Starting phenix.real_space_refine on Tue Mar 3 16:38:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xn5_33311/03_2026/7xn5_33311.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xn5_33311/03_2026/7xn5_33311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xn5_33311/03_2026/7xn5_33311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xn5_33311/03_2026/7xn5_33311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xn5_33311/03_2026/7xn5_33311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xn5_33311/03_2026/7xn5_33311.map" } resolution = 3.18 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= 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 40 5.16 5 C 4392 2.51 5 N 1227 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6955 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1791 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 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: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 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: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'APR': 1, 'NCA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.53, per 1000 atoms: 0.22 Number of scatterers: 6955 At special positions: 0 Unit cell: (106.934, 95.988, 74.938, 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 40 16.00 P 2 15.00 O 1294 8.00 N 1227 7.00 C 4392 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 - 3.00 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: 0.68 Conformation dependent library (CDL) restraints added in 229.0 milliseconds 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 42.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.839A pdb=" N VAL A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 removed outlier: 4.616A pdb=" N LYS A 110 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 142 removed outlier: 4.442A pdb=" N PHE A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'B' and resid 50 through 74 removed outlier: 3.516A pdb=" N LYS B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 93 through 112 removed outlier: 3.646A pdb=" N GLN B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 removed outlier: 3.533A pdb=" N LEU B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.729A pdb=" N ARG B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.508A pdb=" N VAL B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.673A pdb=" N GLU B 257 " --> pdb=" O MET B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 292 removed outlier: 3.614A pdb=" N VAL B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 311 through 316 Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.740A pdb=" N THR B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 392 removed outlier: 3.552A pdb=" N ASN B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 removed outlier: 3.666A pdb=" N PHE B 399 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 416 Processing helix chain 'B' and resid 420 through 430 Processing helix chain 'B' and resid 447 through 455 removed outlier: 3.517A pdb=" N ASN B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'C' and resid 69 through 81 Processing helix chain 'C' and resid 94 through 105 removed outlier: 4.251A pdb=" N GLU C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 141 removed outlier: 3.817A pdb=" N ILE C 139 " --> pdb=" O ASP C 135 " (cutoff:3.500A) 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 92 removed outlier: 3.761A pdb=" N ARG D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 removed outlier: 3.764A pdb=" N ASN D 111 " --> pdb=" O HIS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.871A pdb=" N GLU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.112A pdb=" N LEU A 46 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL A 117 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 48 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 119 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 50 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N HIS A 121 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N HIS A 121 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 126 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.112A pdb=" N LEU A 46 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL A 117 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 48 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 119 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 50 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N HIS A 121 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 163 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS C 264 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 159 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN C 161 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N MET C 44 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL C 115 " --> pdb=" O MET C 44 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU C 46 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL C 117 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE C 48 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU C 119 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE C 50 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ARG C 86 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N CYS C 47 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS C 88 " --> pdb=" O CYS C 47 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE C 49 " --> pdb=" O LYS C 88 " (cutoff:3.500A) 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 152 257 hydrogen bonds defined for protein. 732 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: 0.79 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1161 1.30 - 1.42: 1898 1.42 - 1.55: 3970 1.55 - 1.68: 3 1.68 - 1.81: 66 Bond restraints: 7098 Sorted by residual: bond pdb=" O5D APR B1002 " pdb=" PB APR B1002 " ideal model delta sigma weight residual 1.641 1.519 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" O5' APR B1002 " pdb=" PA APR B1002 " ideal model delta sigma weight residual 1.645 1.527 0.118 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 1.236 1.171 0.065 1.14e-02 7.69e+03 3.21e+01 bond pdb=" CA GLN B 66 " pdb=" C GLN B 66 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.37e-02 5.33e+03 3.17e+01 bond pdb=" C7 NCA B1001 " pdb=" N7 NCA B1001 " ideal model delta sigma weight residual 1.340 1.447 -0.107 2.00e-02 2.50e+03 2.89e+01 ... (remaining 7093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 9344 2.14 - 4.27: 183 4.27 - 6.41: 22 6.41 - 8.54: 4 8.54 - 10.68: 3 Bond angle restraints: 9556 Sorted by residual: angle pdb=" N LYS B 466 " pdb=" CA LYS B 466 " pdb=" C LYS B 466 " ideal model delta sigma weight residual 114.75 107.80 6.95 1.26e+00 6.30e-01 3.04e+01 angle pdb=" N ALA C 227 " pdb=" CA ALA C 227 " pdb=" C ALA C 227 " ideal model delta sigma weight residual 114.56 109.45 5.11 1.27e+00 6.20e-01 1.62e+01 angle pdb=" O ALA B 65 " pdb=" C ALA B 65 " pdb=" N GLN B 66 " ideal model delta sigma weight residual 122.43 117.24 5.19 1.34e+00 5.57e-01 1.50e+01 angle pdb=" C2D APR B1002 " pdb=" C3D APR B1002 " pdb=" O3D APR B1002 " ideal model delta sigma weight residual 108.38 119.06 -10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CA ASN A 89 " pdb=" C ASN A 89 " pdb=" N ASP A 90 " ideal model delta sigma weight residual 116.39 120.53 -4.14 1.17e+00 7.31e-01 1.25e+01 ... (remaining 9551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 3739 17.88 - 35.75: 422 35.75 - 53.63: 67 53.63 - 71.51: 23 71.51 - 89.38: 14 Dihedral angle restraints: 4265 sinusoidal: 1747 harmonic: 2518 Sorted by residual: dihedral pdb=" CA GLU A 190 " pdb=" C GLU A 190 " pdb=" N ALA A 191 " pdb=" CA ALA A 191 " ideal model delta harmonic sigma weight residual -180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE B 465 " pdb=" C ILE B 465 " pdb=" N LYS B 466 " pdb=" CA LYS B 466 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LEU B 117 " pdb=" C LEU B 117 " pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta harmonic sigma weight residual -180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1015 0.134 - 0.268: 6 0.268 - 0.403: 0 0.403 - 0.537: 0 0.537 - 0.671: 1 Chirality restraints: 1022 Sorted by residual: chirality pdb=" C3D APR B1002 " pdb=" C2D APR B1002 " pdb=" C4D APR B1002 " pdb=" O3D APR B1002 " both_signs ideal model delta sigma weight residual False -2.71 -2.03 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C4D APR B1002 " pdb=" C3D APR B1002 " pdb=" C5D APR B1002 " pdb=" O4D APR B1002 " both_signs ideal model delta sigma weight residual False -2.49 -2.66 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA GLN B 66 " pdb=" N GLN B 66 " pdb=" C GLN B 66 " pdb=" CB GLN B 66 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 1019 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' APR B1002 " 0.152 2.00e-02 2.50e+03 6.97e-02 1.34e+02 pdb=" C2 APR B1002 " -0.004 2.00e-02 2.50e+03 pdb=" C4 APR B1002 " -0.077 2.00e-02 2.50e+03 pdb=" C5 APR B1002 " -0.072 2.00e-02 2.50e+03 pdb=" C6 APR B1002 " 0.003 2.00e-02 2.50e+03 pdb=" C8 APR B1002 " -0.016 2.00e-02 2.50e+03 pdb=" N1 APR B1002 " 0.037 2.00e-02 2.50e+03 pdb=" N3 APR B1002 " -0.063 2.00e-02 2.50e+03 pdb=" N6 APR B1002 " 0.105 2.00e-02 2.50e+03 pdb=" N7 APR B1002 " -0.047 2.00e-02 2.50e+03 pdb=" N9 APR B1002 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 328 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO B 329 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 329 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 329 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 66 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C GLN B 66 " 0.040 2.00e-02 2.50e+03 pdb=" O GLN B 66 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 67 " -0.013 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1371 2.77 - 3.31: 6436 3.31 - 3.84: 10933 3.84 - 4.37: 13432 4.37 - 4.90: 23189 Nonbonded interactions: 55361 Sorted by model distance: nonbonded pdb=" OD1 ASP D 122 " pdb=" N GLU D 123 " model vdw 2.242 3.120 nonbonded pdb=" O ARG B 316 " pdb=" OG SER B 320 " model vdw 2.261 3.040 nonbonded pdb=" O LYS C 154 " pdb=" NZ LYS C 156 " model vdw 2.266 3.120 nonbonded pdb=" O ILE D 100 " pdb=" NE2 GLN D 135 " model vdw 2.286 3.120 nonbonded pdb=" O VAL B 303 " pdb=" NE2 GLN B 306 " model vdw 2.288 3.120 ... (remaining 55356 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.570 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.440 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.005 0.122 7098 Z= 0.254 Angle : 0.693 10.677 9556 Z= 0.386 Chirality : 0.047 0.671 1022 Planarity : 0.005 0.070 1236 Dihedral : 16.223 89.383 2641 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.89 (0.28), residues: 851 helix: -0.16 (0.29), residues: 330 sheet: -1.15 (0.50), residues: 127 loop : -2.26 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 207 TYR 0.005 0.001 TYR C 276 PHE 0.017 0.001 PHE D 89 TRP 0.007 0.001 TRP A 214 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 7098) covalent geometry : angle 0.69307 ( 9556) hydrogen bonds : bond 0.17847 ( 253) hydrogen bonds : angle 6.53860 ( 732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: B 194 GLN cc_start: 0.7943 (mp10) cc_final: 0.7493 (mm-40) REVERT: B 205 MET cc_start: 0.7435 (pmm) cc_final: 0.7224 (ptp) REVERT: C 161 GLN cc_start: 0.8407 (tt0) cc_final: 0.8085 (tt0) REVERT: D 114 GLU cc_start: 0.7502 (mp0) cc_final: 0.7166 (mp0) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.0869 time to fit residues: 12.9715 Evaluate side-chains 94 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.138838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103917 restraints weight = 11426.613| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.78 r_work: 0.3218 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7098 Z= 0.138 Angle : 0.572 7.110 9556 Z= 0.297 Chirality : 0.042 0.176 1022 Planarity : 0.004 0.057 1236 Dihedral : 8.893 87.501 995 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.69 % Allowed : 5.93 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.73 (0.28), residues: 851 helix: -0.20 (0.28), residues: 335 sheet: -0.56 (0.52), residues: 124 loop : -2.20 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 126 TYR 0.006 0.001 TYR C 195 PHE 0.012 0.001 PHE B 78 TRP 0.006 0.001 TRP A 214 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7098) covalent geometry : angle 0.57179 ( 9556) hydrogen bonds : bond 0.03733 ( 253) hydrogen bonds : angle 5.01668 ( 732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: B 345 MET cc_start: 0.8563 (ttp) cc_final: 0.8338 (ttm) REVERT: C 197 TYR cc_start: 0.8365 (m-80) cc_final: 0.8116 (m-80) REVERT: D 114 GLU cc_start: 0.7407 (mp0) cc_final: 0.7152 (mp0) outliers start: 5 outliers final: 5 residues processed: 102 average time/residue: 0.0921 time to fit residues: 12.4467 Evaluate side-chains 100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.137449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102542 restraints weight = 11323.296| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.76 r_work: 0.3196 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7098 Z= 0.152 Angle : 0.558 7.099 9556 Z= 0.292 Chirality : 0.042 0.146 1022 Planarity : 0.004 0.055 1236 Dihedral : 8.086 88.518 995 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.97 % Allowed : 8.55 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.71 (0.28), residues: 851 helix: -0.28 (0.28), residues: 334 sheet: -0.40 (0.52), residues: 124 loop : -2.16 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 126 TYR 0.009 0.001 TYR C 226 PHE 0.016 0.001 PHE B 78 TRP 0.006 0.001 TRP C 214 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7098) covalent geometry : angle 0.55795 ( 9556) hydrogen bonds : bond 0.03571 ( 253) hydrogen bonds : angle 4.87627 ( 732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.273 Fit side-chains REVERT: A 61 MET cc_start: 0.7383 (mtt) cc_final: 0.6893 (mtt) REVERT: B 195 ASP cc_start: 0.7300 (m-30) cc_final: 0.7044 (m-30) REVERT: C 197 TYR cc_start: 0.8378 (m-80) cc_final: 0.8113 (m-80) REVERT: D 114 GLU cc_start: 0.7345 (mp0) cc_final: 0.7143 (mp0) REVERT: D 115 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8587 (mmmt) outliers start: 7 outliers final: 5 residues processed: 97 average time/residue: 0.0971 time to fit residues: 12.2702 Evaluate side-chains 98 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 63 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.138266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104879 restraints weight = 11367.055| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.66 r_work: 0.3235 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7098 Z= 0.113 Angle : 0.511 6.961 9556 Z= 0.270 Chirality : 0.040 0.144 1022 Planarity : 0.004 0.052 1236 Dihedral : 7.635 83.567 995 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.38 % Allowed : 9.10 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.48 (0.28), residues: 851 helix: -0.12 (0.28), residues: 336 sheet: -0.08 (0.54), residues: 121 loop : -2.07 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 126 TYR 0.007 0.001 TYR C 226 PHE 0.012 0.001 PHE B 78 TRP 0.006 0.001 TRP A 214 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7098) covalent geometry : angle 0.51069 ( 9556) hydrogen bonds : bond 0.02979 ( 253) hydrogen bonds : angle 4.72123 ( 732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.248 Fit side-chains REVERT: A 61 MET cc_start: 0.7244 (mtt) cc_final: 0.6720 (mtt) REVERT: B 325 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: C 197 TYR cc_start: 0.8320 (m-80) cc_final: 0.8052 (m-80) outliers start: 10 outliers final: 6 residues processed: 108 average time/residue: 0.0923 time to fit residues: 13.1021 Evaluate side-chains 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 0.0370 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.138102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104773 restraints weight = 11381.535| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.68 r_work: 0.3231 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7098 Z= 0.120 Angle : 0.520 7.367 9556 Z= 0.274 Chirality : 0.041 0.143 1022 Planarity : 0.004 0.051 1236 Dihedral : 7.416 89.165 995 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.93 % Allowed : 10.76 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.29), residues: 851 helix: -0.06 (0.28), residues: 337 sheet: -0.11 (0.54), residues: 123 loop : -2.00 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 126 TYR 0.011 0.001 TYR A 197 PHE 0.013 0.001 PHE B 78 TRP 0.007 0.001 TRP C 214 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7098) covalent geometry : angle 0.51968 ( 9556) hydrogen bonds : bond 0.02941 ( 253) hydrogen bonds : angle 4.70657 ( 732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.246 Fit side-chains REVERT: B 325 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: C 197 TYR cc_start: 0.8348 (m-80) cc_final: 0.8108 (m-80) outliers start: 14 outliers final: 9 residues processed: 108 average time/residue: 0.0849 time to fit residues: 12.2049 Evaluate side-chains 104 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 36 optimal weight: 0.2980 chunk 47 optimal weight: 0.1980 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.139585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.106496 restraints weight = 11514.520| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.70 r_work: 0.3264 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7098 Z= 0.098 Angle : 0.506 6.616 9556 Z= 0.266 Chirality : 0.040 0.147 1022 Planarity : 0.003 0.050 1236 Dihedral : 6.814 84.883 995 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.52 % Allowed : 11.86 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.22 (0.29), residues: 851 helix: 0.05 (0.28), residues: 346 sheet: 0.10 (0.55), residues: 120 loop : -1.93 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 126 TYR 0.009 0.001 TYR A 197 PHE 0.009 0.001 PHE B 78 TRP 0.007 0.001 TRP A 214 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7098) covalent geometry : angle 0.50646 ( 9556) hydrogen bonds : bond 0.02558 ( 253) hydrogen bonds : angle 4.58295 ( 732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.329 Fit side-chains REVERT: B 325 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: C 197 TYR cc_start: 0.8337 (m-80) cc_final: 0.8122 (m-80) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.0834 time to fit residues: 12.3199 Evaluate side-chains 104 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 46 optimal weight: 0.0370 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN B 306 GLN B 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.138462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105152 restraints weight = 11459.694| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.69 r_work: 0.3242 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7098 Z= 0.115 Angle : 0.524 9.526 9556 Z= 0.274 Chirality : 0.041 0.134 1022 Planarity : 0.004 0.049 1236 Dihedral : 6.546 79.897 995 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.79 % Allowed : 12.83 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.29), residues: 851 helix: 0.10 (0.28), residues: 344 sheet: -0.03 (0.54), residues: 123 loop : -1.97 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 126 TYR 0.012 0.001 TYR A 197 PHE 0.013 0.001 PHE B 78 TRP 0.007 0.001 TRP C 214 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7098) covalent geometry : angle 0.52410 ( 9556) hydrogen bonds : bond 0.02771 ( 253) hydrogen bonds : angle 4.59518 ( 732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.266 Fit side-chains REVERT: B 154 ASN cc_start: 0.8333 (m-40) cc_final: 0.8115 (m-40) REVERT: B 325 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8477 (tt0) outliers start: 13 outliers final: 10 residues processed: 101 average time/residue: 0.0836 time to fit residues: 11.3685 Evaluate side-chains 106 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099792 restraints weight = 11637.934| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.80 r_work: 0.3149 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7098 Z= 0.246 Angle : 0.649 9.962 9556 Z= 0.337 Chirality : 0.045 0.159 1022 Planarity : 0.004 0.052 1236 Dihedral : 7.060 84.112 995 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 1.93 % Allowed : 13.24 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.73 (0.28), residues: 851 helix: -0.47 (0.27), residues: 346 sheet: -0.23 (0.52), residues: 124 loop : -2.10 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 126 TYR 0.021 0.002 TYR A 197 PHE 0.026 0.002 PHE B 78 TRP 0.012 0.002 TRP C 214 HIS 0.005 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 7098) covalent geometry : angle 0.64898 ( 9556) hydrogen bonds : bond 0.03967 ( 253) hydrogen bonds : angle 5.00343 ( 732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.228 Fit side-chains REVERT: B 325 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: C 197 TYR cc_start: 0.8397 (m-80) cc_final: 0.8154 (m-80) outliers start: 14 outliers final: 11 residues processed: 100 average time/residue: 0.0927 time to fit residues: 12.2461 Evaluate side-chains 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 33 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN B 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103602 restraints weight = 11507.483| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.68 r_work: 0.3210 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7098 Z= 0.131 Angle : 0.566 11.185 9556 Z= 0.294 Chirality : 0.042 0.194 1022 Planarity : 0.004 0.050 1236 Dihedral : 6.590 87.607 995 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.93 % Allowed : 13.66 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.46 (0.29), residues: 851 helix: -0.18 (0.28), residues: 342 sheet: 0.01 (0.54), residues: 121 loop : -2.03 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 126 TYR 0.012 0.001 TYR A 197 PHE 0.016 0.001 PHE D 89 TRP 0.011 0.001 TRP C 214 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7098) covalent geometry : angle 0.56595 ( 9556) hydrogen bonds : bond 0.03035 ( 253) hydrogen bonds : angle 4.85170 ( 732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.201 Fit side-chains REVERT: B 154 ASN cc_start: 0.8361 (m-40) cc_final: 0.8100 (m-40) REVERT: B 325 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: C 197 TYR cc_start: 0.8339 (m-80) cc_final: 0.8102 (m-80) outliers start: 14 outliers final: 12 residues processed: 99 average time/residue: 0.0888 time to fit residues: 11.6801 Evaluate side-chains 106 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102262 restraints weight = 11415.831| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.66 r_work: 0.3190 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7098 Z= 0.168 Angle : 0.590 11.672 9556 Z= 0.306 Chirality : 0.043 0.149 1022 Planarity : 0.004 0.051 1236 Dihedral : 6.643 86.215 995 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.93 % Allowed : 13.79 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.28), residues: 851 helix: -0.23 (0.28), residues: 342 sheet: -0.16 (0.53), residues: 124 loop : -2.06 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 126 TYR 0.016 0.001 TYR A 197 PHE 0.018 0.001 PHE B 78 TRP 0.012 0.001 TRP C 214 HIS 0.004 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 7098) covalent geometry : angle 0.59004 ( 9556) hydrogen bonds : bond 0.03343 ( 253) hydrogen bonds : angle 4.90627 ( 732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.319 Fit side-chains REVERT: B 325 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: C 197 TYR cc_start: 0.8361 (m-80) cc_final: 0.8146 (m-80) outliers start: 14 outliers final: 12 residues processed: 98 average time/residue: 0.0981 time to fit residues: 12.7270 Evaluate side-chains 107 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103350 restraints weight = 11405.292| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.67 r_work: 0.3208 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7098 Z= 0.139 Angle : 0.573 11.231 9556 Z= 0.297 Chirality : 0.042 0.197 1022 Planarity : 0.004 0.051 1236 Dihedral : 6.546 89.794 995 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 1.93 % Allowed : 13.52 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.29), residues: 851 helix: -0.09 (0.28), residues: 342 sheet: 0.04 (0.54), residues: 121 loop : -2.02 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 126 TYR 0.013 0.001 TYR A 197 PHE 0.015 0.001 PHE B 78 TRP 0.012 0.001 TRP C 214 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7098) covalent geometry : angle 0.57288 ( 9556) hydrogen bonds : bond 0.03042 ( 253) hydrogen bonds : angle 4.84251 ( 732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.80 seconds wall clock time: 30 minutes 13.05 seconds (1813.05 seconds total)