Starting phenix.real_space_refine on Thu Jul 2 10:39:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7asa_11891/07_2026/7asa_11891.cif Found real_map, /net/cci-nas-00/data/ceres_data/7asa_11891/07_2026/7asa_11891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7asa_11891/07_2026/7asa_11891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7asa_11891/07_2026/7asa_11891.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7asa_11891/07_2026/7asa_11891.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7asa_11891/07_2026/7asa_11891.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7asa_11891/07_2026/7asa_11891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7asa_11891/07_2026/7asa_11891.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 116 5.49 5 S 18 5.16 5 C 4646 2.51 5 N 1459 2.21 5 O 1865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8104 Number of models: 1 Model: "" Number of chains: 5 Chain: "0" Number of atoms: 3993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 3993 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 26, 'TRANS': 509} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'HIS:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 6, 'TYR:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 9, 'TRP:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 187 Chain: "1" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 659 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "2" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 730 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 13} Link IDs: {'rna2p': 8, 'rna3p': 25} Chain breaks: 1 Chain: "A" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1755 Classifications: {'RNA': 82} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 43, 'rna3p_pyr': 32} Link IDs: {'rna2p': 7, 'rna3p': 74} Chain breaks: 5 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 967 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 10, 'TRANS': 120} Time building chain proxies: 1.69, per 1000 atoms: 0.21 Number of scatterers: 8104 At special positions: 0 Unit cell: (126.28, 146.78, 89.38, 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 18 16.00 P 116 15.00 O 1865 8.00 N 1459 7.00 C 4646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 328.5 milliseconds 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1422 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 43.9% alpha, 18.0% beta 26 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain '0' and resid 4 through 20 removed outlier: 3.593A pdb=" N ASN 0 16 " --> pdb=" O THR 0 12 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS 0 18 " --> pdb=" O GLU 0 14 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET 0 20 " --> pdb=" O ASN 0 16 " (cutoff:3.500A) Processing helix chain '0' and resid 73 through 83 removed outlier: 3.790A pdb=" N LEU 0 78 " --> pdb=" O MET 0 74 " (cutoff:3.500A) Processing helix chain '0' and resid 123 through 127 Processing helix chain '0' and resid 147 through 151 Processing helix chain '0' and resid 180 through 185 Processing helix chain '0' and resid 192 through 200 Processing helix chain '0' and resid 204 through 214 Processing helix chain '0' and resid 223 through 236 Processing helix chain '0' and resid 269 through 279 Processing helix chain '0' and resid 280 through 317 removed outlier: 3.543A pdb=" N PHE 0 297 " --> pdb=" O ASP 0 293 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS 0 314 " --> pdb=" O LYS 0 310 " (cutoff:3.500A) Processing helix chain '0' and resid 321 through 336 removed outlier: 3.610A pdb=" N PHE 0 325 " --> pdb=" O ASN 0 321 " (cutoff:3.500A) Processing helix chain '0' and resid 368 through 414 Processing helix chain '0' and resid 415 through 429 removed outlier: 3.679A pdb=" N GLU 0 421 " --> pdb=" O ARG 0 417 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG 0 423 " --> pdb=" O ILE 0 419 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLU 0 424 " --> pdb=" O SER 0 420 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU 0 425 " --> pdb=" O GLU 0 421 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU 0 426 " --> pdb=" O ILE 0 422 " (cutoff:3.500A) Processing helix chain '0' and resid 466 through 475 Processing helix chain '0' and resid 503 through 516 removed outlier: 4.462A pdb=" N ALA 0 511 " --> pdb=" O ILE 0 507 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR 0 512 " --> pdb=" O MET 0 508 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE 0 513 " --> pdb=" O GLU 0 509 " (cutoff:3.500A) Processing helix chain '0' and resid 561 through 565 Processing helix chain '1' and resid 2 through 10 Processing helix chain '1' and resid 15 through 25 Processing helix chain '1' and resid 68 through 75 removed outlier: 4.141A pdb=" N ALA 1 73 " --> pdb=" O LYS 1 69 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN 1 74 " --> pdb=" O GLU 1 70 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET 1 75 " --> pdb=" O GLU 1 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 32 removed outlier: 4.670A pdb=" N VAL K 24 " --> pdb=" O PRO K 20 " (cutoff:3.500A) Proline residue: K 26 - end of helix removed outlier: 3.529A pdb=" N ALA K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 46 removed outlier: 4.484A pdb=" N LYS K 40 " --> pdb=" O MET K 36 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 84 Processing helix chain 'K' and resid 102 through 113 Processing helix chain 'K' and resid 114 through 116 No H-bonds generated for 'chain 'K' and resid 114 through 116' Processing helix chain 'K' and resid 120 through 134 Processing sheet with id=AA1, first strand: chain '0' and resid 23 through 31 removed outlier: 5.641A pdb=" N ILE 0 24 " --> pdb=" O ARG 0 40 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG 0 40 " --> pdb=" O ILE 0 24 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS 0 26 " --> pdb=" O HIS 0 38 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP 0 34 " --> pdb=" O PRO 0 30 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS 0 47 " --> pdb=" O THR 0 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 87 through 92 removed outlier: 6.607A pdb=" N HIS 0 103 " --> pdb=" O GLU 0 89 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE 0 91 " --> pdb=" O ILE 0 101 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE 0 101 " --> pdb=" O ILE 0 91 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP 0 141 " --> pdb=" O LEU 0 131 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP 0 133 " --> pdb=" O ILE 0 139 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE 0 139 " --> pdb=" O ASP 0 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 249 through 254 removed outlier: 3.790A pdb=" N LYS 0 249 " --> pdb=" O VAL 0 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '0' and resid 345 through 349 Processing sheet with id=AA5, first strand: chain '0' and resid 451 through 454 Processing sheet with id=AA6, first strand: chain '0' and resid 483 through 487 Processing sheet with id=AA7, first strand: chain '1' and resid 33 through 34 removed outlier: 6.858A pdb=" N LEU 1 55 " --> pdb=" O GLU 1 81 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLU 1 81 " --> pdb=" O LEU 1 55 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR 1 57 " --> pdb=" O LEU 1 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 11 through 14 Processing sheet with id=AA9, first strand: chain 'K' and resid 98 through 101 removed outlier: 6.453A pdb=" N ALA K 98 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU K 140 " --> pdb=" O ALA K 98 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL K 100 " --> pdb=" O GLU K 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 290 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1495 1.32 - 1.45: 2573 1.45 - 1.57: 4149 1.57 - 1.70: 224 1.70 - 1.82: 34 Bond restraints: 8475 Sorted by residual: bond pdb=" CA PRO 0 72 " pdb=" C PRO 0 72 " ideal model delta sigma weight residual 1.517 1.554 -0.037 9.30e-03 1.16e+04 1.59e+01 bond pdb=" CZ ARG 0 286 " pdb=" NH2 ARG 0 286 " ideal model delta sigma weight residual 1.330 1.278 0.052 1.30e-02 5.92e+03 1.57e+01 bond pdb=" N ARG 0 265 " pdb=" CA ARG 0 265 " ideal model delta sigma weight residual 1.455 1.503 -0.048 1.25e-02 6.40e+03 1.49e+01 bond pdb=" CZ ARG 0 116 " pdb=" NH2 ARG 0 116 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.29e+01 bond pdb=" CZ ARG 0 395 " pdb=" NH2 ARG 0 395 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.26e+01 ... (remaining 8470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 9394 2.35 - 4.70: 2316 4.70 - 7.04: 264 7.04 - 9.39: 24 9.39 - 11.74: 2 Bond angle restraints: 12000 Sorted by residual: angle pdb=" O3' A 2 44 " pdb=" C3' A 2 44 " pdb=" C2' A 2 44 " ideal model delta sigma weight residual 109.50 121.24 -11.74 1.50e+00 4.44e-01 6.12e+01 angle pdb=" C4' C A2504 " pdb=" C3' C A2504 " pdb=" C2' C A2504 " ideal model delta sigma weight residual 102.60 96.30 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" CA ASN 0 335 " pdb=" CB ASN 0 335 " pdb=" CG ASN 0 335 " ideal model delta sigma weight residual 112.60 106.43 6.17 1.00e+00 1.00e+00 3.80e+01 angle pdb=" C3' U A2502 " pdb=" C2' U A2502 " pdb=" C1' U A2502 " ideal model delta sigma weight residual 101.30 107.27 -5.97 1.00e+00 1.00e+00 3.56e+01 angle pdb=" O3' C 2 13 " pdb=" C3' C 2 13 " pdb=" C2' C 2 13 " ideal model delta sigma weight residual 113.70 122.53 -8.83 1.50e+00 4.44e-01 3.46e+01 ... (remaining 11995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.33: 4759 33.33 - 66.66: 116 66.66 - 99.98: 17 99.98 - 133.31: 2 133.31 - 166.64: 4 Dihedral angle restraints: 4898 sinusoidal: 2714 harmonic: 2184 Sorted by residual: dihedral pdb=" C5' U A1952 " pdb=" C4' U A1952 " pdb=" C3' U A1952 " pdb=" O3' U A1952 " ideal model delta sinusoidal sigma weight residual 147.00 73.30 73.70 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" O4' U A1952 " pdb=" C4' U A1952 " pdb=" C3' U A1952 " pdb=" C2' U A1952 " ideal model delta sinusoidal sigma weight residual 24.00 -38.58 62.58 1 8.00e+00 1.56e-02 8.09e+01 dihedral pdb=" O4' U 2 34 " pdb=" C1' U 2 34 " pdb=" N1 U 2 34 " pdb=" C2 U 2 34 " ideal model delta sinusoidal sigma weight residual 200.00 53.28 146.72 1 1.50e+01 4.44e-03 7.83e+01 ... (remaining 4895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1212 0.133 - 0.266: 225 0.266 - 0.399: 19 0.399 - 0.533: 3 0.533 - 0.666: 1 Chirality restraints: 1460 Sorted by residual: chirality pdb=" CA ASN 0 335 " pdb=" N ASN 0 335 " pdb=" C ASN 0 335 " pdb=" CB ASN 0 335 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ASN 0 151 " pdb=" N ASN 0 151 " pdb=" C ASN 0 151 " pdb=" CB ASN 0 151 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA ASN K 93 " pdb=" N ASN K 93 " pdb=" C ASN K 93 " pdb=" CB ASN K 93 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.51e+00 ... (remaining 1457 not shown) Planarity restraints: 1126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A1113 " -0.286 2.00e-02 2.50e+03 1.17e-01 3.73e+02 pdb=" N9 A A1113 " 0.075 2.00e-02 2.50e+03 pdb=" C8 A A1113 " 0.105 2.00e-02 2.50e+03 pdb=" N7 A A1113 " 0.056 2.00e-02 2.50e+03 pdb=" C5 A A1113 " 0.037 2.00e-02 2.50e+03 pdb=" C6 A A1113 " -0.052 2.00e-02 2.50e+03 pdb=" N6 A A1113 " -0.150 2.00e-02 2.50e+03 pdb=" N1 A A1113 " -0.025 2.00e-02 2.50e+03 pdb=" C2 A A1113 " 0.048 2.00e-02 2.50e+03 pdb=" N3 A A1113 " 0.102 2.00e-02 2.50e+03 pdb=" C4 A A1113 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A2692 " -0.256 2.00e-02 2.50e+03 1.08e-01 3.52e+02 pdb=" N9 G A2692 " 0.050 2.00e-02 2.50e+03 pdb=" C8 G A2692 " 0.066 2.00e-02 2.50e+03 pdb=" N7 G A2692 " 0.039 2.00e-02 2.50e+03 pdb=" C5 G A2692 " 0.053 2.00e-02 2.50e+03 pdb=" C6 G A2692 " -0.024 2.00e-02 2.50e+03 pdb=" O6 G A2692 " -0.161 2.00e-02 2.50e+03 pdb=" N1 G A2692 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G A2692 " 0.071 2.00e-02 2.50e+03 pdb=" N2 G A2692 " -0.072 2.00e-02 2.50e+03 pdb=" N3 G A2692 " 0.119 2.00e-02 2.50e+03 pdb=" C4 G A2692 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1097 " -0.277 2.00e-02 2.50e+03 1.13e-01 3.52e+02 pdb=" N9 A A1097 " 0.073 2.00e-02 2.50e+03 pdb=" C8 A A1097 " 0.106 2.00e-02 2.50e+03 pdb=" N7 A A1097 " 0.050 2.00e-02 2.50e+03 pdb=" C5 A A1097 " 0.038 2.00e-02 2.50e+03 pdb=" C6 A A1097 " -0.033 2.00e-02 2.50e+03 pdb=" N6 A A1097 " -0.153 2.00e-02 2.50e+03 pdb=" N1 A A1097 " -0.029 2.00e-02 2.50e+03 pdb=" C2 A A1097 " 0.044 2.00e-02 2.50e+03 pdb=" N3 A A1097 " 0.096 2.00e-02 2.50e+03 pdb=" C4 A A1097 " 0.086 2.00e-02 2.50e+03 ... (remaining 1123 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 3477 2.97 - 3.45: 8175 3.45 - 3.94: 14307 3.94 - 4.42: 15716 4.42 - 4.90: 22968 Nonbonded interactions: 64643 Sorted by model distance: nonbonded pdb=" O3' G 2 35 " pdb=" O2' G 2 35 " model vdw 2.490 2.432 nonbonded pdb=" O2' G A2688 " pdb=" OP1 A A2689 " model vdw 2.524 3.040 nonbonded pdb=" OD1 ASP 0 34 " pdb=" OG SER 0 51 " model vdw 2.528 3.040 nonbonded pdb=" O3' G 2 39 " pdb=" O2' G 2 39 " model vdw 2.535 2.432 nonbonded pdb=" O THR K 131 " pdb=" OG SER K 134 " model vdw 2.544 3.040 ... (remaining 64638 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.013 0.063 8475 Z= 0.818 Angle : 1.976 11.739 12000 Z= 1.304 Chirality : 0.104 0.666 1460 Planarity : 0.022 0.117 1126 Dihedral : 15.711 166.638 3476 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.68 % Allowed : 3.54 % Favored : 95.78 % Rotamer: Outliers : 0.18 % Allowed : 3.48 % Favored : 96.34 % Cbeta Deviations : 0.84 % 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: -2.30 (0.26), residues: 734 helix: -1.59 (0.24), residues: 297 sheet: -0.45 (0.55), residues: 87 loop : -1.66 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG 1 11 TYR 0.130 0.025 TYR 0 31 PHE 0.091 0.016 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.019 0.004 HIS 0 33 Details of bonding type rmsd/Z covalent geometry : bond 0.01337 / 0.82 ( 8475) covalent geometry : angle 1.97603 / 1.30 (12000) hydrogen bonds : bond 0.12976 / 8.82 ( 361) hydrogen bonds : angle 7.42630 / 5.35 ( 958) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.155 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: 0 9 TYR cc_start: 0.8098 (t80) cc_final: 0.7539 (t80) REVERT: 0 102 PHE cc_start: 0.8000 (m-80) cc_final: 0.7430 (m-80) REVERT: 0 301 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7952 (mm-30) REVERT: 1 2 ARG cc_start: 0.8593 (mtp180) cc_final: 0.8365 (mtp85) REVERT: 1 5 LYS cc_start: 0.8768 (tptt) cc_final: 0.7893 (tptt) REVERT: 1 8 LYS cc_start: 0.9312 (tmtt) cc_final: 0.8638 (tptt) REVERT: 1 21 GLU cc_start: 0.7808 (tp30) cc_final: 0.7557 (tp30) REVERT: K 11 LEU cc_start: 0.9139 (mt) cc_final: 0.8825 (tt) REVERT: K 38 PHE cc_start: 0.6946 (t80) cc_final: 0.6675 (t80) REVERT: K 96 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8193 (mmtt) REVERT: K 129 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7747 (mt-10) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.0924 time to fit residues: 27.4539 Evaluate side-chains 145 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 103 HIS 0 195 GLN 0 300 ASN 0 398 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.117094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.104202 restraints weight = 26176.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.106979 restraints weight = 13786.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108394 restraints weight = 6603.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.108559 restraints weight = 4610.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.109141 restraints weight = 4092.868| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8475 Z= 0.163 Angle : 0.731 11.513 12000 Z= 0.389 Chirality : 0.046 0.238 1460 Planarity : 0.004 0.038 1126 Dihedral : 14.696 179.212 2167 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.18 % Favored : 97.68 % Rotamer: Outliers : 2.75 % Allowed : 16.48 % Favored : 80.77 % 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: -0.59 (0.30), residues: 734 helix: 0.39 (0.29), residues: 299 sheet: -0.30 (0.46), residues: 126 loop : -1.12 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 0 265 TYR 0.014 0.002 TYR 0 153 PHE 0.016 0.002 PHE K 38 TRP 0.000 0.000 TRP 0 484 HIS 0.007 0.001 HIS 0 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 8475) covalent geometry : angle 0.73134 / 0.39 (12000) hydrogen bonds : bond 0.04792 / 3.36 ( 361) hydrogen bonds : angle 4.97752 / 3.63 ( 958) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 9 TYR cc_start: 0.8041 (t80) cc_final: 0.7656 (t80) REVERT: 0 123 MET cc_start: 0.7874 (mtm) cc_final: 0.7403 (mmm) REVERT: 0 171 ILE cc_start: 0.6005 (mp) cc_final: 0.5788 (tp) REVERT: 0 283 GLU cc_start: 0.8490 (mp0) cc_final: 0.8166 (pm20) REVERT: 1 8 LYS cc_start: 0.9337 (tmtt) cc_final: 0.8629 (tptt) REVERT: 1 21 GLU cc_start: 0.7630 (tp30) cc_final: 0.7381 (tp30) REVERT: K 11 LEU cc_start: 0.9151 (mt) cc_final: 0.8944 (tp) REVERT: K 57 GLU cc_start: 0.7582 (tp30) cc_final: 0.6360 (tp30) REVERT: K 72 THR cc_start: 0.9055 (m) cc_final: 0.8747 (t) REVERT: K 91 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7035 (mt-10) REVERT: K 102 ARG cc_start: 0.7165 (mmm-85) cc_final: 0.6879 (tpp80) outliers start: 15 outliers final: 10 residues processed: 180 average time/residue: 0.0806 time to fit residues: 18.9808 Evaluate side-chains 147 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 66 TYR Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 275 ASP Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 67 THR Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 HIS 0 33 HIS ** 0 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 326 GLN 1 31 ASN K 12 GLN K 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.116785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.103908 restraints weight = 25653.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.106978 restraints weight = 13033.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.108156 restraints weight = 6144.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.108349 restraints weight = 4490.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.108827 restraints weight = 3907.957| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8475 Z= 0.152 Angle : 0.662 9.117 12000 Z= 0.347 Chirality : 0.043 0.235 1460 Planarity : 0.004 0.033 1126 Dihedral : 14.500 178.334 2167 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.27 % Favored : 96.59 % Rotamer: Outliers : 4.21 % Allowed : 17.40 % Favored : 78.39 % 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: -0.42 (0.30), residues: 734 helix: 0.59 (0.30), residues: 306 sheet: -0.21 (0.44), residues: 134 loop : -1.16 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 0 154 TYR 0.012 0.002 TYR 0 31 PHE 0.010 0.001 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.014 0.002 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 8475) covalent geometry : angle 0.66182 / 0.35 (12000) hydrogen bonds : bond 0.04298 / 3.06 ( 361) hydrogen bonds : angle 4.59916 / 3.34 ( 958) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7654 (mmm) REVERT: 0 171 ILE cc_start: 0.6074 (mp) cc_final: 0.5821 (tp) REVERT: 0 278 TYR cc_start: 0.8612 (m-10) cc_final: 0.8320 (m-80) REVERT: 0 283 GLU cc_start: 0.8521 (mp0) cc_final: 0.8293 (pm20) REVERT: 1 8 LYS cc_start: 0.9350 (tmtt) cc_final: 0.8726 (tptp) REVERT: 1 21 GLU cc_start: 0.7513 (tp30) cc_final: 0.7220 (tp30) REVERT: 1 70 GLU cc_start: 0.8169 (pm20) cc_final: 0.7839 (pm20) REVERT: K 11 LEU cc_start: 0.9043 (mt) cc_final: 0.8817 (tp) REVERT: K 72 THR cc_start: 0.8986 (m) cc_final: 0.8704 (t) outliers start: 23 outliers final: 13 residues processed: 161 average time/residue: 0.0757 time to fit residues: 16.3372 Evaluate side-chains 142 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 0 residue 66 TYR Chi-restraints excluded: chain 0 residue 123 MET Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 145 HIS K 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.115756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.102716 restraints weight = 26350.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.105570 restraints weight = 14068.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.106878 restraints weight = 6609.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.107019 restraints weight = 4985.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.107315 restraints weight = 4313.223| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8475 Z= 0.183 Angle : 0.667 7.530 12000 Z= 0.348 Chirality : 0.043 0.240 1460 Planarity : 0.005 0.042 1126 Dihedral : 14.759 178.226 2167 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 5.49 % Allowed : 19.96 % Favored : 74.54 % 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: -0.39 (0.31), residues: 734 helix: 0.71 (0.30), residues: 304 sheet: -0.38 (0.44), residues: 140 loop : -1.15 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 0 154 TYR 0.011 0.002 TYR 0 403 PHE 0.012 0.002 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.006 0.002 HIS 0 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 ( 8475) covalent geometry : angle 0.66699 / 0.35 (12000) hydrogen bonds : bond 0.04285 / 3.06 ( 361) hydrogen bonds : angle 4.60806 / 3.34 ( 958) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7874 (mtm) cc_final: 0.7598 (mmm) REVERT: 0 171 ILE cc_start: 0.6179 (mp) cc_final: 0.5920 (tp) REVERT: 0 278 TYR cc_start: 0.8535 (m-10) cc_final: 0.8216 (m-80) REVERT: 0 395 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7454 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9322 (tmtt) cc_final: 0.8699 (tptt) REVERT: 1 21 GLU cc_start: 0.7494 (tp30) cc_final: 0.7243 (tp30) REVERT: K 11 LEU cc_start: 0.9005 (mt) cc_final: 0.8760 (tp) REVERT: K 72 THR cc_start: 0.8973 (m) cc_final: 0.8734 (t) REVERT: K 91 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6649 (mt-10) REVERT: K 134 SER cc_start: 0.8466 (p) cc_final: 0.7967 (p) outliers start: 30 outliers final: 20 residues processed: 160 average time/residue: 0.0796 time to fit residues: 16.8775 Evaluate side-chains 155 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 0 residue 66 TYR Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 275 ASP Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 309 ILE Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.112981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.099670 restraints weight = 26660.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.102302 restraints weight = 15081.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104177 restraints weight = 7147.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.103878 restraints weight = 4863.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.104326 restraints weight = 4610.414| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8475 Z= 0.302 Angle : 0.804 8.939 12000 Z= 0.417 Chirality : 0.048 0.256 1460 Planarity : 0.006 0.054 1126 Dihedral : 15.520 179.358 2167 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.04 % Favored : 94.82 % Rotamer: Outliers : 6.78 % Allowed : 19.78 % Favored : 73.44 % 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: -0.92 (0.30), residues: 734 helix: 0.32 (0.29), residues: 303 sheet: -0.53 (0.47), residues: 124 loop : -1.54 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 133 TYR 0.017 0.002 TYR 0 403 PHE 0.017 0.002 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.017 0.003 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.30 ( 8475) covalent geometry : angle 0.80403 / 0.42 (12000) hydrogen bonds : bond 0.05092 / 3.67 ( 361) hydrogen bonds : angle 5.09963 / 3.71 ( 958) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7916 (mtm) cc_final: 0.7643 (mmm) REVERT: 0 171 ILE cc_start: 0.6238 (mp) cc_final: 0.5975 (tp) REVERT: 0 240 ILE cc_start: 0.5737 (OUTLIER) cc_final: 0.5209 (mm) REVERT: 0 278 TYR cc_start: 0.8523 (m-10) cc_final: 0.8235 (m-80) REVERT: 0 283 GLU cc_start: 0.8567 (mp0) cc_final: 0.8334 (pm20) REVERT: 0 395 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7506 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9333 (tmtt) cc_final: 0.8680 (tptt) REVERT: 1 21 GLU cc_start: 0.7617 (tp30) cc_final: 0.7364 (tp30) REVERT: 1 25 GLN cc_start: 0.8353 (mt0) cc_final: 0.7940 (mt0) REVERT: K 11 LEU cc_start: 0.9041 (mt) cc_final: 0.8774 (tp) REVERT: K 91 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7540 (tt0) outliers start: 37 outliers final: 27 residues processed: 164 average time/residue: 0.0773 time to fit residues: 17.0741 Evaluate side-chains 157 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 59 VAL Chi-restraints excluded: chain 0 residue 74 MET Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 275 ASP Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 309 ILE Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 0 residue 421 GLU Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.0060 chunk 78 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.116518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.103350 restraints weight = 25643.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.106228 restraints weight = 13419.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107664 restraints weight = 6312.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.107621 restraints weight = 4447.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.108045 restraints weight = 4213.915| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8475 Z= 0.137 Angle : 0.645 9.208 12000 Z= 0.333 Chirality : 0.041 0.233 1460 Planarity : 0.004 0.047 1126 Dihedral : 14.973 178.197 2167 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 6.04 % Allowed : 21.25 % Favored : 72.71 % 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: -0.39 (0.31), residues: 734 helix: 0.71 (0.30), residues: 307 sheet: -0.22 (0.46), residues: 135 loop : -1.27 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 133 TYR 0.009 0.001 TYR 0 153 PHE 0.008 0.001 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.012 0.001 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 8475) covalent geometry : angle 0.64541 / 0.33 (12000) hydrogen bonds : bond 0.04176 / 2.98 ( 361) hydrogen bonds : angle 4.49647 / 3.25 ( 958) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 ARG cc_start: 0.7712 (tpt-90) cc_final: 0.7510 (tpt-90) REVERT: 0 123 MET cc_start: 0.7914 (mtm) cc_final: 0.7711 (mmm) REVERT: 0 171 ILE cc_start: 0.6209 (mp) cc_final: 0.5933 (tp) REVERT: 0 240 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5580 (mp) REVERT: 0 278 TYR cc_start: 0.8535 (m-10) cc_final: 0.8225 (m-80) REVERT: 0 283 GLU cc_start: 0.8547 (mp0) cc_final: 0.8334 (pm20) REVERT: 0 395 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7434 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9301 (tmtt) cc_final: 0.8661 (tptt) REVERT: 1 25 GLN cc_start: 0.8256 (mt0) cc_final: 0.7985 (mt0) REVERT: K 11 LEU cc_start: 0.8960 (mt) cc_final: 0.8718 (tp) outliers start: 33 outliers final: 22 residues processed: 163 average time/residue: 0.0718 time to fit residues: 15.8922 Evaluate side-chains 155 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 33 HIS Chi-restraints excluded: chain 0 residue 66 TYR Chi-restraints excluded: chain 0 residue 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 146 LEU Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 30 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.115062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.101954 restraints weight = 26089.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.104643 restraints weight = 13950.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.106091 restraints weight = 6705.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.106019 restraints weight = 4715.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.106398 restraints weight = 4443.463| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8475 Z= 0.196 Angle : 0.693 9.148 12000 Z= 0.359 Chirality : 0.043 0.238 1460 Planarity : 0.005 0.057 1126 Dihedral : 15.126 178.348 2167 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 5.68 % Allowed : 23.44 % Favored : 70.88 % 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: -0.48 (0.31), residues: 734 helix: 0.67 (0.30), residues: 307 sheet: -0.34 (0.45), residues: 135 loop : -1.32 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 106 TYR 0.010 0.002 TYR 0 162 PHE 0.011 0.001 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.007 0.001 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 ( 8475) covalent geometry : angle 0.69264 / 0.36 (12000) hydrogen bonds : bond 0.04359 / 3.10 ( 361) hydrogen bonds : angle 4.60330 / 3.33 ( 958) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.6005 (mp) cc_final: 0.5766 (tp) REVERT: 0 240 ILE cc_start: 0.5757 (OUTLIER) cc_final: 0.5393 (mp) REVERT: 0 278 TYR cc_start: 0.8522 (m-10) cc_final: 0.8223 (m-80) REVERT: 0 395 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7465 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9308 (tmtt) cc_final: 0.8676 (tptt) REVERT: 1 62 GLU cc_start: 0.7764 (mp0) cc_final: 0.7544 (mp0) REVERT: K 11 LEU cc_start: 0.8964 (mt) cc_final: 0.8721 (tp) outliers start: 31 outliers final: 25 residues processed: 148 average time/residue: 0.0754 time to fit residues: 14.9235 Evaluate side-chains 147 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 33 HIS Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 146 LEU Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 275 ASP Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 30 ILE Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 134 SER Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 50 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.116382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.103289 restraints weight = 25935.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.106107 restraints weight = 13664.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.107669 restraints weight = 6507.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107666 restraints weight = 4671.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.107976 restraints weight = 4065.263| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8475 Z= 0.153 Angle : 0.666 8.282 12000 Z= 0.342 Chirality : 0.042 0.230 1460 Planarity : 0.005 0.053 1126 Dihedral : 14.965 178.075 2167 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 6.04 % Allowed : 23.63 % Favored : 70.33 % 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: -0.44 (0.31), residues: 734 helix: 0.70 (0.30), residues: 306 sheet: -0.24 (0.46), residues: 135 loop : -1.34 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 106 TYR 0.009 0.001 TYR 0 31 PHE 0.008 0.001 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.007 0.001 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 8475) covalent geometry : angle 0.66610 / 0.34 (12000) hydrogen bonds : bond 0.04162 / 2.96 ( 361) hydrogen bonds : angle 4.44686 / 3.21 ( 958) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.5964 (mp) cc_final: 0.5755 (tp) REVERT: 0 240 ILE cc_start: 0.5844 (OUTLIER) cc_final: 0.5508 (mp) REVERT: 0 272 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7324 (tp30) REVERT: 0 278 TYR cc_start: 0.8508 (m-10) cc_final: 0.8187 (m-80) REVERT: 0 382 LYS cc_start: 0.8592 (tppt) cc_final: 0.8362 (tppt) REVERT: 0 395 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7447 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9278 (tmtt) cc_final: 0.8650 (tptt) REVERT: 1 62 GLU cc_start: 0.7620 (mp0) cc_final: 0.7411 (mp0) REVERT: 1 70 GLU cc_start: 0.7942 (pm20) cc_final: 0.7731 (pm20) REVERT: K 11 LEU cc_start: 0.8903 (mt) cc_final: 0.8667 (tp) REVERT: K 125 MET cc_start: 0.7733 (ttm) cc_final: 0.7465 (ttt) outliers start: 33 outliers final: 29 residues processed: 151 average time/residue: 0.0822 time to fit residues: 16.4599 Evaluate side-chains 157 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 33 HIS Chi-restraints excluded: chain 0 residue 74 MET Chi-restraints excluded: chain 0 residue 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 272 GLU Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 0 residue 421 GLU Chi-restraints excluded: chain 1 residue 3 LEU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 30 ILE Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 134 SER Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.115005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.101845 restraints weight = 25650.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.104644 restraints weight = 13370.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.106006 restraints weight = 6324.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.105936 restraints weight = 4469.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.106320 restraints weight = 4266.788| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8475 Z= 0.201 Angle : 0.709 7.846 12000 Z= 0.364 Chirality : 0.044 0.252 1460 Planarity : 0.005 0.050 1126 Dihedral : 15.169 178.370 2167 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.04 % Favored : 94.82 % Rotamer: Outliers : 6.78 % Allowed : 22.71 % Favored : 70.51 % 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: -0.60 (0.31), residues: 734 helix: 0.59 (0.29), residues: 307 sheet: -0.46 (0.45), residues: 140 loop : -1.38 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 94 TYR 0.010 0.002 TYR 0 403 PHE 0.010 0.001 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.007 0.001 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 ( 8475) covalent geometry : angle 0.70887 / 0.36 (12000) hydrogen bonds : bond 0.04374 / 3.13 ( 361) hydrogen bonds : angle 4.62617 / 3.36 ( 958) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7551 (mmm) cc_final: 0.7275 (mmt) REVERT: 0 171 ILE cc_start: 0.6024 (mp) cc_final: 0.5811 (tp) REVERT: 0 240 ILE cc_start: 0.5751 (OUTLIER) cc_final: 0.5252 (mm) REVERT: 0 272 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7372 (tp30) REVERT: 0 278 TYR cc_start: 0.8518 (m-10) cc_final: 0.8185 (m-80) REVERT: 0 382 LYS cc_start: 0.8578 (tppt) cc_final: 0.8353 (tppt) REVERT: 0 395 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7491 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9335 (tmtt) cc_final: 0.8688 (tptt) REVERT: 1 70 GLU cc_start: 0.7972 (pm20) cc_final: 0.7769 (pm20) REVERT: K 11 LEU cc_start: 0.8928 (mt) cc_final: 0.8679 (tp) REVERT: K 129 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7701 (mt-10) outliers start: 37 outliers final: 30 residues processed: 150 average time/residue: 0.0802 time to fit residues: 16.2219 Evaluate side-chains 155 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 33 HIS Chi-restraints excluded: chain 0 residue 57 SER Chi-restraints excluded: chain 0 residue 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 146 LEU Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 272 GLU Chi-restraints excluded: chain 0 residue 275 ASP Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 0 residue 421 GLU Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 30 ILE Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 134 SER Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 0.0770 chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.0270 chunk 4 optimal weight: 0.4980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.117622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.104658 restraints weight = 25908.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.107497 restraints weight = 13322.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.108841 restraints weight = 6307.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.108906 restraints weight = 4392.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.109201 restraints weight = 4048.040| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8475 Z= 0.130 Angle : 0.655 8.179 12000 Z= 0.337 Chirality : 0.041 0.228 1460 Planarity : 0.005 0.051 1126 Dihedral : 14.821 177.728 2167 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 4.58 % Allowed : 25.82 % Favored : 69.60 % 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: -0.36 (0.31), residues: 734 helix: 0.82 (0.29), residues: 302 sheet: -0.23 (0.46), residues: 136 loop : -1.30 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 102 TYR 0.008 0.001 TYR 0 31 PHE 0.006 0.001 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.005 0.001 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8475) covalent geometry : angle 0.65458 / 0.34 (12000) hydrogen bonds : bond 0.03940 / 2.78 ( 361) hydrogen bonds : angle 4.41551 / 3.20 ( 958) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 31 TYR cc_start: 0.6998 (m-10) cc_final: 0.6798 (m-10) REVERT: 0 123 MET cc_start: 0.7544 (mmm) cc_final: 0.7281 (mmt) REVERT: 0 240 ILE cc_start: 0.5864 (OUTLIER) cc_final: 0.5548 (mp) REVERT: 0 272 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: 0 278 TYR cc_start: 0.8505 (m-10) cc_final: 0.8217 (m-80) REVERT: 0 382 LYS cc_start: 0.8559 (tppt) cc_final: 0.8328 (tppt) REVERT: 0 395 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7405 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9310 (tmtt) cc_final: 0.8660 (tptt) REVERT: 1 70 GLU cc_start: 0.7963 (pm20) cc_final: 0.7757 (pm20) REVERT: K 11 LEU cc_start: 0.8867 (mt) cc_final: 0.8652 (tp) outliers start: 25 outliers final: 20 residues processed: 147 average time/residue: 0.0810 time to fit residues: 15.7287 Evaluate side-chains 148 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 33 HIS Chi-restraints excluded: chain 0 residue 57 SER Chi-restraints excluded: chain 0 residue 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 272 GLU Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 30 ILE Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 SER Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.0470 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.116795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.103817 restraints weight = 25630.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.106604 restraints weight = 13302.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.107903 restraints weight = 6404.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.107822 restraints weight = 4576.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.108213 restraints weight = 4360.426| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8475 Z= 0.154 Angle : 0.673 7.973 12000 Z= 0.346 Chirality : 0.042 0.233 1460 Planarity : 0.005 0.063 1126 Dihedral : 14.857 177.817 2167 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.36 % Favored : 95.50 % Rotamer: Outliers : 4.95 % Allowed : 25.64 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.31), residues: 734 helix: 0.82 (0.29), residues: 303 sheet: -0.28 (0.46), residues: 136 loop : -1.27 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 94 TYR 0.011 0.001 TYR 0 31 PHE 0.007 0.001 PHE 0 75 TRP 0.000 0.000 TRP 0 484 HIS 0.006 0.001 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8475) covalent geometry : angle 0.67296 / 0.35 (12000) hydrogen bonds : bond 0.03995 / 2.82 ( 361) hydrogen bonds : angle 4.45840 / 3.23 ( 958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1381.00 seconds wall clock time: 24 minutes 26.09 seconds (1466.09 seconds total)