Starting phenix.real_space_refine on Fri Sep 11 07:09:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7asa_11891/09_2026/7asa_11891.cif Found real_map, /net/cci-nas-00/data/ceres_data/7asa_11891/09_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_11891/09_2026/7asa_11891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7asa_11891/09_2026/7asa_11891.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7asa_11891/09_2026/7asa_11891.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7asa_11891/09_2026/7asa_11891.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7asa_11891/09_2026/7asa_11891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7asa_11891/09_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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 2.33, per 1000 atoms: 0.29 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: 0.74 Conformation dependent library (CDL) restraints added in 395.6 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: 1.06 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: 1.46 Time building geometry restraints manager: 0.90 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 - 2.19: 8939 2.19 - 4.38: 2628 4.38 - 6.57: 386 6.57 - 8.76: 42 8.76 - 10.95: 5 Bond angle restraints: 12000 Sorted by residual: 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=" N PRO K 22 " pdb=" CA PRO K 22 " pdb=" C PRO K 22 " ideal model delta sigma weight residual 110.70 117.76 -7.06 1.22e+00 6.72e-01 3.35e+01 angle pdb=" N PRO 0 448 " pdb=" CA PRO 0 448 " pdb=" CB PRO 0 448 " ideal model delta sigma weight residual 103.33 108.66 -5.33 9.30e-01 1.16e+00 3.29e+01 angle pdb=" N PRO 0 491 " pdb=" CA PRO 0 491 " pdb=" CB PRO 0 491 " ideal model delta sigma weight residual 103.25 109.26 -6.01 1.05e+00 9.07e-01 3.27e+01 angle pdb=" C4' A 2 44 " pdb=" C3' A 2 44 " pdb=" O3' A 2 44 " ideal model delta sigma weight residual 112.50 101.55 10.95 2.00e+00 2.50e-01 3.00e+01 ... (remaining 11995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.65: 4555 27.65 - 55.30: 280 55.30 - 82.95: 59 82.95 - 110.60: 3 110.60 - 138.25: 1 Dihedral angle restraints: 4898 sinusoidal: 2714 harmonic: 2184 Sorted by residual: dihedral pdb=" C4' A A1115 " pdb=" C3' A A1115 " pdb=" C2' A A1115 " pdb=" C1' A A1115 " ideal model delta sinusoidal sigma weight residual 36.34 -41.02 77.36 1 3.10e+00 1.04e-01 7.80e+02 dihedral pdb=" C4' G 2 22 " pdb=" C3' G 2 22 " pdb=" C2' G 2 22 " pdb=" C1' G 2 22 " ideal model delta sinusoidal sigma weight residual 36.34 -38.20 74.54 1 3.10e+00 1.04e-01 7.33e+02 dihedral pdb=" C4' A 2 9 " pdb=" C3' A 2 9 " pdb=" C2' A 2 9 " pdb=" C1' A 2 9 " ideal model delta sinusoidal sigma weight residual 36.35 -36.97 73.32 1 3.10e+00 1.04e-01 7.12e+02 ... (remaining 4895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1110 0.133 - 0.266: 301 0.266 - 0.399: 38 0.399 - 0.533: 10 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=" P C A1949 " pdb=" OP1 C A1949 " pdb=" OP2 C A1949 " pdb=" O5' C A1949 " both_signs ideal model delta sigma weight residual True 2.17 -2.70 -0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" P A 2 21 " pdb=" OP1 A 2 21 " pdb=" OP2 A 2 21 " pdb=" O5' A 2 21 " both_signs ideal model delta sigma weight residual True 2.17 -2.66 -0.49 2.00e-01 2.50e+01 6.03e+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: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.240 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- 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= 0.785 Angle : 2.020 10.952 12000 Z= 1.177 Chirality : 0.121 0.666 1460 Planarity : 0.022 0.117 1126 Dihedral : 17.331 138.249 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 0.01343 / 0.79 ( 8475) covalent geometry : angle 2.01999 / 1.18 (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 : 0.253 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: 0.1219 time to fit residues: 36.0485 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 : 0.257 ------------------------------------------------------------------------------- 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: 0.9990 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 0 126 HIS 0 195 GLN 0 300 ASN 0 398 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.117534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105070 restraints weight = 26353.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.107895 restraints weight = 13675.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.109235 restraints weight = 6614.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.109371 restraints weight = 4763.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.109888 restraints weight = 4063.066| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8475 Z= 0.189 Angle : 1.084 13.961 12000 Z= 0.475 Chirality : 0.086 0.718 1460 Planarity : 0.005 0.039 1126 Dihedral : 16.638 175.292 2167 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.32 % Favored : 97.55 % Rotamer: Outliers : 2.93 % Allowed : 16.48 % 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: -0.64 (0.30), residues: 734 helix: 0.37 (0.29), residues: 299 sheet: -0.34 (0.46), residues: 126 loop : -1.16 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 0 265 TYR 0.015 0.002 TYR 0 153 PHE 0.017 0.002 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.008 0.001 HIS 0 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 ( 8475) covalent geometry : angle 1.08407 / 0.47 (12000) hydrogen bonds : bond 0.04884 / 3.42 ( 361) hydrogen bonds : angle 5.00205 / 3.65 ( 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 186 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 9 TYR cc_start: 0.8024 (t80) cc_final: 0.7641 (t80) REVERT: 0 123 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7440 (mmm) REVERT: 0 171 ILE cc_start: 0.6053 (mp) cc_final: 0.5820 (tp) REVERT: 0 283 GLU cc_start: 0.8487 (mp0) cc_final: 0.8168 (pm20) REVERT: 1 8 LYS cc_start: 0.9349 (tmtt) cc_final: 0.8697 (tptt) REVERT: 1 21 GLU cc_start: 0.7628 (tp30) cc_final: 0.7389 (tp30) REVERT: 1 68 LYS cc_start: 0.8613 (mptt) cc_final: 0.8300 (mmtt) REVERT: K 11 LEU cc_start: 0.9117 (mt) cc_final: 0.8885 (tp) REVERT: K 57 GLU cc_start: 0.7557 (tp30) cc_final: 0.6319 (tp30) REVERT: K 72 THR cc_start: 0.9055 (m) cc_final: 0.8744 (t) outliers start: 16 outliers final: 11 residues processed: 177 average time/residue: 0.1059 time to fit residues: 24.6958 Evaluate side-chains 148 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 66 TYR Chi-restraints excluded: chain 0 residue 123 MET 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 Chi-restraints excluded: chain K residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 0 13 HIS ** 0 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 326 GLN 1 31 ASN K 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.117577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.104841 restraints weight = 25809.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.107357 restraints weight = 10973.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.108925 restraints weight = 6072.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.109901 restraints weight = 3951.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.110500 restraints weight = 2923.700| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4266 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= 0.169 Angle : 0.921 12.212 12000 Z= 0.406 Chirality : 0.075 0.758 1460 Planarity : 0.005 0.037 1126 Dihedral : 16.404 175.412 2167 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 4.03 % Allowed : 17.58 % 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: -0.40 (0.30), residues: 734 helix: 0.69 (0.30), residues: 305 sheet: -0.33 (0.43), residues: 139 loop : -1.18 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 1 27 TYR 0.011 0.002 TYR 0 153 PHE 0.009 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/Z covalent geometry : bond 0.00355 / 0.17 ( 8475) covalent geometry : angle 0.92083 / 0.41 (12000) hydrogen bonds : bond 0.04402 / 3.11 ( 361) hydrogen bonds : angle 4.61897 / 3.35 ( 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 176 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.6059 (mp) cc_final: 0.5817 (tp) REVERT: 0 278 TYR cc_start: 0.8523 (m-10) cc_final: 0.8280 (m-80) REVERT: 0 283 GLU cc_start: 0.8539 (mp0) cc_final: 0.8281 (pm20) REVERT: 1 8 LYS cc_start: 0.9403 (tmtt) cc_final: 0.8702 (tptp) REVERT: 1 21 GLU cc_start: 0.7594 (tp30) cc_final: 0.7283 (tp30) REVERT: 1 68 LYS cc_start: 0.8396 (mptt) cc_final: 0.8122 (mmtt) REVERT: K 11 LEU cc_start: 0.9024 (mt) cc_final: 0.8753 (tp) REVERT: K 72 THR cc_start: 0.8977 (m) cc_final: 0.8677 (t) outliers start: 22 outliers final: 14 residues processed: 169 average time/residue: 0.1050 time to fit residues: 23.3907 Evaluate side-chains 145 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 55 SER 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 54 ILE 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: 0.8980 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3869 r_free = 0.3869 target = 0.113909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.101495 restraints weight = 26724.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.104262 restraints weight = 13918.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.105361 restraints weight = 6510.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.105562 restraints weight = 4969.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.106052 restraints weight = 4262.221| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 8475 Z= 0.276 Angle : 1.045 12.473 12000 Z= 0.456 Chirality : 0.079 0.761 1460 Planarity : 0.006 0.058 1126 Dihedral : 16.868 179.477 2167 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 5.86 % Allowed : 18.86 % Favored : 75.27 % 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: -0.63 (0.30), residues: 734 helix: 0.53 (0.29), residues: 303 sheet: -0.31 (0.45), residues: 135 loop : -1.40 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 1 2 TYR 0.016 0.002 TYR 0 403 PHE 0.017 0.002 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 0.00569 / 0.28 ( 8475) covalent geometry : angle 1.04495 / 0.46 (12000) hydrogen bonds : bond 0.04800 / 3.45 ( 361) hydrogen bonds : angle 4.97597 / 3.61 ( 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 178 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.6185 (mp) cc_final: 0.5936 (tp) REVERT: 0 278 TYR cc_start: 0.8472 (m-10) cc_final: 0.8153 (m-80) REVERT: 0 395 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7515 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9367 (tmtt) cc_final: 0.8718 (tptt) REVERT: K 72 THR cc_start: 0.9048 (m) cc_final: 0.8810 (t) outliers start: 32 outliers final: 24 residues processed: 169 average time/residue: 0.1024 time to fit residues: 22.9381 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 : 0.256 ------------------------------------------------------------------------------- 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 133 ASP 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 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 18 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 THR 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 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: 0.4980 chunk 22 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 31 ASN ** K 93 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 = 0.3872 r_free = 0.3872 target = 0.114030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.101552 restraints weight = 26376.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.104566 restraints weight = 13291.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105724 restraints weight = 6010.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.106021 restraints weight = 4750.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.106560 restraints weight = 3764.106| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8475 Z= 0.254 Angle : 1.002 12.288 12000 Z= 0.439 Chirality : 0.077 0.747 1460 Planarity : 0.005 0.055 1126 Dihedral : 16.742 178.400 2167 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.63 % Favored : 95.23 % Rotamer: Outliers : 6.59 % Allowed : 21.06 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.78 (0.31), residues: 734 helix: 0.41 (0.29), residues: 306 sheet: -0.52 (0.46), residues: 130 loop : -1.43 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 1 2 TYR 0.014 0.002 TYR 0 9 PHE 0.014 0.002 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.013 0.002 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.25 ( 8475) covalent geometry : angle 1.00224 / 0.44 (12000) hydrogen bonds : bond 0.04731 / 3.40 ( 361) hydrogen bonds : angle 4.92516 / 3.57 ( 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 173 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.6134 (mp) cc_final: 0.5910 (tp) REVERT: 0 240 ILE cc_start: 0.5616 (OUTLIER) cc_final: 0.5170 (mm) REVERT: 0 278 TYR cc_start: 0.8470 (m-10) cc_final: 0.8218 (m-80) REVERT: 0 283 GLU cc_start: 0.8507 (mp0) cc_final: 0.8299 (pm20) REVERT: 0 395 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7457 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9345 (tmtt) cc_final: 0.8742 (tptp) REVERT: K 72 THR cc_start: 0.9001 (m) cc_final: 0.8771 (t) outliers start: 36 outliers final: 26 residues processed: 163 average time/residue: 0.0982 time to fit residues: 21.5822 Evaluate side-chains 160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 66 TYR 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 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 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 41 VAL Chi-restraints excluded: chain 1 residue 57 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.0170 chunk 78 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 0 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3928 r_free = 0.3928 target = 0.117527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.105250 restraints weight = 25950.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.108146 restraints weight = 13290.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.109414 restraints weight = 6177.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.109583 restraints weight = 4485.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.110011 restraints weight = 3835.486| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5281 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= 0.150 Angle : 0.883 11.356 12000 Z= 0.388 Chirality : 0.069 0.728 1460 Planarity : 0.005 0.046 1126 Dihedral : 16.288 177.418 2167 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 6.04 % Allowed : 21.43 % Favored : 72.53 % 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: -0.40 (0.31), residues: 734 helix: 0.71 (0.30), residues: 305 sheet: -0.17 (0.46), residues: 136 loop : -1.30 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 64 TYR 0.010 0.001 TYR 0 31 PHE 0.008 0.001 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.013 0.001 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 8475) covalent geometry : angle 0.88321 / 0.39 (12000) hydrogen bonds : bond 0.04174 / 2.93 ( 361) hydrogen bonds : angle 4.50161 / 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 178 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 171 ILE cc_start: 0.6038 (mp) cc_final: 0.5830 (tp) REVERT: 0 240 ILE cc_start: 0.5898 (OUTLIER) cc_final: 0.5575 (mp) REVERT: 0 278 TYR cc_start: 0.8470 (m-10) cc_final: 0.8173 (m-80) REVERT: 0 283 GLU cc_start: 0.8539 (mp0) cc_final: 0.8286 (pm20) REVERT: 0 324 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7605 (tp30) REVERT: 0 382 LYS cc_start: 0.8475 (tppt) cc_final: 0.8249 (tppt) REVERT: 0 395 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7429 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9349 (tmtt) cc_final: 0.8759 (tptp) REVERT: K 72 THR cc_start: 0.8906 (m) cc_final: 0.8652 (t) outliers start: 33 outliers final: 24 residues processed: 165 average time/residue: 0.0991 time to fit residues: 21.9191 Evaluate side-chains 161 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 66 TYR Chi-restraints excluded: chain 0 residue 74 MET 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 243 ILE Chi-restraints excluded: chain 0 residue 254 LEU Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 324 GLU 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 67 THR 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 134 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: 2.9990 chunk 57 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.0770 chunk 22 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.117778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.105478 restraints weight = 26105.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.108368 restraints weight = 13218.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.109397 restraints weight = 6039.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.109655 restraints weight = 4688.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.110127 restraints weight = 3935.795| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8475 Z= 0.155 Angle : 0.879 11.781 12000 Z= 0.390 Chirality : 0.068 0.706 1460 Planarity : 0.005 0.043 1126 Dihedral : 16.203 177.174 2167 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Rotamer: Outliers : 6.04 % Allowed : 22.71 % Favored : 71.25 % 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: -0.25 (0.31), residues: 734 helix: 0.77 (0.29), residues: 307 sheet: -0.06 (0.46), residues: 136 loop : -1.18 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 64 TYR 0.007 0.001 TYR 0 162 PHE 0.008 0.001 PHE 0 207 TRP 0.000 0.000 TRP 0 484 HIS 0.009 0.001 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 8475) covalent geometry : angle 0.87868 / 0.39 (12000) hydrogen bonds : bond 0.04039 / 2.85 ( 361) hydrogen bonds : angle 4.39824 / 3.17 ( 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 170 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 240 ILE cc_start: 0.5858 (OUTLIER) cc_final: 0.5556 (mp) REVERT: 0 272 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: 0 278 TYR cc_start: 0.8443 (m-10) cc_final: 0.8167 (m-80) REVERT: 0 324 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7610 (tp30) REVERT: 0 382 LYS cc_start: 0.8493 (tppt) cc_final: 0.8256 (tppt) REVERT: 0 395 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7394 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9341 (tmtt) cc_final: 0.8752 (tptp) REVERT: K 72 THR cc_start: 0.8891 (m) cc_final: 0.8663 (t) outliers start: 33 outliers final: 23 residues processed: 158 average time/residue: 0.0975 time to fit residues: 20.7653 Evaluate side-chains 149 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 74 MET 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 254 LEU Chi-restraints excluded: chain 0 residue 272 GLU Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 324 GLU 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 12 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 THR 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 108 ILE 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: 3.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 0.0170 chunk 78 optimal weight: 0.9990 chunk 40 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.8542 > 50:) chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 overall best weight: 0.9222 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.116803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.104498 restraints weight = 26097.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.107938 restraints weight = 13328.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108474 restraints weight = 5839.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108731 restraints weight = 4380.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.108922 restraints weight = 3875.672| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8475 Z= 0.187 Angle : 0.910 11.357 12000 Z= 0.402 Chirality : 0.069 0.680 1460 Planarity : 0.005 0.042 1126 Dihedral : 16.276 177.233 2167 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 6.41 % Allowed : 22.16 % Favored : 71.43 % 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: -0.28 (0.31), residues: 734 helix: 0.79 (0.29), residues: 307 sheet: -0.09 (0.46), residues: 135 loop : -1.24 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 64 TYR 0.011 0.001 TYR 0 31 PHE 0.012 0.001 PHE 0 279 TRP 0.000 0.000 TRP 0 484 HIS 0.010 0.001 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 ( 8475) covalent geometry : angle 0.91037 / 0.40 (12000) hydrogen bonds : bond 0.04175 / 2.97 ( 361) hydrogen bonds : angle 4.47506 / 3.24 ( 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 163 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 122 ILE cc_start: 0.8991 (mm) cc_final: 0.8742 (mm) REVERT: 0 240 ILE cc_start: 0.5845 (OUTLIER) cc_final: 0.5520 (mp) REVERT: 0 272 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: 0 278 TYR cc_start: 0.8463 (m-10) cc_final: 0.8153 (m-80) REVERT: 0 324 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7613 (tp30) REVERT: 0 382 LYS cc_start: 0.8504 (tppt) cc_final: 0.8282 (tppt) REVERT: 0 395 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7425 (mmm-85) REVERT: 1 8 LYS cc_start: 0.9334 (tmtt) cc_final: 0.8697 (tptt) REVERT: 1 82 GLU cc_start: 0.7688 (mp0) cc_final: 0.7269 (mp0) REVERT: K 72 THR cc_start: 0.8942 (m) cc_final: 0.8720 (t) outliers start: 35 outliers final: 26 residues processed: 150 average time/residue: 0.0983 time to fit residues: 19.8117 Evaluate side-chains 155 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 74 MET 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 272 GLU Chi-restraints excluded: chain 0 residue 299 VAL Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 324 GLU 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 12 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 THR 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 108 ILE 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: 0.0970 chunk 52 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 0.0370 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 80 optimal weight: 0.0570 overall best weight: 0.1952 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.120927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.108977 restraints weight = 25838.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.112389 restraints weight = 12658.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.112986 restraints weight = 5560.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.113362 restraints weight = 4370.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.113599 restraints weight = 3608.431| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5944 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= 0.131 Angle : 0.836 10.921 12000 Z= 0.372 Chirality : 0.065 0.655 1460 Planarity : 0.005 0.063 1126 Dihedral : 15.828 175.997 2167 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Rotamer: Outliers : 3.48 % Allowed : 25.46 % Favored : 71.06 % 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: -0.04 (0.31), residues: 734 helix: 1.05 (0.30), residues: 301 sheet: 0.05 (0.47), residues: 136 loop : -1.14 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 64 TYR 0.010 0.001 TYR 0 31 PHE 0.017 0.001 PHE 0 279 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 0.00276 / 0.13 ( 8475) covalent geometry : angle 0.83648 / 0.37 (12000) hydrogen bonds : bond 0.03765 / 2.61 ( 361) hydrogen bonds : angle 4.26269 / 3.07 ( 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 158 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 122 ILE cc_start: 0.8810 (mm) cc_final: 0.8592 (mm) REVERT: 0 240 ILE cc_start: 0.5847 (OUTLIER) cc_final: 0.5586 (mp) REVERT: 0 324 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: 0 382 LYS cc_start: 0.8577 (tppt) cc_final: 0.8370 (tppt) REVERT: 1 8 LYS cc_start: 0.9287 (tmtt) cc_final: 0.8710 (tptp) REVERT: K 57 GLU cc_start: 0.7617 (tp30) cc_final: 0.7182 (tp30) REVERT: K 72 THR cc_start: 0.8804 (m) cc_final: 0.8573 (t) outliers start: 19 outliers final: 15 residues processed: 151 average time/residue: 0.1003 time to fit residues: 20.3301 Evaluate side-chains 143 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 74 MET Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 324 GLU 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 41 VAL Chi-restraints excluded: chain 1 residue 57 THR 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 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 0.0040 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.119360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.106671 restraints weight = 26117.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.109227 restraints weight = 10775.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.110788 restraints weight = 5844.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.111698 restraints weight = 3798.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.112343 restraints weight = 2866.799| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8475 Z= 0.150 Angle : 0.854 10.795 12000 Z= 0.381 Chirality : 0.065 0.653 1460 Planarity : 0.005 0.059 1126 Dihedral : 15.910 176.741 2167 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Rotamer: Outliers : 4.40 % Allowed : 25.82 % Favored : 69.78 % 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: 0.01 (0.31), residues: 734 helix: 1.07 (0.29), residues: 302 sheet: -0.00 (0.46), residues: 136 loop : -1.06 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 94 TYR 0.016 0.001 TYR 0 31 PHE 0.013 0.001 PHE 0 279 TRP 0.000 0.000 TRP 0 484 HIS 0.008 0.001 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8475) covalent geometry : angle 0.85383 / 0.38 (12000) hydrogen bonds : bond 0.03840 / 2.70 ( 361) hydrogen bonds : angle 4.32927 / 3.12 ( 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 152 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 195 GLN cc_start: 0.7174 (tp40) cc_final: 0.6928 (tt0) REVERT: 0 240 ILE cc_start: 0.5708 (OUTLIER) cc_final: 0.5446 (mp) REVERT: 0 278 TYR cc_start: 0.8565 (m-80) cc_final: 0.8041 (m-80) REVERT: 0 324 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: 0 382 LYS cc_start: 0.8567 (tppt) cc_final: 0.8339 (tppt) REVERT: 1 8 LYS cc_start: 0.9341 (tmtt) cc_final: 0.8676 (tptt) REVERT: K 57 GLU cc_start: 0.7480 (tp30) cc_final: 0.7078 (tp30) outliers start: 24 outliers final: 17 residues processed: 144 average time/residue: 0.0954 time to fit residues: 18.5901 Evaluate side-chains 140 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 HIS Chi-restraints excluded: chain 0 residue 74 MET Chi-restraints excluded: chain 0 residue 140 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 324 GLU Chi-restraints excluded: chain 0 residue 336 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 1 residue 12 LEU Chi-restraints excluded: chain 1 residue 41 VAL Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 71 GLU Chi-restraints excluded: chain 1 residue 83 LYS 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 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.116574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.104227 restraints weight = 25764.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.107558 restraints weight = 12780.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.108127 restraints weight = 5580.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108492 restraints weight = 4353.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.108586 restraints weight = 3627.366| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8475 Z= 0.204 Angle : 0.930 11.124 12000 Z= 0.414 Chirality : 0.070 0.667 1460 Planarity : 0.005 0.056 1126 Dihedral : 16.159 177.526 2167 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 4.21 % Allowed : 26.92 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.28 (0.31), residues: 734 helix: 0.75 (0.29), residues: 306 sheet: -0.12 (0.46), residues: 135 loop : -1.16 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 94 TYR 0.018 0.002 TYR 0 31 PHE 0.019 0.002 PHE 0 279 TRP 0.000 0.000 TRP 0 484 HIS 0.011 0.002 HIS 0 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 ( 8475) covalent geometry : angle 0.93035 / 0.41 (12000) hydrogen bonds : bond 0.04198 / 3.02 ( 361) hydrogen bonds : angle 4.58535 / 3.33 ( 958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1808.20 seconds wall clock time: 31 minutes 54.28 seconds (1914.28 seconds total)