Starting phenix.real_space_refine on Tue Mar 3 19:42:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7asa_11891/03_2026/7asa_11891.cif Found real_map, /net/cci-nas-00/data/ceres_data/7asa_11891/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7asa_11891/03_2026/7asa_11891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7asa_11891/03_2026/7asa_11891.map" model { file = "/net/cci-nas-00/data/ceres_data/7asa_11891/03_2026/7asa_11891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7asa_11891/03_2026/7asa_11891.cif" } 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-5986/lib/python3.9/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: 1.84, per 1000 atoms: 0.23 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: 0.63 Conformation dependent library (CDL) restraints added in 205.9 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: 0.90 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: 1.49 Time building geometry restraints manager: 0.88 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: 4970 33.33 - 66.66: 284 66.66 - 99.98: 52 99.98 - 133.31: 2 133.31 - 166.64: 4 Dihedral angle restraints: 5312 sinusoidal: 3128 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 5309 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: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.620 Find NCS groups from input model: 0.030 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 20.131 166.638 3890 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 covalent geometry : bond 0.01337 ( 8475) covalent geometry : angle 1.97603 (12000) hydrogen bonds : bond 0.12976 ( 361) hydrogen bonds : angle 7.42630 ( 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 : 0.242 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: 0.1109 time to fit residues: 32.6326 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 : 0.261 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3920 r_free = 0.3920 target = 0.117053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.104056 restraints weight = 26178.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.106964 restraints weight = 13765.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108411 restraints weight = 6584.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.108534 restraints weight = 4729.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.109156 restraints weight = 4055.301| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3222 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= 0.165 Angle : 0.740 11.548 12000 Z= 0.394 Chirality : 0.046 0.253 1460 Planarity : 0.004 0.038 1126 Dihedral : 21.538 178.821 2581 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.18 % Favored : 97.68 % Rotamer: Outliers : 2.75 % Allowed : 16.67 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.62 (0.30), residues: 734 helix: 0.37 (0.29), residues: 299 sheet: -0.32 (0.46), residues: 126 loop : -1.14 (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 0.017 0.002 PHE K 38 TRP 0.000 0.000 TRP 0 484 HIS 0.008 0.002 HIS 0 259 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8475) covalent geometry : angle 0.73951 (12000) hydrogen bonds : bond 0.04845 ( 361) hydrogen bonds : angle 4.99063 ( 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 : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 9 TYR cc_start: 0.8039 (t80) cc_final: 0.7653 (t80) REVERT: 0 123 MET cc_start: 0.7900 (mtm) cc_final: 0.7428 (mmm) REVERT: 0 171 ILE cc_start: 0.6040 (mp) cc_final: 0.5814 (tp) REVERT: 0 283 GLU cc_start: 0.8493 (mp0) cc_final: 0.8166 (pm20) REVERT: 1 8 LYS cc_start: 0.9343 (tmtt) cc_final: 0.8627 (tptt) REVERT: 1 21 GLU cc_start: 0.7653 (tp30) cc_final: 0.7413 (tp30) REVERT: 1 68 LYS cc_start: 0.8590 (mptt) cc_final: 0.8308 (mmtm) REVERT: K 11 LEU cc_start: 0.9135 (mt) cc_final: 0.8929 (tp) REVERT: K 57 GLU cc_start: 0.7597 (tp30) cc_final: 0.6371 (tp30) REVERT: K 72 THR cc_start: 0.9066 (m) cc_final: 0.8756 (t) REVERT: K 91 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7025 (mt-10) outliers start: 15 outliers final: 10 residues processed: 180 average time/residue: 0.1015 time to fit residues: 23.8959 Evaluate side-chains 146 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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: 0.9980 chunk 6 optimal weight: 0.0050 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 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: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3915 r_free = 0.3915 target = 0.116533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.103761 restraints weight = 25804.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.106727 restraints weight = 13386.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.107726 restraints weight = 6247.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.107955 restraints weight = 4878.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.108301 restraints weight = 4161.617| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4037 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= 0.160 Angle : 0.678 9.035 12000 Z= 0.354 Chirality : 0.044 0.238 1460 Planarity : 0.005 0.035 1126 Dihedral : 21.497 178.543 2581 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.54 % Favored : 96.32 % Rotamer: Outliers : 4.40 % Allowed : 17.77 % Favored : 77.84 % 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: -0.50 (0.30), residues: 734 helix: 0.55 (0.29), residues: 306 sheet: -0.33 (0.43), residues: 139 loop : -1.22 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 1 27 TYR 0.011 0.002 TYR 0 153 PHE 0.010 0.001 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.011 0.002 HIS 0 60 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8475) covalent geometry : angle 0.67783 (12000) hydrogen bonds : bond 0.04312 ( 361) hydrogen bonds : angle 4.64266 ( 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 173 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7908 (mtm) cc_final: 0.7634 (mmm) REVERT: 0 171 ILE cc_start: 0.6043 (mp) cc_final: 0.5806 (tp) REVERT: 0 278 TYR cc_start: 0.8585 (m-10) cc_final: 0.8298 (m-80) REVERT: 0 283 GLU cc_start: 0.8502 (mp0) cc_final: 0.8260 (pm20) REVERT: 1 8 LYS cc_start: 0.9336 (tmtt) cc_final: 0.8730 (tptp) REVERT: 1 21 GLU cc_start: 0.7494 (tp30) cc_final: 0.7209 (tp30) REVERT: 1 68 LYS cc_start: 0.8376 (mptt) cc_final: 0.8085 (mmtm) REVERT: K 11 LEU cc_start: 0.9048 (mt) cc_final: 0.8836 (tp) REVERT: K 72 THR cc_start: 0.8979 (m) cc_final: 0.8707 (t) outliers start: 24 outliers final: 15 residues processed: 162 average time/residue: 0.1037 time to fit residues: 21.9758 Evaluate side-chains 145 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 24 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 Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3918 r_free = 0.3918 target = 0.116856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.104125 restraints weight = 26328.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107149 restraints weight = 13564.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.108336 restraints weight = 6332.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.108454 restraints weight = 4532.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.108931 restraints weight = 4080.201| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8475 Z= 0.152 Angle : 0.638 7.753 12000 Z= 0.333 Chirality : 0.042 0.234 1460 Planarity : 0.004 0.036 1126 Dihedral : 21.536 177.987 2581 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.27 % Favored : 96.59 % Rotamer: Outliers : 4.58 % Allowed : 21.25 % Favored : 74.18 % 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: -0.30 (0.31), residues: 734 helix: 0.80 (0.30), residues: 305 sheet: -0.34 (0.44), residues: 140 loop : -1.13 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 0 154 TYR 0.011 0.001 TYR 0 31 PHE 0.010 0.001 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.009 0.002 HIS 0 60 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8475) covalent geometry : angle 0.63829 (12000) hydrogen bonds : bond 0.04090 ( 361) hydrogen bonds : angle 4.46116 ( 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 164 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 50 LEU cc_start: 0.8866 (mt) cc_final: 0.8660 (mt) REVERT: 0 123 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7546 (mmm) REVERT: 0 171 ILE cc_start: 0.6102 (mp) cc_final: 0.5850 (tp) REVERT: 0 278 TYR cc_start: 0.8568 (m-10) cc_final: 0.8313 (m-80) REVERT: 0 395 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7422 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9333 (tmtt) cc_final: 0.8713 (tptp) REVERT: 1 21 GLU cc_start: 0.7491 (tp30) cc_final: 0.7248 (tp30) REVERT: 1 68 LYS cc_start: 0.8250 (mptt) cc_final: 0.7965 (mmtm) REVERT: 1 70 GLU cc_start: 0.8392 (pm20) cc_final: 0.8166 (pm20) REVERT: K 11 LEU cc_start: 0.8998 (mt) cc_final: 0.8786 (tp) REVERT: K 72 THR cc_start: 0.8934 (m) cc_final: 0.8668 (t) outliers start: 25 outliers final: 18 residues processed: 155 average time/residue: 0.0916 time to fit residues: 19.0436 Evaluate side-chains 145 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 83 ILE 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 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 395 ARG Chi-restraints excluded: chain 1 residue 18 LEU Chi-restraints excluded: chain 1 residue 41 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 Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.0010 chunk 45 optimal weight: 0.0570 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 31 ASN K 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.116684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.103757 restraints weight = 26121.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.106724 restraints weight = 13764.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.108188 restraints weight = 6413.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.108250 restraints weight = 4642.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.108545 restraints weight = 4002.150| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8475 Z= 0.155 Angle : 0.639 10.221 12000 Z= 0.332 Chirality : 0.041 0.235 1460 Planarity : 0.005 0.055 1126 Dihedral : 21.545 178.157 2581 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.81 % Favored : 96.05 % Rotamer: Outliers : 5.13 % Allowed : 20.33 % 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: -0.16 (0.31), residues: 734 helix: 0.94 (0.30), residues: 304 sheet: -0.21 (0.45), residues: 140 loop : -1.12 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 94 TYR 0.010 0.001 TYR 0 31 PHE 0.020 0.001 PHE 0 267 TRP 0.000 0.000 TRP 0 484 HIS 0.010 0.001 HIS 0 60 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8475) covalent geometry : angle 0.63889 (12000) hydrogen bonds : bond 0.04018 ( 361) hydrogen bonds : angle 4.43016 ( 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 167 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7651 (mmm) REVERT: 0 171 ILE cc_start: 0.6203 (mp) cc_final: 0.5958 (tp) REVERT: 0 240 ILE cc_start: 0.5881 (OUTLIER) cc_final: 0.5613 (mp) REVERT: 0 278 TYR cc_start: 0.8509 (m-10) cc_final: 0.8251 (m-80) REVERT: 0 382 LYS cc_start: 0.8455 (tppt) cc_final: 0.8254 (tppt) REVERT: 1 8 LYS cc_start: 0.9308 (tmtt) cc_final: 0.8683 (tptt) REVERT: 1 21 GLU cc_start: 0.7448 (tp30) cc_final: 0.7203 (tp30) REVERT: K 11 LEU cc_start: 0.8965 (mt) cc_final: 0.8746 (tp) REVERT: K 72 THR cc_start: 0.8933 (m) cc_final: 0.8695 (t) outliers start: 28 outliers final: 21 residues processed: 156 average time/residue: 0.0916 time to fit residues: 19.0035 Evaluate side-chains 151 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 123 MET 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 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 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 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 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: 0.1980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.0370 chunk 70 optimal weight: 2.9990 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.121009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.108120 restraints weight = 26035.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.110657 restraints weight = 11049.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.112214 restraints weight = 6075.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.113206 restraints weight = 3979.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.113811 restraints weight = 2961.293| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8475 Z= 0.110 Angle : 0.589 9.820 12000 Z= 0.303 Chirality : 0.039 0.219 1460 Planarity : 0.004 0.051 1126 Dihedral : 21.265 177.214 2581 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 4.95 % Allowed : 21.43 % Favored : 73.63 % 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: 0.09 (0.31), residues: 734 helix: 1.12 (0.30), residues: 305 sheet: -0.09 (0.45), residues: 141 loop : -0.95 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 94 TYR 0.008 0.001 TYR 0 31 PHE 0.009 0.001 PHE 0 37 TRP 0.000 0.000 TRP 0 484 HIS 0.008 0.001 HIS 0 60 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8475) covalent geometry : angle 0.58944 (12000) hydrogen bonds : bond 0.03710 ( 361) hydrogen bonds : angle 4.16094 ( 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: 27 poor density : 149 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 31 TYR cc_start: 0.6837 (m-80) cc_final: 0.6632 (m-80) REVERT: 0 133 ASP cc_start: 0.5006 (OUTLIER) cc_final: 0.4737 (t0) REVERT: 0 141 ASP cc_start: 0.7577 (t0) cc_final: 0.7368 (p0) REVERT: 0 171 ILE cc_start: 0.6008 (mp) cc_final: 0.5774 (tp) REVERT: 0 317 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7174 (mm-30) REVERT: 0 382 LYS cc_start: 0.8573 (tppt) cc_final: 0.8333 (tppt) REVERT: 0 395 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7370 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9340 (tmtt) cc_final: 0.8719 (tptp) REVERT: 1 25 GLN cc_start: 0.8088 (mt0) cc_final: 0.7730 (mt0) REVERT: 1 67 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7468 (m) REVERT: K 57 GLU cc_start: 0.7340 (tp30) cc_final: 0.7015 (tp30) REVERT: K 72 THR cc_start: 0.8735 (m) cc_final: 0.8515 (t) outliers start: 27 outliers final: 13 residues processed: 166 average time/residue: 0.0940 time to fit residues: 20.6675 Evaluate side-chains 145 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 317 GLU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 395 ARG Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 67 THR Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 13 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 30 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.118305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.105492 restraints weight = 26060.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.108229 restraints weight = 13487.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.109737 restraints weight = 6463.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.109585 restraints weight = 4471.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.109971 restraints weight = 4262.178| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8475 Z= 0.149 Angle : 0.630 8.051 12000 Z= 0.324 Chirality : 0.041 0.227 1460 Planarity : 0.005 0.059 1126 Dihedral : 21.389 177.948 2581 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 4.95 % Allowed : 22.16 % Favored : 72.89 % 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: 0.07 (0.31), residues: 734 helix: 1.01 (0.30), residues: 305 sheet: -0.02 (0.45), residues: 141 loop : -0.88 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 94 TYR 0.014 0.001 TYR 0 9 PHE 0.009 0.001 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.010 0.001 HIS 0 60 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8475) covalent geometry : angle 0.62956 (12000) hydrogen bonds : bond 0.03793 ( 361) hydrogen bonds : angle 4.28649 ( 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 158 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.6081 (mp) cc_final: 0.5881 (tp) REVERT: 0 278 TYR cc_start: 0.8641 (m-80) cc_final: 0.8171 (m-80) REVERT: 0 382 LYS cc_start: 0.8553 (tppt) cc_final: 0.8317 (tppt) REVERT: 0 395 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7387 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9325 (tmtt) cc_final: 0.8701 (tptt) REVERT: 1 21 GLU cc_start: 0.7446 (tp30) cc_final: 0.7204 (tp30) REVERT: 1 62 GLU cc_start: 0.7409 (mp0) cc_final: 0.7137 (mp0) REVERT: K 11 LEU cc_start: 0.8688 (tp) cc_final: 0.8425 (tt) REVERT: K 72 THR cc_start: 0.8738 (m) cc_final: 0.8480 (t) REVERT: K 77 VAL cc_start: 0.8931 (m) cc_final: 0.8679 (p) outliers start: 27 outliers final: 20 residues processed: 151 average time/residue: 0.0940 time to fit residues: 18.9103 Evaluate side-chains 138 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 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 126 HIS Chi-restraints excluded: chain 0 residue 133 ASP Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 254 LEU 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 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 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=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: 2.9990 chunk 2 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 151 ASN 0 188 GLN ** 1 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.112901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.099849 restraints weight = 26195.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.101801 restraints weight = 14251.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.103852 restraints weight = 7307.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.103751 restraints weight = 5063.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.103929 restraints weight = 4323.275| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 8475 Z= 0.333 Angle : 0.849 9.278 12000 Z= 0.437 Chirality : 0.049 0.257 1460 Planarity : 0.006 0.058 1126 Dihedral : 22.066 179.544 2581 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.96 % Rotamer: Outliers : 7.14 % Allowed : 19.96 % Favored : 72.89 % 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: -0.75 (0.30), residues: 734 helix: 0.32 (0.29), residues: 304 sheet: -0.32 (0.45), residues: 135 loop : -1.37 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 94 TYR 0.014 0.003 TYR 0 162 PHE 0.017 0.002 PHE K 66 TRP 0.000 0.000 TRP 0 484 HIS 0.010 0.003 HIS 0 60 Details of bonding type rmsd covalent geometry : bond 0.00673 ( 8475) covalent geometry : angle 0.84876 (12000) hydrogen bonds : bond 0.05079 ( 361) hydrogen bonds : angle 5.13545 ( 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 167 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 123 MET cc_start: 0.7682 (mmm) cc_final: 0.7238 (mtp) REVERT: 0 171 ILE cc_start: 0.5984 (mp) cc_final: 0.5757 (tp) REVERT: 0 278 TYR cc_start: 0.8518 (m-80) cc_final: 0.7951 (m-80) REVERT: 0 395 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7615 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9322 (tmtt) cc_final: 0.8660 (tptt) REVERT: 1 17 THR cc_start: 0.8510 (m) cc_final: 0.8118 (p) REVERT: K 11 LEU cc_start: 0.8840 (tp) cc_final: 0.8491 (tt) outliers start: 39 outliers final: 32 residues processed: 156 average time/residue: 0.0931 time to fit residues: 19.4909 Evaluate side-chains 153 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS 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 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 274 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 332 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 30 ILE 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 89 SER Chi-restraints excluded: chain K residue 127 MET 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: 0.0470 chunk 52 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.0670 chunk 60 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 80 optimal weight: 0.0370 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.117733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104691 restraints weight = 25749.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107319 restraints weight = 13054.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108901 restraints weight = 6279.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.108881 restraints weight = 4215.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.109259 restraints weight = 4045.898| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5509 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= 0.129 Angle : 0.671 9.496 12000 Z= 0.345 Chirality : 0.041 0.232 1460 Planarity : 0.005 0.057 1126 Dihedral : 21.592 177.755 2581 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.54 % Favored : 96.32 % Rotamer: Outliers : 4.76 % Allowed : 23.08 % Favored : 72.16 % 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: -0.29 (0.31), residues: 734 helix: 0.71 (0.29), residues: 308 sheet: -0.21 (0.44), residues: 141 loop : -1.09 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 94 TYR 0.018 0.001 TYR 0 9 PHE 0.008 0.001 PHE 0 87 TRP 0.000 0.000 TRP 0 484 HIS 0.008 0.001 HIS 0 60 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8475) covalent geometry : angle 0.67123 (12000) hydrogen bonds : bond 0.03962 ( 361) hydrogen bonds : angle 4.51891 ( 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 159 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 31 TYR cc_start: 0.7060 (m-10) cc_final: 0.6850 (m-10) REVERT: 0 171 ILE cc_start: 0.6016 (mp) cc_final: 0.5798 (tp) REVERT: 0 278 TYR cc_start: 0.8582 (m-80) cc_final: 0.8170 (m-80) REVERT: 0 382 LYS cc_start: 0.8578 (tppt) cc_final: 0.8332 (tppt) REVERT: 0 395 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7429 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9248 (tmtt) cc_final: 0.8626 (tptp) REVERT: K 57 GLU cc_start: 0.7652 (tp30) cc_final: 0.7193 (tp30) REVERT: K 77 VAL cc_start: 0.8920 (m) cc_final: 0.8625 (p) outliers start: 26 outliers final: 19 residues processed: 148 average time/residue: 0.0953 time to fit residues: 18.7011 Evaluate side-chains 144 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 169 ASP Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 332 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 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 56 VAL Chi-restraints excluded: chain K residue 60 VAL 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: 3.9990 chunk 43 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 151 ASN 1 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.115801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.102709 restraints weight = 26138.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.105381 restraints weight = 13837.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.106845 restraints weight = 6662.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.106691 restraints weight = 4697.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.107067 restraints weight = 4480.559| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8475 Z= 0.190 Angle : 0.724 7.870 12000 Z= 0.369 Chirality : 0.044 0.238 1460 Planarity : 0.005 0.056 1126 Dihedral : 21.641 178.128 2581 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 4.21 % Allowed : 23.99 % Favored : 71.79 % 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 (0.31), residues: 734 helix: 0.62 (0.29), residues: 303 sheet: -0.40 (0.44), residues: 142 loop : -1.09 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 94 TYR 0.019 0.002 TYR 0 9 PHE 0.010 0.002 PHE 0 75 TRP 0.000 0.000 TRP 0 484 HIS 0.009 0.002 HIS 0 60 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8475) covalent geometry : angle 0.72352 (12000) hydrogen bonds : bond 0.04222 ( 361) hydrogen bonds : angle 4.68485 ( 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 146 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.6017 (mp) cc_final: 0.5797 (tp) REVERT: 0 278 TYR cc_start: 0.8532 (m-80) cc_final: 0.8148 (m-80) REVERT: 0 283 GLU cc_start: 0.8443 (pm20) cc_final: 0.8032 (pm20) REVERT: 0 382 LYS cc_start: 0.8566 (tppt) cc_final: 0.8317 (tppt) REVERT: 0 395 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7435 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9291 (tmtt) cc_final: 0.8660 (tptt) REVERT: 1 14 LYS cc_start: 0.8466 (mptt) cc_final: 0.8135 (mmtp) REVERT: 1 17 THR cc_start: 0.8412 (m) cc_final: 0.8034 (p) REVERT: K 77 VAL cc_start: 0.8953 (m) cc_final: 0.8661 (p) outliers start: 23 outliers final: 19 residues processed: 139 average time/residue: 0.0928 time to fit residues: 17.1876 Evaluate side-chains 138 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 169 ASP Chi-restraints excluded: chain 0 residue 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 332 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 41 VAL Chi-restraints excluded: chain 1 residue 79 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 127 MET 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: 0.9980 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 31 ASN ** 1 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.114607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.101580 restraints weight = 25987.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.103953 restraints weight = 13907.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.105521 restraints weight = 6975.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.105441 restraints weight = 4715.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.105745 restraints weight = 4591.056| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8475 Z= 0.222 Angle : 0.757 10.499 12000 Z= 0.386 Chirality : 0.045 0.242 1460 Planarity : 0.005 0.058 1126 Dihedral : 21.785 178.034 2581 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.96 % Rotamer: Outliers : 4.03 % Allowed : 23.99 % Favored : 71.98 % 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: -0.61 (0.31), residues: 734 helix: 0.47 (0.29), residues: 306 sheet: -0.33 (0.44), residues: 144 loop : -1.32 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 94 TYR 0.022 0.002 TYR 0 9 PHE 0.010 0.002 PHE 0 377 TRP 0.000 0.000 TRP 0 484 HIS 0.009 0.002 HIS 0 60 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8475) covalent geometry : angle 0.75736 (12000) hydrogen bonds : bond 0.04465 ( 361) hydrogen bonds : angle 4.90302 ( 958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1673.94 seconds wall clock time: 29 minutes 25.86 seconds (1765.86 seconds total)