1211 7.00 C 4346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.3 seconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 42.3% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.541A pdb=" N THR A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 214 through 226 removed outlier: 4.355A pdb=" N CYS A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'B' and resid 52 through 74 removed outlier: 4.209A pdb=" N PHE B 58 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 82 removed outlier: 3.547A pdb=" N GLU B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 114 removed outlier: 3.927A pdb=" N LEU B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.568A pdb=" N LEU B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 176' Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.570A pdb=" N CYS B 221 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 222' Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.715A pdb=" N VAL B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.035A pdb=" N GLY B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'B' and resid 280 through 292 removed outlier: 4.028A pdb=" N ALA B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.882A pdb=" N TYR B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.800A pdb=" N SER B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.821A pdb=" N GLY B 361 " --> pdb=" O PRO B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 378 removed outlier: 4.148A pdb=" N THR B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 378 " --> pdb=" O TRP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 392 Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 420 through 431 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.783A pdb=" N GLU C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 107 through 111 removed outlier: 4.015A pdb=" N LYS C 110 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 213 through 226 Processing helix chain 'C' and resid 231 through 246 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 102 through 112 removed outlier: 3.628A pdb=" N THR D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN D 111 " --> pdb=" O HIS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 128 removed outlier: 4.042A pdb=" N GLU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.208A pdb=" N LEU A 46 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL A 117 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 48 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 119 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 50 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE A 114 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE A 159 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N CYS A 116 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 156 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ALA A 196 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE A 158 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 227 Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 87 removed outlier: 7.079A pdb=" N CYS C 47 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU C 46 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL C 117 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE C 48 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU C 119 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE C 50 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 194 " --> pdb=" O LYS C 156 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 654 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: 1.61 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1150 1.29 - 1.42: 1879 1.42 - 1.55: 3918 1.55 - 1.68: 6 1.68 - 1.81: 64 Bond restraints: 7017 Sorted by residual: bond pdb=" C2D APR A1001 " pdb=" O2D APR A1001 " ideal model delta sigma weight residual 1.397 1.573 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" CA TYR B 68 " pdb=" C TYR B 68 " ideal model delta sigma weight residual 1.522 1.413 0.109 1.34e-02 5.57e+03 6.65e+01 bond pdb=" C1D APR A1001 " pdb=" C2D APR A1001 " ideal model delta sigma weight residual 1.529 1.675 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" CA ALA B 141 " pdb=" C ALA B 141 " ideal model delta sigma weight residual 1.528 1.449 0.080 1.39e-02 5.18e+03 3.28e+01 bond pdb=" CA SER B 139 " pdb=" C SER B 139 " ideal model delta sigma weight residual 1.522 1.453 0.070 1.23e-02 6.61e+03 3.20e+01 ... (remaining 7012 not shown) Histogram of bond angle deviations from ideal: 87.63 - 97.30: 2 97.30 - 106.96: 187 106.96 - 116.63: 4523 116.63 - 126.29: 4642 126.29 - 135.96: 93 Bond angle restraints: 9447 Sorted by residual: angle pdb=" O3A APR A1001 " pdb=" PB APR A1001 " pdb=" O5D APR A1001 " ideal model delta sigma weight residual 101.31 124.38 -23.07 3.00e+00 1.11e-01 5.91e+01 angle pdb=" C1D APR A1001 " pdb=" C2D APR A1001 " pdb=" O2D APR A1001 " ideal model delta sigma weight residual 110.00 87.63 22.37 3.00e+00 1.11e-01 5.56e+01 angle pdb=" N TYR B 68 " pdb=" CA TYR B 68 " pdb=" C TYR B 68 " ideal model delta sigma weight residual 113.38 105.51 7.87 1.23e+00 6.61e-01 4.09e+01 angle pdb=" C5D APR A1001 " pdb=" C4D APR A1001 " pdb=" O4D APR A1001 " ideal model delta sigma weight residual 111.97 130.75 -18.78 3.00e+00 1.11e-01 3.92e+01 angle pdb=" O3A APR A1001 " pdb=" PA APR A1001 " pdb=" O5' APR A1001 " ideal model delta sigma weight residual 102.36 121.10 -18.74 3.00e+00 1.11e-01 3.90e+01 ... (remaining 9442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 3681 17.82 - 35.64: 426 35.64 - 53.46: 89 53.46 - 71.28: 11 71.28 - 89.09: 10 Dihedral angle restraints: 4217 sinusoidal: 1729 harmonic: 2488 Sorted by residual: dihedral pdb=" CA GLU D 140 " pdb=" C GLU D 140 " pdb=" N PHE D 141 " pdb=" CA PHE D 141 " ideal model delta harmonic sigma weight residual 180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA LYS B 300 " pdb=" C LYS B 300 " pdb=" N ALA B 301 " pdb=" CA ALA B 301 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" C ASN B 355 " pdb=" N ASN B 355 " pdb=" CA ASN B 355 " pdb=" CB ASN B 355 " ideal model delta harmonic sigma weight residual -122.60 -110.04 -12.56 0 2.50e+00 1.60e-01 2.52e+01 ... (remaining 4214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 1002 0.185 - 0.370: 5 0.370 - 0.556: 1 0.556 - 0.741: 0 0.741 - 0.926: 2 Chirality restraints: 1010 Sorted by residual: chirality pdb=" C2D APR A1001 " pdb=" C1D APR A1001 " pdb=" C3D APR A1001 " pdb=" O2D APR A1001 " both_signs ideal model delta sigma weight residual False -2.45 -3.38 0.93 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" C3D APR A1001 " pdb=" C2D APR A1001 " pdb=" C4D APR A1001 " pdb=" O3D APR A1001 " both_signs ideal model delta sigma weight residual False -2.71 -1.96 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" C4D APR A1001 " pdb=" C3D APR A1001 " pdb=" C5D APR A1001 " pdb=" O4D APR A1001 " both_signs ideal model delta sigma weight residual False -2.49 -2.04 -0.45 2.00e-01 2.50e+01 5.05e+00 ... (remaining 1007 not shown) Planarity restraints: 1221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' APR A1001 " -0.124 2.00e-02 2.50e+03 5.80e-02 9.25e+01 pdb=" C2 APR A1001 " 0.007 2.00e-02 2.50e+03 pdb=" C4 APR A1001 " 0.060 2.00e-02 2.50e+03 pdb=" C5 APR A1001 " 0.057 2.00e-02 2.50e+03 pdb=" C6 APR A1001 " -0.001 2.00e-02 2.50e+03 pdb=" C8 APR A1001 " 0.016 2.00e-02 2.50e+03 pdb=" N1 APR A1001 " -0.024 2.00e-02 2.50e+03 pdb=" N3 APR A1001 " 0.051 2.00e-02 2.50e+03 pdb=" N6 APR A1001 " -0.095 2.00e-02 2.50e+03 pdb=" N7 APR A1001 " 0.046 2.00e-02 2.50e+03 pdb=" N9 APR A1001 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 66 " 0.024 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C GLN B 66 " -0.082 2.00e-02 2.50e+03 pdb=" O GLN B 66 " 0.030 2.00e-02 2.50e+03 pdb=" N SER B 67 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 443 " -0.016 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C ASN B 443 " 0.053 2.00e-02 2.50e+03 pdb=" O ASN B 443 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 444 " -0.018 2.00e-02 2.50e+03 ... (remaining 1218 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 4 2.26 - 2.92: 2852 2.92 - 3.58: 9411 3.58 - 4.24: 15202 4.24 - 4.90: 26010 Nonbonded interactions: 53479 Sorted by model distance: nonbonded pdb=" NE ARG A 207 " pdb=" C1D APR A1001 " model vdw 1.596 3.550 nonbonded pdb=" C3D APR A1001 " pdb=" O5D APR A1001 " model vdw 2.029 2.776 nonbonded pdb=" CZ ARG A 207 " pdb=" C1D APR A1001 " model vdw 2.227 2.960 nonbonded pdb=" OH TYR A 37 " pdb=" O GLY A 153 " model vdw 2.238 2.440 nonbonded pdb=" O PHE B 72 " pdb=" N LEU B 85 " model vdw 2.261 2.520 ... (remaining 53474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.970 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.560 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.007 0.176 7017 Z= 0.457 Angle : 0.965 23.071 9447 Z= 0.518 Chirality : 0.061 0.926 1010 Planarity : 0.006 0.069 1221 Dihedral : 15.940 89.095 2611 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.70 % Allowed : 0.98 % Favored : 98.33 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.27), residues: 839 helix: -0.96 (0.28), residues: 342 sheet: -2.81 (0.47), residues: 119 loop : -2.98 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 261 HIS 0.007 0.001 HIS A 121 PHE 0.007 0.001 PHE A 78 TYR 0.016 0.001 TYR B 68 ARG 0.007 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: B 306 GLN cc_start: 0.6926 (pp30) cc_final: 0.6716 (pp30) REVERT: B 332 MET cc_start: 0.8470 (tmm) cc_final: 0.8254 (tmm) REVERT: C 89 ASN cc_start: 0.7856 (p0) cc_final: 0.7637 (p0) REVERT: C 102 ASP cc_start: 0.7464 (m-30) cc_final: 0.6305 (m-30) outliers start: 5 outliers final: 2 residues processed: 135 average time/residue: 0.1852 time to fit residues: 33.1484 Evaluate side-chains 106 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain B residue 139 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 121 HIS A 208 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN B 309 GLN B 443 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7017 Z= 0.185 Angle : 0.557 5.676 9447 Z= 0.296 Chirality : 0.041 0.151 1010 Planarity : 0.005 0.066 1221 Dihedral : 7.945 79.231 986 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.09 % Allowed : 8.23 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.28), residues: 839 helix: -0.52 (0.28), residues: 341 sheet: -2.76 (0.47), residues: 122 loop : -2.71 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 PHE 0.029 0.001 PHE A 247 TYR 0.017 0.001 TYR A 37 ARG 0.004 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.4681 (OUTLIER) cc_final: 0.4204 (m100) outliers start: 15 outliers final: 12 residues processed: 111 average time/residue: 0.2101 time to fit residues: 30.4867 Evaluate side-chains 118 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain C residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7017 Z= 0.359 Angle : 0.624 6.471 9447 Z= 0.330 Chirality : 0.044 0.143 1010 Planarity : 0.005 0.062 1221 Dihedral : 8.066 79.124 985 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.23 % Allowed : 13.67 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.28), residues: 839 helix: -0.72 (0.28), residues: 355 sheet: -2.67 (0.46), residues: 120 loop : -2.72 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 261 HIS 0.011 0.001 HIS A 121 PHE 0.014 0.002 PHE B 299 TYR 0.024 0.002 TYR A 37 ARG 0.004 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 140 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6987 (mm-30) outliers start: 16 outliers final: 13 residues processed: 116 average time/residue: 0.2019 time to fit residues: 31.1639 Evaluate side-chains 112 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7017 Z= 0.213 Angle : 0.541 5.095 9447 Z= 0.288 Chirality : 0.042 0.134 1010 Planarity : 0.004 0.062 1221 Dihedral : 7.650 75.785 985 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.79 % Allowed : 14.64 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.29), residues: 839 helix: -0.60 (0.28), residues: 357 sheet: -2.48 (0.47), residues: 120 loop : -2.61 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 261 HIS 0.005 0.001 HIS B 202 PHE 0.011 0.001 PHE B 233 TYR 0.016 0.001 TYR A 37 ARG 0.002 0.000 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 302 TYR cc_start: 0.7291 (t80) cc_final: 0.7000 (t80) REVERT: D 140 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6863 (mm-30) outliers start: 20 outliers final: 17 residues processed: 110 average time/residue: 0.1785 time to fit residues: 26.9309 Evaluate side-chains 113 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7017 Z= 0.213 Angle : 0.535 6.976 9447 Z= 0.282 Chirality : 0.041 0.133 1010 Planarity : 0.004 0.054 1221 Dihedral : 7.567 72.502 985 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 3.21 % Allowed : 15.34 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.29), residues: 839 helix: -0.60 (0.28), residues: 367 sheet: -2.39 (0.47), residues: 120 loop : -2.69 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 261 HIS 0.005 0.001 HIS B 202 PHE 0.027 0.001 PHE A 247 TYR 0.009 0.001 TYR B 225 ARG 0.002 0.000 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.7308 (mmt) cc_final: 0.7054 (mmt) REVERT: A 228 ASP cc_start: 0.8062 (p0) cc_final: 0.7542 (p0) REVERT: B 306 GLN cc_start: 0.6534 (pp30) cc_final: 0.6328 (pp30) REVERT: B 467 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8239 (m-70) REVERT: C 262 ILE cc_start: 0.8126 (mp) cc_final: 0.7845 (mm) REVERT: D 140 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6983 (mm-30) outliers start: 23 outliers final: 19 residues processed: 114 average time/residue: 0.1900 time to fit residues: 29.1173 Evaluate side-chains 118 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7017 Z= 0.254 Angle : 0.548 5.858 9447 Z= 0.289 Chirality : 0.042 0.133 1010 Planarity : 0.004 0.055 1221 Dihedral : 7.709 75.104 985 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 3.77 % Allowed : 16.18 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.29), residues: 839 helix: -0.56 (0.28), residues: 367 sheet: -2.52 (0.46), residues: 123 loop : -2.68 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.005 0.001 HIS B 202 PHE 0.024 0.001 PHE A 247 TYR 0.014 0.001 TYR A 37 ARG 0.002 0.000 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8083 (p0) cc_final: 0.7786 (p0) REVERT: A 229 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8471 (pttt) REVERT: B 302 TYR cc_start: 0.7402 (t80) cc_final: 0.7123 (t80) REVERT: B 467 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.8199 (m-70) REVERT: C 262 ILE cc_start: 0.8126 (mp) cc_final: 0.7840 (mm) outliers start: 27 outliers final: 20 residues processed: 117 average time/residue: 0.1788 time to fit residues: 29.4759 Evaluate side-chains 120 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 89 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 0.0770 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7017 Z= 0.224 Angle : 0.545 8.110 9447 Z= 0.286 Chirality : 0.041 0.136 1010 Planarity : 0.004 0.055 1221 Dihedral : 7.673 76.726 985 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 3.49 % Allowed : 17.02 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.29), residues: 839 helix: -0.54 (0.28), residues: 376 sheet: -2.46 (0.47), residues: 123 loop : -2.66 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 261 HIS 0.010 0.001 HIS A 121 PHE 0.021 0.001 PHE A 247 TYR 0.009 0.001 TYR A 37 ARG 0.003 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 MET cc_start: 0.7289 (mmt) cc_final: 0.7047 (mmt) REVERT: A 228 ASP cc_start: 0.8068 (p0) cc_final: 0.7781 (p0) REVERT: A 229 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8464 (pttt) REVERT: B 261 TRP cc_start: 0.8128 (OUTLIER) cc_final: 0.7286 (p-90) REVERT: B 302 TYR cc_start: 0.7430 (t80) cc_final: 0.7146 (t80) REVERT: B 306 GLN cc_start: 0.6541 (pp30) cc_final: 0.6340 (pp30) REVERT: B 467 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.8229 (m-70) REVERT: C 236 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7713 (mp) REVERT: C 262 ILE cc_start: 0.8125 (mp) cc_final: 0.7757 (mm) REVERT: C 271 LYS cc_start: 0.7902 (mttt) cc_final: 0.7589 (mttm) outliers start: 25 outliers final: 18 residues processed: 117 average time/residue: 0.1681 time to fit residues: 27.1245 Evaluate side-chains 119 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 141 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7017 Z= 0.317 Angle : 0.598 9.807 9447 Z= 0.311 Chirality : 0.042 0.134 1010 Planarity : 0.005 0.055 1221 Dihedral : 8.103 85.363 985 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 3.91 % Allowed : 17.29 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.29), residues: 839 helix: -0.61 (0.27), residues: 377 sheet: -2.65 (0.45), residues: 123 loop : -2.69 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 261 HIS 0.006 0.001 HIS B 202 PHE 0.019 0.001 PHE A 247 TYR 0.023 0.002 TYR A 37 ARG 0.003 0.000 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7151 (t80) REVERT: A 228 ASP cc_start: 0.8060 (p0) cc_final: 0.7814 (p0) REVERT: A 229 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8508 (pttt) REVERT: B 233 PHE cc_start: 0.6318 (m-80) cc_final: 0.6012 (m-80) REVERT: B 261 TRP cc_start: 0.8247 (OUTLIER) cc_final: 0.7960 (p-90) REVERT: B 302 TYR cc_start: 0.7509 (t80) cc_final: 0.7234 (t80) REVERT: B 467 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8216 (m-70) REVERT: C 236 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7794 (mp) REVERT: C 262 ILE cc_start: 0.8155 (mp) cc_final: 0.7877 (mm) REVERT: C 271 LYS cc_start: 0.7977 (mttt) cc_final: 0.7664 (mttm) outliers start: 28 outliers final: 19 residues processed: 120 average time/residue: 0.1818 time to fit residues: 29.5947 Evaluate side-chains 125 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 142 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 50 optimal weight: 0.3980 chunk 80 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7017 Z= 0.184 Angle : 0.555 11.405 9447 Z= 0.290 Chirality : 0.041 0.154 1010 Planarity : 0.004 0.057 1221 Dihedral : 7.749 84.760 985 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.93 % Allowed : 19.39 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.29), residues: 839 helix: -0.51 (0.28), residues: 377 sheet: -2.39 (0.47), residues: 123 loop : -2.62 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 PHE 0.018 0.001 PHE A 247 TYR 0.014 0.001 TYR D 138 ARG 0.004 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7153 (t80) REVERT: A 228 ASP cc_start: 0.7961 (p0) cc_final: 0.7671 (p0) REVERT: A 229 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8532 (pttm) REVERT: B 261 TRP cc_start: 0.8100 (OUTLIER) cc_final: 0.7153 (p-90) REVERT: B 302 TYR cc_start: 0.7458 (t80) cc_final: 0.7204 (t80) REVERT: B 467 HIS cc_start: 0.8668 (OUTLIER) cc_final: 0.8319 (m-70) REVERT: C 236 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7671 (mp) REVERT: C 262 ILE cc_start: 0.8120 (mp) cc_final: 0.7813 (mm) REVERT: C 271 LYS cc_start: 0.7972 (mttt) cc_final: 0.7667 (mttm) outliers start: 21 outliers final: 16 residues processed: 113 average time/residue: 0.1778 time to fit residues: 27.5102 Evaluate side-chains 115 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.0020 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7017 Z= 0.199 Angle : 0.571 12.732 9447 Z= 0.298 Chirality : 0.041 0.139 1010 Planarity : 0.004 0.056 1221 Dihedral : 7.733 88.238 985 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.93 % Allowed : 19.67 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.29), residues: 839 helix: -0.47 (0.28), residues: 377 sheet: -2.33 (0.48), residues: 123 loop : -2.58 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.004 0.001 HIS B 202 PHE 0.018 0.001 PHE A 247 TYR 0.015 0.001 TYR D 138 ARG 0.003 0.000 ARG D 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7195 (t80) REVERT: A 229 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8371 (pttt) REVERT: B 261 TRP cc_start: 0.8108 (OUTLIER) cc_final: 0.7100 (p-90) REVERT: B 302 TYR cc_start: 0.7492 (t80) cc_final: 0.7223 (t80) REVERT: B 467 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.8390 (m-70) REVERT: C 236 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7668 (mp) REVERT: C 262 ILE cc_start: 0.8124 (mp) cc_final: 0.7852 (mm) REVERT: C 271 LYS cc_start: 0.7977 (mttt) cc_final: 0.7682 (mttm) outliers start: 21 outliers final: 16 residues processed: 109 average time/residue: 0.1841 time to fit residues: 27.5948 Evaluate side-chains 114 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 28 optimal weight: 0.0000 chunk 69 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.138695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109553 restraints weight = 11878.483| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.88 r_work: 0.3359 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7017 Z= 0.146 Angle : 0.534 12.574 9447 Z= 0.279 Chirality : 0.040 0.141 1010 Planarity : 0.004 0.057 1221 Dihedral : 7.442 89.347 985 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.09 % Allowed : 20.78 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.30), residues: 839 helix: -0.18 (0.29), residues: 367 sheet: -2.18 (0.48), residues: 122 loop : -2.50 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 214 HIS 0.003 0.001 HIS B 202 PHE 0.017 0.001 PHE A 247 TYR 0.016 0.001 TYR D 138 ARG 0.003 0.000 ARG D 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1694.53 seconds wall clock time: 31 minutes 0.56 seconds (1860.56 seconds total)