Starting phenix.real_space_refine on Sat Dec 28 00:37:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xn5_33311/12_2024/7xn5_33311.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xn5_33311/12_2024/7xn5_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_33311/12_2024/7xn5_33311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xn5_33311/12_2024/7xn5_33311.map" model { file = "/net/cci-nas-00/data/ceres_data/7xn5_33311/12_2024/7xn5_33311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xn5_33311/12_2024/7xn5_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-5532/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: 5.05, per 1000 atoms: 0.73 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: 1.73 Conformation dependent library (CDL) restraints added in 1.5 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: 0.73 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: 1.72 Time building geometry restraints manager: 2.01 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.670 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.800 ------------------------------------------------------------------------------- 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= 0.323 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 *********************** 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 : 0.780 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: 0.1971 time to fit residues: 29.2532 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 : 0.855 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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= 0.211 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 *********************** 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 : 0.779 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 102 average time/residue: 0.2060 time to fit residues: 27.9259 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 : 1.564 ------------------------------------------------------------------------------- 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 43 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 0.0770 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.0270 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7098 Z= 0.206 Angle : 0.542 7.060 9556 Z= 0.284 Chirality : 0.041 0.148 1022 Planarity : 0.004 0.054 1236 Dihedral : 8.017 87.560 995 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.97 % Allowed : 8.28 % Favored : 90.76 % 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: -1.61 (0.28), residues: 851 helix: -0.18 (0.28), residues: 335 sheet: -0.25 (0.53), residues: 121 loop : -2.15 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 214 HIS 0.004 0.001 HIS B 202 PHE 0.014 0.001 PHE B 78 TYR 0.008 0.001 TYR B 302 ARG 0.005 0.000 ARG D 126 *********************** 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 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.6781 (mtt) cc_final: 0.6360 (mtt) REVERT: B 183 PHE cc_start: 0.8482 (m-10) cc_final: 0.8270 (m-80) outliers start: 7 outliers final: 5 residues processed: 99 average time/residue: 0.2167 time to fit residues: 28.0711 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 : 1.095 ------------------------------------------------------------------------------- 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 77 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.0050 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1426 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= 0.215 Angle : 0.537 7.245 9556 Z= 0.281 Chirality : 0.041 0.146 1022 Planarity : 0.004 0.053 1236 Dihedral : 7.810 85.167 995 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.52 % Allowed : 8.83 % Favored : 89.66 % 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: -1.58 (0.28), residues: 851 helix: -0.17 (0.28), residues: 335 sheet: -0.27 (0.53), residues: 124 loop : -2.11 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 214 HIS 0.003 0.001 HIS A 185 PHE 0.015 0.001 PHE B 78 TYR 0.008 0.001 TYR C 226 ARG 0.005 0.000 ARG D 126 *********************** 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 110 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.836 Fit side-chains REVERT: A 61 MET cc_start: 0.6885 (mtt) cc_final: 0.6493 (mtt) REVERT: B 325 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8201 (tt0) outliers start: 11 outliers final: 8 residues processed: 105 average time/residue: 0.2128 time to fit residues: 29.4931 Evaluate side-chains 101 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 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 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1542 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= 0.220 Angle : 0.538 6.873 9556 Z= 0.282 Chirality : 0.041 0.142 1022 Planarity : 0.004 0.052 1236 Dihedral : 7.680 85.905 995 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.79 % Allowed : 10.62 % Favored : 87.59 % 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: -1.56 (0.28), residues: 851 helix: -0.18 (0.28), residues: 336 sheet: -0.24 (0.53), residues: 123 loop : -2.08 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 214 HIS 0.003 0.001 HIS B 137 PHE 0.016 0.001 PHE B 78 TYR 0.013 0.001 TYR A 197 ARG 0.005 0.000 ARG D 126 *********************** 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 109 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.786 Fit side-chains REVERT: B 325 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8228 (tt0) outliers start: 13 outliers final: 10 residues processed: 103 average time/residue: 0.2294 time to fit residues: 31.2087 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 : 0.764 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7098 Z= 0.248 Angle : 0.560 7.417 9556 Z= 0.293 Chirality : 0.042 0.148 1022 Planarity : 0.004 0.052 1236 Dihedral : 7.427 86.115 995 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.07 % Allowed : 12.00 % Favored : 85.93 % 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: -1.62 (0.28), residues: 851 helix: -0.30 (0.28), residues: 343 sheet: -0.22 (0.53), residues: 124 loop : -2.10 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 214 HIS 0.004 0.001 HIS B 137 PHE 0.018 0.001 PHE B 78 TYR 0.016 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 *********************** 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 115 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.764 Fit side-chains REVERT: A 61 MET cc_start: 0.6811 (mtt) cc_final: 0.6382 (mtt) REVERT: B 325 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: C 197 TYR cc_start: 0.7821 (m-80) cc_final: 0.7585 (m-80) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.2069 time to fit residues: 28.7372 Evaluate side-chains 105 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 51 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1733 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= 0.188 Angle : 0.526 9.190 9556 Z= 0.275 Chirality : 0.041 0.137 1022 Planarity : 0.004 0.051 1236 Dihedral : 6.716 81.940 995 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.07 % Allowed : 12.97 % 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: -1.40 (0.29), residues: 851 helix: -0.08 (0.28), residues: 344 sheet: -0.00 (0.54), residues: 121 loop : -2.05 (0.30), residues: 386 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 0.014 0.001 PHE D 89 TYR 0.012 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 *********************** 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 113 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.832 Fit side-chains REVERT: B 325 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: C 197 TYR cc_start: 0.7831 (m-80) cc_final: 0.7617 (m-80) outliers start: 15 outliers final: 10 residues processed: 105 average time/residue: 0.2098 time to fit residues: 29.9117 Evaluate side-chains 105 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7098 Z= 0.282 Angle : 0.583 10.032 9556 Z= 0.302 Chirality : 0.043 0.149 1022 Planarity : 0.004 0.052 1236 Dihedral : 6.868 88.801 995 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 1.66 % Allowed : 13.93 % 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 (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: -1.57 (0.28), residues: 851 helix: -0.23 (0.28), residues: 342 sheet: -0.18 (0.53), residues: 124 loop : -2.09 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 214 HIS 0.004 0.001 HIS B 387 PHE 0.018 0.002 PHE B 78 TYR 0.017 0.001 TYR A 197 ARG 0.006 0.000 ARG D 126 *********************** 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 107 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.804 Fit side-chains REVERT: B 325 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: C 197 TYR cc_start: 0.7839 (m-80) cc_final: 0.7637 (m-80) outliers start: 12 outliers final: 10 residues processed: 100 average time/residue: 0.2114 time to fit residues: 28.5025 Evaluate side-chains 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 79 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1828 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= 0.210 Angle : 0.554 11.193 9556 Z= 0.287 Chirality : 0.041 0.144 1022 Planarity : 0.004 0.051 1236 Dihedral : 6.563 87.583 995 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.66 % Allowed : 14.07 % 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: -1.42 (0.29), residues: 851 helix: -0.11 (0.28), residues: 344 sheet: 0.02 (0.54), residues: 121 loop : -2.05 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 214 HIS 0.003 0.001 HIS B 202 PHE 0.015 0.001 PHE D 89 TYR 0.013 0.001 TYR A 197 ARG 0.007 0.000 ARG D 126 *********************** 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 109 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.754 Fit side-chains REVERT: B 325 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: C 197 TYR cc_start: 0.7753 (m-80) cc_final: 0.7529 (m-80) outliers start: 12 outliers final: 10 residues processed: 102 average time/residue: 0.2184 time to fit residues: 29.3366 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 : 0.869 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 54 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.3084 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.005 0.040 7098 Z= 0.314 Angle : 0.610 11.666 9556 Z= 0.315 Chirality : 0.043 0.153 1022 Planarity : 0.004 0.052 1236 Dihedral : 6.769 84.428 995 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 1.66 % Allowed : 14.34 % 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: -1.63 (0.28), residues: 851 helix: -0.37 (0.27), residues: 348 sheet: -0.18 (0.53), residues: 124 loop : -2.07 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 214 HIS 0.004 0.001 HIS B 137 PHE 0.022 0.002 PHE B 78 TYR 0.019 0.001 TYR A 197 ARG 0.007 0.000 ARG D 126 ********************** 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 105 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.808 Fit side-chains REVERT: B 325 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: C 197 TYR cc_start: 0.7789 (m-80) cc_final: 0.7545 (m-80) outliers start: 12 outliers final: 10 residues processed: 98 average time/residue: 0.1996 time to fit residues: 26.2370 Evaluate side-chains 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 0.0270 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.137536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104422 restraints weight = 11278.689| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.65 r_work: 0.3224 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1898 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= 0.186 Angle : 0.547 11.708 9556 Z= 0.283 Chirality : 0.041 0.143 1022 Planarity : 0.004 0.051 1236 Dihedral : 6.432 86.961 995 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.79 % Allowed : 14.34 % Favored : 83.86 % 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: -1.34 (0.29), residues: 851 helix: -0.03 (0.28), residues: 344 sheet: 0.04 (0.54), residues: 121 loop : -2.01 (0.30), residues: 386 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 0.013 0.001 PHE B 78 TYR 0.012 0.001 TYR A 197 ARG 0.007 0.000 ARG D 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1831.23 seconds wall clock time: 34 minutes 46.42 seconds (2086.42 seconds total)