Starting phenix.real_space_refine on Fri Jul 25 05:47:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xn5_33311/07_2025/7xn5_33311.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xn5_33311/07_2025/7xn5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xn5_33311/07_2025/7xn5_33311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xn5_33311/07_2025/7xn5_33311.map" model { file = "/net/cci-nas-00/data/ceres_data/7xn5_33311/07_2025/7xn5_33311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xn5_33311/07_2025/7xn5_33311.cif" } resolution = 3.18 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 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.95, per 1000 atoms: 0.86 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: 1.76 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 0.78 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: 1.95 Time building geometry restraints manager: 2.10 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: 26.140 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: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 23.090 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (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 TRP 0.007 0.001 TRP A 214 HIS 0.003 0.001 HIS B 202 PHE 0.017 0.001 PHE D 89 TYR 0.005 0.001 TYR C 276 ARG 0.020 0.001 ARG A 207 Details of bonding type rmsd hydrogen bonds : bond 0.17847 ( 253) hydrogen bonds : angle 6.53860 ( 732) covalent geometry : bond 0.00466 ( 7098) covalent geometry : angle 0.69307 ( 9556) *********************** 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 : 0.801 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: 0.1991 time to fit residues: 29.5840 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 : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 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 = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104085 restraints weight = 11121.524| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.75 r_work: 0.3222 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (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 TRP 0.006 0.001 TRP A 214 HIS 0.004 0.001 HIS A 185 PHE 0.012 0.001 PHE B 78 TYR 0.006 0.001 TYR C 195 ARG 0.005 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 253) hydrogen bonds : angle 5.01668 ( 732) covalent geometry : bond 0.00321 ( 7098) covalent geometry : angle 0.57179 ( 9556) *********************** 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 : 0.838 Fit side-chains revert: symmetry clash REVERT: B 345 MET cc_start: 0.8561 (ttp) cc_final: 0.8339 (ttm) REVERT: C 197 TYR cc_start: 0.8358 (m-80) cc_final: 0.8111 (m-80) REVERT: D 114 GLU cc_start: 0.7404 (mp0) cc_final: 0.7154 (mp0) outliers start: 5 outliers final: 5 residues processed: 102 average time/residue: 0.2161 time to fit residues: 29.1951 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 : 0.802 ------------------------------------------------------------------------------- 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 81 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100831 restraints weight = 11371.612| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.76 r_work: 0.3164 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7098 Z= 0.202 Angle : 0.605 7.320 9556 Z= 0.316 Chirality : 0.043 0.154 1022 Planarity : 0.004 0.056 1236 Dihedral : 8.330 88.023 995 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.83 % Allowed : 8.83 % Favored : 90.34 % 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: -1.89 (0.28), residues: 851 helix: -0.50 (0.28), residues: 337 sheet: -0.44 (0.52), residues: 124 loop : -2.21 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 261 HIS 0.005 0.001 HIS B 137 PHE 0.021 0.002 PHE B 78 TYR 0.011 0.001 TYR C 226 ARG 0.005 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 253) hydrogen bonds : angle 5.01481 ( 732) covalent geometry : bond 0.00483 ( 7098) covalent geometry : angle 0.60499 ( 9556) *********************** 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 100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.7495 (mtt) cc_final: 0.7065 (mtt) REVERT: A 197 TYR cc_start: 0.7893 (m-80) cc_final: 0.7609 (m-80) REVERT: B 195 ASP cc_start: 0.7342 (m-30) cc_final: 0.7050 (m-30) REVERT: C 197 TYR cc_start: 0.8373 (m-80) cc_final: 0.8091 (m-80) REVERT: D 114 GLU cc_start: 0.7385 (mp0) cc_final: 0.7156 (mp0) outliers start: 6 outliers final: 5 residues processed: 96 average time/residue: 0.2445 time to fit residues: 30.9621 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 : 1.086 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.9990 chunk 56 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.136948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103337 restraints weight = 11359.702| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.66 r_work: 0.3209 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7098 Z= 0.134 Angle : 0.537 7.052 9556 Z= 0.282 Chirality : 0.041 0.144 1022 Planarity : 0.004 0.054 1236 Dihedral : 7.888 83.777 995 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.79 % Allowed : 10.07 % Favored : 88.14 % 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: -1.64 (0.28), residues: 851 helix: -0.27 (0.28), residues: 334 sheet: -0.27 (0.53), residues: 124 loop : -2.11 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 214 HIS 0.004 0.001 HIS B 202 PHE 0.014 0.001 PHE B 78 TYR 0.007 0.001 TYR C 226 ARG 0.005 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03197 ( 253) hydrogen bonds : angle 4.78405 ( 732) covalent geometry : bond 0.00318 ( 7098) covalent geometry : angle 0.53702 ( 9556) *********************** 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 112 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 2.192 Fit side-chains REVERT: A 61 MET cc_start: 0.7374 (mtt) cc_final: 0.6903 (mtt) REVERT: B 325 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: C 197 TYR cc_start: 0.8354 (m-80) cc_final: 0.8070 (m-80) outliers start: 13 outliers final: 8 residues processed: 105 average time/residue: 0.3245 time to fit residues: 46.2768 Evaluate side-chains 106 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 2.334 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 0.0870 chunk 61 optimal weight: 0.0470 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 0.0060 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.0050 overall best weight: 0.4288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 387 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.139015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105757 restraints weight = 11329.488| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.68 r_work: 0.3249 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7098 Z= 0.101 Angle : 0.502 7.341 9556 Z= 0.264 Chirality : 0.040 0.142 1022 Planarity : 0.004 0.052 1236 Dihedral : 7.301 89.137 995 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.52 % Allowed : 11.72 % Favored : 86.76 % 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: -1.35 (0.29), residues: 851 helix: -0.01 (0.28), residues: 338 sheet: -0.01 (0.54), residues: 120 loop : -2.00 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 214 HIS 0.002 0.001 HIS B 202 PHE 0.012 0.001 PHE D 89 TYR 0.007 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.02677 ( 253) hydrogen bonds : angle 4.61652 ( 732) covalent geometry : bond 0.00234 ( 7098) covalent geometry : angle 0.50181 ( 9556) *********************** 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 119 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.055 Fit side-chains REVERT: B 325 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: C 197 TYR cc_start: 0.8348 (m-80) cc_final: 0.8126 (m-80) outliers start: 11 outliers final: 6 residues processed: 113 average time/residue: 0.2576 time to fit residues: 39.4119 Evaluate side-chains 102 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.136165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102935 restraints weight = 11397.383| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.66 r_work: 0.3182 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7098 Z= 0.178 Angle : 0.573 8.130 9556 Z= 0.300 Chirality : 0.043 0.149 1022 Planarity : 0.004 0.053 1236 Dihedral : 7.370 88.315 995 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.07 % Allowed : 12.28 % Favored : 85.66 % 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: -1.61 (0.28), residues: 851 helix: -0.28 (0.28), residues: 342 sheet: -0.21 (0.53), residues: 123 loop : -2.09 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 214 HIS 0.005 0.001 HIS B 137 PHE 0.019 0.001 PHE B 78 TYR 0.014 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 253) hydrogen bonds : angle 4.83582 ( 732) covalent geometry : bond 0.00426 ( 7098) covalent geometry : angle 0.57274 ( 9556) *********************** 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 113 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.768 Fit side-chains REVERT: A 61 MET cc_start: 0.7239 (mtt) cc_final: 0.6714 (mtt) REVERT: B 325 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8610 (tt0) REVERT: C 197 TYR cc_start: 0.8393 (m-80) cc_final: 0.8180 (m-80) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 0.3669 time to fit residues: 50.2029 Evaluate side-chains 110 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 80 optimal weight: 0.0270 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.139434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106974 restraints weight = 11153.480| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.63 r_work: 0.3253 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7098 Z= 0.099 Angle : 0.509 9.327 9556 Z= 0.267 Chirality : 0.040 0.140 1022 Planarity : 0.004 0.051 1236 Dihedral : 6.467 76.492 995 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.93 % Allowed : 13.10 % Favored : 84.97 % 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: -1.28 (0.29), residues: 851 helix: 0.01 (0.28), residues: 344 sheet: 0.12 (0.55), residues: 119 loop : -1.98 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 214 HIS 0.003 0.001 HIS B 202 PHE 0.015 0.001 PHE D 89 TYR 0.009 0.001 TYR A 197 ARG 0.007 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.02531 ( 253) hydrogen bonds : angle 4.62269 ( 732) covalent geometry : bond 0.00228 ( 7098) covalent geometry : angle 0.50900 ( 9556) *********************** 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 111 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.751 Fit side-chains REVERT: A 61 MET cc_start: 0.6907 (mtt) cc_final: 0.6348 (mtt) REVERT: B 325 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8485 (tt0) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.1885 time to fit residues: 26.7187 Evaluate side-chains 108 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.137999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105020 restraints weight = 11292.033| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.66 r_work: 0.3225 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1808 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= 0.128 Angle : 0.547 10.443 9556 Z= 0.285 Chirality : 0.042 0.149 1022 Planarity : 0.004 0.050 1236 Dihedral : 6.487 82.519 995 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.93 % Allowed : 14.07 % Favored : 84.00 % 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: -1.35 (0.29), residues: 851 helix: -0.04 (0.28), residues: 344 sheet: -0.11 (0.53), residues: 124 loop : -1.99 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 214 HIS 0.003 0.001 HIS B 202 PHE 0.017 0.001 PHE B 78 TYR 0.013 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 253) hydrogen bonds : angle 4.68386 ( 732) covalent geometry : bond 0.00305 ( 7098) covalent geometry : angle 0.54704 ( 9556) *********************** 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 110 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.796 Fit side-chains REVERT: B 325 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: C 197 TYR cc_start: 0.8354 (m-80) cc_final: 0.8145 (m-80) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.2056 time to fit residues: 28.7171 Evaluate side-chains 104 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 61 optimal weight: 0.0770 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 81 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.136964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103423 restraints weight = 11475.730| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.68 r_work: 0.3208 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1862 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= 0.145 Angle : 0.568 11.116 9556 Z= 0.296 Chirality : 0.042 0.146 1022 Planarity : 0.004 0.051 1236 Dihedral : 6.550 85.288 995 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.07 % Allowed : 13.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.29), residues: 851 helix: -0.10 (0.28), residues: 344 sheet: -0.13 (0.53), residues: 124 loop : -2.00 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 214 HIS 0.003 0.001 HIS B 202 PHE 0.016 0.001 PHE B 78 TYR 0.014 0.001 TYR A 197 ARG 0.007 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 253) hydrogen bonds : angle 4.77583 ( 732) covalent geometry : bond 0.00347 ( 7098) covalent geometry : angle 0.56832 ( 9556) *********************** 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 107 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.781 Fit side-chains REVERT: B 325 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: C 197 TYR cc_start: 0.8340 (m-80) cc_final: 0.8122 (m-80) outliers start: 15 outliers final: 10 residues processed: 98 average time/residue: 0.2027 time to fit residues: 26.9499 Evaluate side-chains 101 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 65 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3797 r_free = 0.3797 target = 0.134873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101553 restraints weight = 11517.635| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.66 r_work: 0.3167 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7098 Z= 0.221 Angle : 0.635 11.654 9556 Z= 0.330 Chirality : 0.045 0.159 1022 Planarity : 0.004 0.052 1236 Dihedral : 6.891 84.273 995 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 1.79 % Allowed : 14.07 % Favored : 84.14 % 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: -1.68 (0.28), residues: 851 helix: -0.44 (0.27), residues: 346 sheet: -0.23 (0.53), residues: 124 loop : -2.05 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 214 HIS 0.005 0.001 HIS B 137 PHE 0.022 0.002 PHE B 78 TYR 0.019 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 253) hydrogen bonds : angle 5.02814 ( 732) covalent geometry : bond 0.00532 ( 7098) covalent geometry : angle 0.63524 ( 9556) ********************** 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 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.907 Fit side-chains REVERT: B 325 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8662 (tt0) REVERT: C 197 TYR cc_start: 0.8370 (m-80) cc_final: 0.8138 (m-80) outliers start: 13 outliers final: 11 residues processed: 96 average time/residue: 0.2248 time to fit residues: 29.2591 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 : 0.784 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3821 r_free = 0.3821 target = 0.136349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.102942 restraints weight = 11380.848| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.67 r_work: 0.3204 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1905 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= 0.144 Angle : 0.577 11.720 9556 Z= 0.299 Chirality : 0.043 0.197 1022 Planarity : 0.004 0.051 1236 Dihedral : 6.617 88.820 995 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.93 % Allowed : 13.93 % Favored : 84.14 % 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: -1.49 (0.29), residues: 851 helix: -0.24 (0.28), residues: 345 sheet: -0.03 (0.54), residues: 121 loop : -2.01 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 214 HIS 0.003 0.001 HIS B 202 PHE 0.015 0.001 PHE B 78 TYR 0.013 0.001 TYR A 197 ARG 0.007 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 253) hydrogen bonds : angle 4.87853 ( 732) covalent geometry : bond 0.00343 ( 7098) covalent geometry : angle 0.57724 ( 9556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4063.07 seconds wall clock time: 73 minutes 55.42 seconds (4435.42 seconds total)