Starting phenix.real_space_refine on Mon Apr 6 03:03:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q6y_72281/04_2026/9q6y_72281.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q6y_72281/04_2026/9q6y_72281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q6y_72281/04_2026/9q6y_72281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q6y_72281/04_2026/9q6y_72281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q6y_72281/04_2026/9q6y_72281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q6y_72281/04_2026/9q6y_72281.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.006 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 S 54 5.16 5 C 4759 2.51 5 N 1301 2.21 5 O 1462 1.98 5 H 7345 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14921 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 9224 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 560} Chain: "B" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1992 Classifications: {'peptide': 131} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "C" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1879 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "E" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1826 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Time building chain proxies: 1.91, per 1000 atoms: 0.13 Number of scatterers: 14921 At special positions: 0 Unit cell: (80.868, 105.48, 141.519, 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 54 16.00 O 1462 8.00 N 1301 7.00 C 4759 6.00 H 7345 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.04 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 340 " - pdb=" SG CYS A 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.04 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 117 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 126 " distance=2.04 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: 1.17 Conformation dependent library (CDL) restraints added in 456.6 milliseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 53.8% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.567A pdb=" N HIS A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 37 " --> pdb=" O HIS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 55 Processing helix chain 'A' and resid 59 through 80 Processing helix chain 'A' and resid 89 through 99 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 154 through 169 removed outlier: 3.557A pdb=" N PHE A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 195 Processing helix chain 'A' and resid 197 through 247 Proline residue: A 204 - end of helix removed outlier: 3.657A pdb=" N LYS A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 272 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.538A pdb=" N ILE A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 4.361A pdb=" N CYS A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.716A pdb=" N LEU A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 396 through 423 removed outlier: 3.524A pdb=" N GLU A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Proline residue: A 403 - end of helix Proline residue: A 408 - end of helix removed outlier: 3.866A pdb=" N GLN A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 439 Processing helix chain 'A' and resid 443 through 462 Processing helix chain 'A' and resid 465 through 491 removed outlier: 4.220A pdb=" N MET A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Proline residue: A 471 - end of helix removed outlier: 3.680A pdb=" N THR A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 removed outlier: 3.805A pdb=" N THR A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 515 Processing helix chain 'A' and resid 534 through 540 removed outlier: 4.054A pdb=" N CYS A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 564 through 585 Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.641A pdb=" N ARG C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.762A pdb=" N ASN E 53 " --> pdb=" O THR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 112 Processing helix chain 'E' and resid 128 through 132 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 30 removed outlier: 7.229A pdb=" N VAL B 29 " --> pdb=" O SER B 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.785A pdb=" N THR B 73 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE B 63 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG B 54 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 65 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 109 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 136 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.785A pdb=" N THR B 73 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE B 63 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG B 54 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 65 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 109 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'C' and resid 25 through 29 removed outlier: 3.991A pdb=" N THR C 99 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.966A pdb=" N ALA C 113 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.966A pdb=" N ALA C 113 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 27 through 29 removed outlier: 3.586A pdb=" N VAL E 27 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR E 99 " --> pdb=" O ASP E 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 33 through 35 removed outlier: 3.510A pdb=" N ALA E 113 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY E 120 " --> pdb=" O CYS E 55 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS E 55 " --> pdb=" O GLY E 120 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG E 60 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU E 68 " --> pdb=" O ARG E 60 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1302 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: 3.15 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7344 1.04 - 1.23: 441 1.23 - 1.43: 2885 1.43 - 1.63: 4340 1.63 - 1.83: 66 Bond restraints: 15076 Sorted by residual: bond pdb=" N HIS B 18 " pdb=" H1 HIS B 18 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" CB PRO A 561 " pdb=" CG PRO A 561 " ideal model delta sigma weight residual 1.492 1.660 -0.168 5.00e-02 4.00e+02 1.12e+01 bond pdb=" N PRO A 561 " pdb=" CD PRO A 561 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.55e+00 bond pdb=" N PRO A 561 " pdb=" CA PRO A 561 " ideal model delta sigma weight residual 1.470 1.446 0.024 1.01e-02 9.80e+03 5.84e+00 bond pdb=" CB CYS A 193 " pdb=" SG CYS A 193 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.78e+00 ... (remaining 15071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 27123 3.12 - 6.23: 70 6.23 - 9.35: 4 9.35 - 12.47: 1 12.47 - 15.59: 1 Bond angle restraints: 27199 Sorted by residual: angle pdb=" CA PRO A 561 " pdb=" N PRO A 561 " pdb=" CD PRO A 561 " ideal model delta sigma weight residual 112.00 96.41 15.59 1.40e+00 5.10e-01 1.24e+02 angle pdb=" N PRO A 561 " pdb=" CD PRO A 561 " pdb=" CG PRO A 561 " ideal model delta sigma weight residual 103.20 95.81 7.39 1.50e+00 4.44e-01 2.42e+01 angle pdb=" C PRO A 561 " pdb=" CA PRO A 561 " pdb=" CB PRO A 561 " ideal model delta sigma weight residual 110.00 114.95 -4.95 1.12e+00 7.97e-01 1.96e+01 angle pdb=" CA LYS C 108 " pdb=" CB LYS C 108 " pdb=" CG LYS C 108 " ideal model delta sigma weight residual 114.10 120.09 -5.99 2.00e+00 2.50e-01 8.96e+00 angle pdb=" N PRO A 561 " pdb=" CD PRO A 561 " pdb=" HD2 PRO A 561 " ideal model delta sigma weight residual 109.00 117.65 -8.65 3.00e+00 1.11e-01 8.32e+00 ... (remaining 27194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6333 17.99 - 35.98: 601 35.98 - 53.96: 187 53.96 - 71.95: 43 71.95 - 89.94: 21 Dihedral angle restraints: 7185 sinusoidal: 3859 harmonic: 3326 Sorted by residual: dihedral pdb=" CB CYS A 461 " pdb=" SG CYS A 461 " pdb=" SG CYS A 472 " pdb=" CB CYS A 472 " ideal model delta sinusoidal sigma weight residual 93.00 20.83 72.17 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS A 340 " pdb=" SG CYS A 340 " pdb=" SG CYS A 385 " pdb=" CB CYS A 385 " ideal model delta sinusoidal sigma weight residual 93.00 160.78 -67.78 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" CA CYS A 193 " pdb=" C CYS A 193 " pdb=" N GLN A 194 " pdb=" CA GLN A 194 " ideal model delta harmonic sigma weight residual 180.00 147.09 32.91 0 5.00e+00 4.00e-02 4.33e+01 ... (remaining 7182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 951 0.049 - 0.097: 149 0.097 - 0.145: 36 0.145 - 0.194: 1 0.194 - 0.242: 1 Chirality restraints: 1138 Sorted by residual: chirality pdb=" CA PRO A 561 " pdb=" N PRO A 561 " pdb=" C PRO A 561 " pdb=" CB PRO A 561 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA CYS A 193 " pdb=" N CYS A 193 " pdb=" C CYS A 193 " pdb=" CB CYS A 193 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA PRO C 109 " pdb=" N PRO C 109 " pdb=" C PRO C 109 " pdb=" CB PRO C 109 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 1135 not shown) Planarity restraints: 2291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 560 " -0.079 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO A 561 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 491 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO A 492 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 492 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 492 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 135 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C ASN A 135 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN A 135 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 136 " -0.013 2.00e-02 2.50e+03 ... (remaining 2288 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 236 2.07 - 2.70: 23634 2.70 - 3.33: 42851 3.33 - 3.97: 51384 3.97 - 4.60: 82040 Nonbonded interactions: 200145 Sorted by model distance: nonbonded pdb=" OE1 GLU C 110 " pdb=" H GLU C 110 " model vdw 1.432 2.450 nonbonded pdb=" OE1 GLU B 105 " pdb=" H GLU B 105 " model vdw 1.455 2.450 nonbonded pdb=" OE1 GLU C 129 " pdb=" H GLU C 129 " model vdw 1.468 2.450 nonbonded pdb=" OE1 GLU C 66 " pdb=" H GLU C 66 " model vdw 1.474 2.450 nonbonded pdb="HH21 ARG B 128 " pdb=" OD1 ASP B 130 " model vdw 1.543 2.450 ... (remaining 200140 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 group one per residue 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: 4.180 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: 0.080 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.540 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 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 : 0.004 0.168 7752 Z= 0.175 Angle : 0.664 15.585 10491 Z= 0.375 Chirality : 0.039 0.242 1138 Planarity : 0.006 0.108 1364 Dihedral : 16.398 89.939 2855 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.74 % Allowed : 18.35 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.29), residues: 959 helix: 1.64 (0.25), residues: 447 sheet: 0.63 (0.43), residues: 162 loop : -0.36 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 221 TYR 0.021 0.001 TYR A 185 PHE 0.017 0.001 PHE A 419 TRP 0.007 0.001 TRP B 69 HIS 0.011 0.001 HIS E 78 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 7731) covalent geometry : angle 0.65557 (10449) SS BOND : bond 0.00375 ( 21) SS BOND : angle 1.75956 ( 42) hydrogen bonds : bond 0.16144 ( 440) hydrogen bonds : angle 6.91534 ( 1302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 167 average time/residue: 0.2410 time to fit residues: 50.9457 Evaluate side-chains 105 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain B residue 69 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 245 GLN A 391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.031341 restraints weight = 143927.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.033355 restraints weight = 68047.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.034808 restraints weight = 40327.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.035863 restraints weight = 27082.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.036616 restraints weight = 19701.124| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7752 Z= 0.217 Angle : 0.608 4.872 10491 Z= 0.333 Chirality : 0.036 0.145 1138 Planarity : 0.005 0.051 1364 Dihedral : 5.212 39.689 1062 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.08 % Allowed : 19.33 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.28), residues: 959 helix: 1.82 (0.24), residues: 448 sheet: 0.00 (0.40), residues: 174 loop : -0.31 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 138 TYR 0.015 0.002 TYR A 185 PHE 0.014 0.001 PHE C 69 TRP 0.011 0.001 TRP E 58 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 7731) covalent geometry : angle 0.60334 (10449) SS BOND : bond 0.00413 ( 21) SS BOND : angle 1.32185 ( 42) hydrogen bonds : bond 0.03890 ( 440) hydrogen bonds : angle 5.16624 ( 1302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.9148 (mtp) cc_final: 0.8942 (mtp) REVERT: A 191 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8837 (tm-30) REVERT: A 242 ARG cc_start: 0.9653 (OUTLIER) cc_final: 0.9241 (tpt90) REVERT: A 309 GLU cc_start: 0.9651 (mt-10) cc_final: 0.9418 (mp0) REVERT: B 48 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8737 (m-10) REVERT: B 81 LYS cc_start: 0.9703 (ttmt) cc_final: 0.9472 (ttmm) REVERT: B 96 TYR cc_start: 0.9066 (m-80) cc_final: 0.8808 (m-80) REVERT: E 25 GLN cc_start: 0.8107 (tp40) cc_final: 0.7623 (mm-40) REVERT: E 90 THR cc_start: 0.9661 (OUTLIER) cc_final: 0.9403 (p) outliers start: 25 outliers final: 14 residues processed: 118 average time/residue: 0.2208 time to fit residues: 33.4674 Evaluate side-chains 102 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 604 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 127 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 26 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.041553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.031525 restraints weight = 144278.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.033538 restraints weight = 67189.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.034995 restraints weight = 39490.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.036020 restraints weight = 26303.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.036765 restraints weight = 19086.382| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7752 Z= 0.126 Angle : 0.533 4.939 10491 Z= 0.282 Chirality : 0.035 0.124 1138 Planarity : 0.004 0.038 1364 Dihedral : 4.717 40.013 1059 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.71 % Allowed : 17.73 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.28), residues: 959 helix: 2.10 (0.24), residues: 452 sheet: 0.15 (0.41), residues: 167 loop : -0.19 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 88 TYR 0.014 0.001 TYR A 185 PHE 0.008 0.001 PHE C 69 TRP 0.007 0.001 TRP E 58 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7731) covalent geometry : angle 0.52808 (10449) SS BOND : bond 0.00513 ( 21) SS BOND : angle 1.25483 ( 42) hydrogen bonds : bond 0.03411 ( 440) hydrogen bonds : angle 4.76280 ( 1302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8893 (tm-30) REVERT: A 242 ARG cc_start: 0.9638 (OUTLIER) cc_final: 0.9295 (tpt90) REVERT: A 309 GLU cc_start: 0.9635 (mt-10) cc_final: 0.9381 (mp0) REVERT: A 409 GLN cc_start: 0.9725 (tt0) cc_final: 0.9391 (tm-30) REVERT: B 48 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.8806 (m-10) REVERT: B 81 LYS cc_start: 0.9702 (ttmt) cc_final: 0.9477 (ttmm) REVERT: B 96 TYR cc_start: 0.9042 (m-80) cc_final: 0.8776 (m-80) REVERT: E 25 GLN cc_start: 0.8067 (tp40) cc_final: 0.7552 (mm-40) REVERT: E 86 GLU cc_start: 0.8915 (tp30) cc_final: 0.8703 (tp30) REVERT: E 101 TYR cc_start: 0.9552 (m-80) cc_final: 0.9088 (m-80) outliers start: 22 outliers final: 11 residues processed: 115 average time/residue: 0.2456 time to fit residues: 35.7097 Evaluate side-chains 99 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 38 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.3097 r_free = 0.3097 target = 0.041518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.031352 restraints weight = 146783.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.033373 restraints weight = 68684.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.034824 restraints weight = 40532.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.035867 restraints weight = 27171.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.036611 restraints weight = 19734.894| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7752 Z= 0.126 Angle : 0.536 9.496 10491 Z= 0.284 Chirality : 0.036 0.201 1138 Planarity : 0.004 0.037 1364 Dihedral : 4.660 39.461 1059 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.34 % Allowed : 18.10 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.29), residues: 959 helix: 2.14 (0.25), residues: 452 sheet: 0.24 (0.41), residues: 174 loop : -0.17 (0.38), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.013 0.001 TYR A 185 PHE 0.009 0.001 PHE B 71 TRP 0.006 0.001 TRP E 58 HIS 0.002 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7731) covalent geometry : angle 0.52984 (10449) SS BOND : bond 0.00376 ( 21) SS BOND : angle 1.43195 ( 42) hydrogen bonds : bond 0.03291 ( 440) hydrogen bonds : angle 4.61864 ( 1302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.9197 (mtp) cc_final: 0.8963 (mtp) REVERT: A 191 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8913 (tm-30) REVERT: A 197 ASP cc_start: 0.9702 (m-30) cc_final: 0.9323 (p0) REVERT: A 242 ARG cc_start: 0.9674 (OUTLIER) cc_final: 0.9386 (tpt90) REVERT: A 309 GLU cc_start: 0.9629 (mt-10) cc_final: 0.9378 (mp0) REVERT: A 322 MET cc_start: 0.9229 (mtp) cc_final: 0.8954 (ttp) REVERT: A 409 GLN cc_start: 0.9738 (tt0) cc_final: 0.9404 (tm-30) REVERT: A 470 MET cc_start: 0.8378 (ttm) cc_final: 0.8065 (tpp) REVERT: B 48 TYR cc_start: 0.9263 (OUTLIER) cc_final: 0.8849 (m-10) REVERT: B 81 LYS cc_start: 0.9720 (ttmt) cc_final: 0.9513 (ttmm) REVERT: B 96 TYR cc_start: 0.9053 (m-80) cc_final: 0.8789 (m-80) REVERT: C 132 TYR cc_start: 0.9120 (m-80) cc_final: 0.8520 (m-80) REVERT: E 25 GLN cc_start: 0.8108 (tp40) cc_final: 0.7548 (mm-40) outliers start: 19 outliers final: 16 residues processed: 107 average time/residue: 0.2459 time to fit residues: 33.7580 Evaluate side-chains 103 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 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 = 0.3037 r_free = 0.3037 target = 0.039160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.029371 restraints weight = 154348.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.031277 restraints weight = 71645.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.032647 restraints weight = 42319.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.033623 restraints weight = 28442.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.034311 restraints weight = 20869.930| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7752 Z= 0.215 Angle : 0.562 7.545 10491 Z= 0.307 Chirality : 0.035 0.144 1138 Planarity : 0.004 0.041 1364 Dihedral : 4.760 39.159 1059 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.08 % Allowed : 17.98 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.28), residues: 959 helix: 1.65 (0.24), residues: 462 sheet: 0.29 (0.40), residues: 180 loop : -0.33 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 60 TYR 0.012 0.001 TYR A 185 PHE 0.012 0.001 PHE C 69 TRP 0.010 0.001 TRP E 58 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7731) covalent geometry : angle 0.55336 (10449) SS BOND : bond 0.00336 ( 21) SS BOND : angle 1.62023 ( 42) hydrogen bonds : bond 0.03454 ( 440) hydrogen bonds : angle 4.82901 ( 1302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.9340 (tp30) cc_final: 0.9085 (tp30) REVERT: A 147 MET cc_start: 0.9223 (mtp) cc_final: 0.8969 (mtp) REVERT: A 191 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8836 (tm-30) REVERT: A 212 GLU cc_start: 0.9265 (tp30) cc_final: 0.9031 (tp30) REVERT: A 242 ARG cc_start: 0.9658 (OUTLIER) cc_final: 0.9389 (tpt90) REVERT: A 309 GLU cc_start: 0.9609 (mt-10) cc_final: 0.9391 (mp0) REVERT: A 409 GLN cc_start: 0.9753 (tt0) cc_final: 0.9415 (tm-30) REVERT: A 470 MET cc_start: 0.8403 (ttm) cc_final: 0.8074 (tpp) REVERT: B 48 TYR cc_start: 0.9312 (OUTLIER) cc_final: 0.9108 (m-10) REVERT: B 81 LYS cc_start: 0.9763 (ttmt) cc_final: 0.9558 (ttmm) REVERT: B 96 TYR cc_start: 0.9156 (m-80) cc_final: 0.8915 (m-80) outliers start: 25 outliers final: 20 residues processed: 109 average time/residue: 0.2483 time to fit residues: 34.8015 Evaluate side-chains 105 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 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 = 0.3031 r_free = 0.3031 target = 0.039061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.029263 restraints weight = 152464.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.031207 restraints weight = 69742.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.032588 restraints weight = 40810.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.033590 restraints weight = 27249.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.034303 restraints weight = 19771.789| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7752 Z= 0.159 Angle : 0.531 6.389 10491 Z= 0.284 Chirality : 0.035 0.128 1138 Planarity : 0.004 0.039 1364 Dihedral : 4.654 38.190 1059 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.82 % Allowed : 17.36 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.28), residues: 959 helix: 1.77 (0.24), residues: 463 sheet: -0.01 (0.39), residues: 182 loop : -0.23 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 133 TYR 0.014 0.001 TYR A 185 PHE 0.008 0.001 PHE C 69 TRP 0.008 0.001 TRP E 58 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7731) covalent geometry : angle 0.52550 (10449) SS BOND : bond 0.00347 ( 21) SS BOND : angle 1.29987 ( 42) hydrogen bonds : bond 0.03258 ( 440) hydrogen bonds : angle 4.71103 ( 1302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.9358 (tp30) cc_final: 0.9093 (tp30) REVERT: A 147 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8936 (mtp) REVERT: A 156 GLU cc_start: 0.9417 (tt0) cc_final: 0.8992 (mt-10) REVERT: A 191 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8829 (tm-30) REVERT: A 212 GLU cc_start: 0.9320 (tp30) cc_final: 0.9083 (tp30) REVERT: A 242 ARG cc_start: 0.9660 (OUTLIER) cc_final: 0.9390 (tpt90) REVERT: A 309 GLU cc_start: 0.9601 (mt-10) cc_final: 0.9389 (mp0) REVERT: A 409 GLN cc_start: 0.9762 (tt0) cc_final: 0.9400 (tm-30) REVERT: A 470 MET cc_start: 0.8372 (ttm) cc_final: 0.8098 (tpp) REVERT: B 48 TYR cc_start: 0.9318 (OUTLIER) cc_final: 0.9089 (m-10) REVERT: B 96 TYR cc_start: 0.9150 (m-80) cc_final: 0.8910 (m-80) REVERT: C 72 LEU cc_start: 0.9329 (tt) cc_final: 0.8983 (tt) REVERT: C 132 TYR cc_start: 0.9166 (m-80) cc_final: 0.8554 (m-80) outliers start: 31 outliers final: 21 residues processed: 113 average time/residue: 0.2371 time to fit residues: 34.4135 Evaluate side-chains 106 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 143 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 78 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 0.0010 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 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 = 0.3030 r_free = 0.3030 target = 0.039026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.029272 restraints weight = 151174.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.031204 restraints weight = 69048.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.032588 restraints weight = 40437.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033578 restraints weight = 27047.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.034261 restraints weight = 19740.397| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7752 Z= 0.145 Angle : 0.530 6.114 10491 Z= 0.282 Chirality : 0.035 0.128 1138 Planarity : 0.004 0.038 1364 Dihedral : 4.604 37.317 1059 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.45 % Allowed : 18.23 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.29), residues: 959 helix: 1.99 (0.24), residues: 457 sheet: -0.09 (0.39), residues: 178 loop : -0.22 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 361 TYR 0.014 0.001 TYR A 185 PHE 0.007 0.001 PHE A 333 TRP 0.007 0.001 TRP E 58 HIS 0.008 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7731) covalent geometry : angle 0.52373 (10449) SS BOND : bond 0.00284 ( 21) SS BOND : angle 1.36557 ( 42) hydrogen bonds : bond 0.03201 ( 440) hydrogen bonds : angle 4.61929 ( 1302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.9366 (tp30) cc_final: 0.9113 (tp30) REVERT: A 147 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8942 (mtp) REVERT: A 212 GLU cc_start: 0.9314 (tp30) cc_final: 0.9057 (tp30) REVERT: A 242 ARG cc_start: 0.9656 (OUTLIER) cc_final: 0.9390 (tpt90) REVERT: A 309 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9391 (mp0) REVERT: A 322 MET cc_start: 0.9238 (mtp) cc_final: 0.8997 (ttp) REVERT: A 409 GLN cc_start: 0.9763 (tt0) cc_final: 0.9392 (tm-30) REVERT: A 470 MET cc_start: 0.8401 (ttm) cc_final: 0.8122 (tpp) REVERT: B 48 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.9100 (m-10) REVERT: B 96 TYR cc_start: 0.9163 (m-80) cc_final: 0.8918 (m-80) REVERT: C 72 LEU cc_start: 0.9369 (tt) cc_final: 0.9021 (tt) REVERT: C 132 TYR cc_start: 0.9161 (m-80) cc_final: 0.8518 (m-80) outliers start: 28 outliers final: 23 residues processed: 102 average time/residue: 0.2373 time to fit residues: 31.1689 Evaluate side-chains 104 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 0.0170 chunk 77 optimal weight: 0.8980 overall best weight: 1.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 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 = 0.3044 r_free = 0.3044 target = 0.039466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.029637 restraints weight = 151512.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.031608 restraints weight = 68816.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.033015 restraints weight = 40156.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.034023 restraints weight = 26765.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.034747 restraints weight = 19456.310| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7752 Z= 0.119 Angle : 0.516 5.697 10491 Z= 0.271 Chirality : 0.035 0.123 1138 Planarity : 0.004 0.040 1364 Dihedral : 4.458 36.756 1059 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.83 % Allowed : 18.47 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.29), residues: 959 helix: 2.21 (0.24), residues: 456 sheet: -0.04 (0.39), residues: 178 loop : -0.25 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 361 TYR 0.013 0.001 TYR A 185 PHE 0.007 0.001 PHE B 71 TRP 0.005 0.001 TRP E 58 HIS 0.007 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7731) covalent geometry : angle 0.51004 (10449) SS BOND : bond 0.00314 ( 21) SS BOND : angle 1.33472 ( 42) hydrogen bonds : bond 0.03043 ( 440) hydrogen bonds : angle 4.46067 ( 1302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.9372 (tp30) cc_final: 0.9114 (tp30) REVERT: A 147 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8906 (mtp) REVERT: A 212 GLU cc_start: 0.9304 (tp30) cc_final: 0.9034 (tp30) REVERT: A 242 ARG cc_start: 0.9647 (OUTLIER) cc_final: 0.9371 (tpt90) REVERT: A 309 GLU cc_start: 0.9597 (mt-10) cc_final: 0.9384 (mp0) REVERT: A 322 MET cc_start: 0.9225 (mtp) cc_final: 0.9021 (ttp) REVERT: A 409 GLN cc_start: 0.9770 (tt0) cc_final: 0.9361 (tm-30) REVERT: A 470 MET cc_start: 0.8419 (ttm) cc_final: 0.8174 (tpp) REVERT: A 595 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8707 (mm-30) REVERT: B 48 TYR cc_start: 0.9339 (OUTLIER) cc_final: 0.9114 (m-10) REVERT: B 81 LYS cc_start: 0.9759 (ttmt) cc_final: 0.9553 (ttmm) REVERT: B 96 TYR cc_start: 0.9139 (m-80) cc_final: 0.8897 (m-80) REVERT: C 72 LEU cc_start: 0.9421 (tt) cc_final: 0.9082 (tt) REVERT: C 132 TYR cc_start: 0.9141 (m-80) cc_final: 0.8514 (m-80) REVERT: E 101 TYR cc_start: 0.9641 (m-80) cc_final: 0.9392 (m-80) outliers start: 23 outliers final: 19 residues processed: 98 average time/residue: 0.2540 time to fit residues: 31.7091 Evaluate side-chains 100 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 TYR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 10 optimal weight: 0.0050 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 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 = 0.3020 r_free = 0.3020 target = 0.038454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.028735 restraints weight = 155688.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.030650 restraints weight = 70780.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.032028 restraints weight = 41475.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.033000 restraints weight = 27771.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033696 restraints weight = 20328.622| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7752 Z= 0.176 Angle : 0.535 5.418 10491 Z= 0.287 Chirality : 0.034 0.121 1138 Planarity : 0.004 0.042 1364 Dihedral : 4.566 36.394 1059 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.33 % Allowed : 18.23 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.28), residues: 959 helix: 1.91 (0.24), residues: 464 sheet: -0.07 (0.38), residues: 184 loop : -0.23 (0.38), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 361 TYR 0.013 0.001 TYR A 185 PHE 0.009 0.001 PHE C 69 TRP 0.007 0.001 TRP E 58 HIS 0.007 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7731) covalent geometry : angle 0.52672 (10449) SS BOND : bond 0.00280 ( 21) SS BOND : angle 1.55496 ( 42) hydrogen bonds : bond 0.03206 ( 440) hydrogen bonds : angle 4.59924 ( 1302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.9364 (tp30) cc_final: 0.9108 (tp30) REVERT: A 147 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8891 (mtp) REVERT: A 212 GLU cc_start: 0.9310 (tp30) cc_final: 0.9036 (tp30) REVERT: A 242 ARG cc_start: 0.9640 (OUTLIER) cc_final: 0.9376 (tpt90) REVERT: A 409 GLN cc_start: 0.9775 (tt0) cc_final: 0.9375 (tm-30) REVERT: A 470 MET cc_start: 0.8397 (ttm) cc_final: 0.8149 (tpp) REVERT: B 96 TYR cc_start: 0.9183 (m-80) cc_final: 0.8943 (m-80) REVERT: C 72 LEU cc_start: 0.9466 (tt) cc_final: 0.9160 (tt) REVERT: C 132 TYR cc_start: 0.9200 (m-80) cc_final: 0.8560 (m-80) outliers start: 27 outliers final: 23 residues processed: 97 average time/residue: 0.2423 time to fit residues: 30.1266 Evaluate side-chains 100 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 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 = 0.3042 r_free = 0.3042 target = 0.039054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.029275 restraints weight = 151748.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.031245 restraints weight = 68858.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.032663 restraints weight = 40051.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.033667 restraints weight = 26576.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.034375 restraints weight = 19267.325| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7752 Z= 0.115 Angle : 0.541 6.777 10491 Z= 0.281 Chirality : 0.035 0.122 1138 Planarity : 0.004 0.043 1364 Dihedral : 4.481 35.658 1059 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.34 % Allowed : 19.58 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.29), residues: 959 helix: 2.22 (0.24), residues: 457 sheet: -0.12 (0.39), residues: 179 loop : -0.21 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 361 TYR 0.015 0.001 TYR A 185 PHE 0.006 0.001 PHE B 71 TRP 0.004 0.001 TRP C 75 HIS 0.007 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7731) covalent geometry : angle 0.53392 (10449) SS BOND : bond 0.00282 ( 21) SS BOND : angle 1.49146 ( 42) hydrogen bonds : bond 0.03049 ( 440) hydrogen bonds : angle 4.40584 ( 1302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.9370 (tp30) cc_final: 0.9114 (tp30) REVERT: A 147 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.9003 (mtp) REVERT: A 212 GLU cc_start: 0.9294 (tp30) cc_final: 0.9009 (tp30) REVERT: A 242 ARG cc_start: 0.9628 (OUTLIER) cc_final: 0.9351 (tpt90) REVERT: A 409 GLN cc_start: 0.9772 (tt0) cc_final: 0.9386 (tm-30) REVERT: A 470 MET cc_start: 0.8371 (ttm) cc_final: 0.8138 (tpp) REVERT: C 132 TYR cc_start: 0.9137 (m-80) cc_final: 0.8492 (m-80) REVERT: E 86 GLU cc_start: 0.9045 (tp30) cc_final: 0.8760 (tp30) outliers start: 19 outliers final: 17 residues processed: 93 average time/residue: 0.2475 time to fit residues: 29.5600 Evaluate side-chains 92 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 77 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 98 ASN ** 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 = 0.3053 r_free = 0.3053 target = 0.039460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.029647 restraints weight = 153284.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.031630 restraints weight = 69127.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.033058 restraints weight = 40254.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.034045 restraints weight = 26760.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034772 restraints weight = 19477.659| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7752 Z= 0.113 Angle : 0.541 6.614 10491 Z= 0.283 Chirality : 0.035 0.120 1138 Planarity : 0.004 0.043 1364 Dihedral : 4.418 36.133 1059 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.46 % Allowed : 19.58 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.28), residues: 959 helix: 2.23 (0.24), residues: 456 sheet: -0.05 (0.39), residues: 179 loop : -0.22 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 361 TYR 0.013 0.001 TYR A 185 PHE 0.006 0.001 PHE E 69 TRP 0.004 0.001 TRP C 75 HIS 0.007 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7731) covalent geometry : angle 0.53463 (10449) SS BOND : bond 0.00284 ( 21) SS BOND : angle 1.43682 ( 42) hydrogen bonds : bond 0.02958 ( 440) hydrogen bonds : angle 4.36488 ( 1302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2438.46 seconds wall clock time: 42 minutes 15.95 seconds (2535.95 seconds total)