Starting phenix.real_space_refine on Tue Mar 3 14:34:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q65_13852/03_2026/7q65_13852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q65_13852/03_2026/7q65_13852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q65_13852/03_2026/7q65_13852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q65_13852/03_2026/7q65_13852.map" model { file = "/net/cci-nas-00/data/ceres_data/7q65_13852/03_2026/7q65_13852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q65_13852/03_2026/7q65_13852.cif" } resolution = 3.32 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= 0.001 sd= 0.008 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: 3 Type Number sf(0) Gaussians C 3806 2.51 5 N 1056 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 6204 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 282 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, D, F, H, J, L, N, P, R, T, V Time building chain proxies: 0.73, per 1000 atoms: 0.12 Number of scatterers: 6204 At special positions: 0 Unit cell: (79.8, 65.1, 77.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1342 8.00 N 1056 7.00 C 3806 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: 0.46 Conformation dependent library (CDL) restraints added in 411.5 milliseconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 103 removed outlier: 6.526A pdb=" N THR A 99 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE C 102 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU A 101 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR C 99 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE E 102 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU C 101 " --> pdb=" O PHE E 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR E 99 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE G 102 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU E 101 " --> pdb=" O PHE G 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR G 99 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE I 102 " --> pdb=" O THR G 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU G 101 " --> pdb=" O PHE I 102 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR I 99 " --> pdb=" O SER K 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE K 102 " --> pdb=" O THR I 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU I 101 " --> pdb=" O PHE K 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR K 99 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE M 102 " --> pdb=" O THR K 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU K 101 " --> pdb=" O PHE M 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR M 99 " --> pdb=" O SER O 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE O 102 " --> pdb=" O THR M 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU M 101 " --> pdb=" O PHE O 102 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR O 99 " --> pdb=" O SER Q 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE Q 102 " --> pdb=" O THR O 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU O 101 " --> pdb=" O PHE Q 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR Q 99 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE S 102 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU Q 101 " --> pdb=" O PHE S 102 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR S 99 " --> pdb=" O SER U 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE U 102 " --> pdb=" O THR S 99 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU S 101 " --> pdb=" O PHE U 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.805A pdb=" N GLY C 121 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY E 121 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY G 121 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY I 121 " --> pdb=" O PHE G 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY K 121 " --> pdb=" O PHE I 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY M 121 " --> pdb=" O PHE K 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY O 121 " --> pdb=" O PHE M 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY Q 121 " --> pdb=" O PHE O 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY S 121 " --> pdb=" O PHE Q 120 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY U 121 " --> pdb=" O PHE S 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 89 Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.544A pdb=" N SER B 100 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER D 100 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER F 100 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER H 100 " --> pdb=" O LEU J 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER J 100 " --> pdb=" O LEU L 101 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER L 100 " --> pdb=" O LEU N 101 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER N 100 " --> pdb=" O LEU P 101 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER P 100 " --> pdb=" O LEU R 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER R 100 " --> pdb=" O LEU T 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER T 100 " --> pdb=" O LEU V 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 106 removed outlier: 6.323A pdb=" N SER B 104 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER D 104 " --> pdb=" O GLN F 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER F 104 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER H 104 " --> pdb=" O GLN J 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER J 104 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER L 104 " --> pdb=" O GLN N 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER N 104 " --> pdb=" O GLN P 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER P 104 " --> pdb=" O GLN R 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER R 104 " --> pdb=" O GLN T 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER T 104 " --> pdb=" O GLN V 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 111 through 112 Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 123 removed outlier: 6.843A pdb=" N ASN D 119 " --> pdb=" O GLY B 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE B 120 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY D 121 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN F 119 " --> pdb=" O GLY D 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE D 120 " --> pdb=" O ASN F 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY F 121 " --> pdb=" O PHE D 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN H 119 " --> pdb=" O GLY F 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE F 120 " --> pdb=" O ASN H 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY H 121 " --> pdb=" O PHE F 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN J 119 " --> pdb=" O GLY H 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE H 120 " --> pdb=" O ASN J 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY J 121 " --> pdb=" O PHE H 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN L 119 " --> pdb=" O GLY J 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE J 120 " --> pdb=" O ASN L 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY L 121 " --> pdb=" O PHE J 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN N 119 " --> pdb=" O GLY L 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE L 120 " --> pdb=" O ASN N 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY N 121 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN P 119 " --> pdb=" O GLY N 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE N 120 " --> pdb=" O ASN P 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY P 121 " --> pdb=" O PHE N 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN R 119 " --> pdb=" O GLY P 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE P 120 " --> pdb=" O ASN R 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY R 121 " --> pdb=" O PHE P 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN T 119 " --> pdb=" O GLY R 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE R 120 " --> pdb=" O ASN T 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY T 121 " --> pdb=" O PHE R 120 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN V 119 " --> pdb=" O GLY T 118 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE T 120 " --> pdb=" O ASN V 119 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY V 121 " --> pdb=" O PHE T 120 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.28: 1034 1.28 - 1.35: 1023 1.35 - 1.42: 766 1.42 - 1.49: 1544 1.49 - 1.57: 1947 Bond restraints: 6314 Sorted by residual: bond pdb=" CA ASN S 106 " pdb=" CB ASN S 106 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.75e-02 3.27e+03 6.56e+00 bond pdb=" CA ASN U 106 " pdb=" CB ASN U 106 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.75e-02 3.27e+03 6.49e+00 bond pdb=" CA ASN Q 106 " pdb=" CB ASN Q 106 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.75e-02 3.27e+03 6.48e+00 bond pdb=" CA ASN M 106 " pdb=" CB ASN M 106 " ideal model delta sigma weight residual 1.527 1.482 0.044 1.75e-02 3.27e+03 6.43e+00 bond pdb=" CA ASN C 106 " pdb=" CB ASN C 106 " ideal model delta sigma weight residual 1.527 1.482 0.044 1.75e-02 3.27e+03 6.42e+00 ... (remaining 6309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 7559 2.02 - 4.04: 724 4.04 - 6.07: 154 6.07 - 8.09: 88 8.09 - 10.11: 33 Bond angle restraints: 8558 Sorted by residual: angle pdb=" CA ASN N 106 " pdb=" CB ASN N 106 " pdb=" CG ASN N 106 " ideal model delta sigma weight residual 112.60 118.08 -5.48 1.00e+00 1.00e+00 3.00e+01 angle pdb=" CA ASN V 106 " pdb=" CB ASN V 106 " pdb=" CG ASN V 106 " ideal model delta sigma weight residual 112.60 118.06 -5.46 1.00e+00 1.00e+00 2.99e+01 angle pdb=" CA ASN P 106 " pdb=" CB ASN P 106 " pdb=" CG ASN P 106 " ideal model delta sigma weight residual 112.60 118.06 -5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CA ASN H 106 " pdb=" CB ASN H 106 " pdb=" CG ASN H 106 " ideal model delta sigma weight residual 112.60 118.06 -5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CA ASN L 106 " pdb=" CB ASN L 106 " pdb=" CG ASN L 106 " ideal model delta sigma weight residual 112.60 118.05 -5.45 1.00e+00 1.00e+00 2.97e+01 ... (remaining 8553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.47: 2641 7.47 - 14.94: 604 14.94 - 22.40: 143 22.40 - 29.87: 66 29.87 - 37.34: 22 Dihedral angle restraints: 3476 sinusoidal: 1122 harmonic: 2354 Sorted by residual: dihedral pdb=" CA THR K 85 " pdb=" C THR K 85 " pdb=" N GLY K 86 " pdb=" CA GLY K 86 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA THR I 85 " pdb=" C THR I 85 " pdb=" N GLY I 86 " pdb=" CA GLY I 86 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA THR G 85 " pdb=" C THR G 85 " pdb=" N GLY G 86 " pdb=" CA GLY G 86 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 3473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 654 0.069 - 0.139: 248 0.139 - 0.208: 22 0.208 - 0.277: 33 0.277 - 0.347: 33 Chirality restraints: 990 Sorted by residual: chirality pdb=" CB THR O 94 " pdb=" CA THR O 94 " pdb=" OG1 THR O 94 " pdb=" CG2 THR O 94 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CB THR E 94 " pdb=" CA THR E 94 " pdb=" OG1 THR E 94 " pdb=" CG2 THR E 94 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB THR S 94 " pdb=" CA THR S 94 " pdb=" OG1 THR S 94 " pdb=" CG2 THR S 94 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 987 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN N 106 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C ASN N 106 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN N 106 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN N 107 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 106 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ASN F 106 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN F 106 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN F 107 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 106 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ASN L 106 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN L 106 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN L 107 " -0.012 2.00e-02 2.50e+03 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 576 2.71 - 3.26: 6253 3.26 - 3.80: 12009 3.80 - 4.35: 14019 4.35 - 4.90: 28813 Nonbonded interactions: 61670 Sorted by model distance: nonbonded pdb=" O GLY E 93 " pdb=" OG SER G 96 " model vdw 2.159 3.040 nonbonded pdb=" O GLY O 93 " pdb=" OG SER Q 96 " model vdw 2.159 3.040 nonbonded pdb=" O GLY Q 93 " pdb=" OG SER S 96 " model vdw 2.159 3.040 nonbonded pdb=" O GLY K 93 " pdb=" OG SER M 96 " model vdw 2.159 3.040 nonbonded pdb=" O GLY S 93 " pdb=" OG SER U 96 " model vdw 2.159 3.040 ... (remaining 61665 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.310 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 : 0.016 0.073 6314 Z= 0.724 Angle : 1.561 10.109 8558 Z= 0.897 Chirality : 0.097 0.347 990 Planarity : 0.006 0.021 1144 Dihedral : 10.100 37.337 1980 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 8.33 % Allowed : 3.18 % Favored : 88.48 % 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: -5.74 (0.13), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.10), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.005 PHE V 102 Details of bonding type rmsd covalent geometry : bond 0.01584 ( 6314) covalent geometry : angle 1.56092 ( 8558) hydrogen bonds : bond 0.21683 ( 60) hydrogen bonds : angle 10.54056 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 217 time to evaluate : 0.158 Fit side-chains REVERT: A 89 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8661 (p0) REVERT: A 113 LYS cc_start: 0.8860 (ptpt) cc_final: 0.8125 (mmpt) REVERT: C 89 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8626 (p0) REVERT: H 124 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9127 (p) REVERT: L 112 ASN cc_start: 0.8513 (t0) cc_final: 0.8291 (t0) REVERT: L 124 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.9024 (p) REVERT: M 115 THR cc_start: 0.8611 (p) cc_final: 0.8184 (m) REVERT: N 104 SER cc_start: 0.8834 (m) cc_final: 0.8614 (m) REVERT: N 112 ASN cc_start: 0.8251 (t0) cc_final: 0.7984 (t0) REVERT: O 115 THR cc_start: 0.8658 (p) cc_final: 0.8406 (m) REVERT: R 87 THR cc_start: 0.9106 (t) cc_final: 0.8903 (m) REVERT: S 89 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8671 (p0) REVERT: U 89 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8522 (p0) REVERT: U 113 LYS cc_start: 0.8978 (ptpt) cc_final: 0.8593 (ptpp) outliers start: 55 outliers final: 34 residues processed: 254 average time/residue: 0.0574 time to fit residues: 20.6834 Evaluate side-chains 194 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 89 ASN Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 91 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN H 112 ASN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 ASN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.093091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.078496 restraints weight = 10319.366| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.26 r_work: 0.3199 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6314 Z= 0.147 Angle : 0.661 6.716 8558 Z= 0.348 Chirality : 0.033 0.124 990 Planarity : 0.004 0.024 1144 Dihedral : 8.871 57.759 917 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 9.09 % Allowed : 10.61 % Favored : 80.30 % 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: -5.65 (0.14), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.30 (0.10), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE O 92 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6314) covalent geometry : angle 0.66086 ( 8558) hydrogen bonds : bond 0.03765 ( 60) hydrogen bonds : angle 4.55908 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 96 SER cc_start: 0.8874 (m) cc_final: 0.8664 (m) REVERT: A 112 ASN cc_start: 0.8463 (t0) cc_final: 0.8112 (t0) REVERT: A 113 LYS cc_start: 0.9082 (ptpt) cc_final: 0.7523 (mmmt) REVERT: E 115 THR cc_start: 0.8777 (t) cc_final: 0.8485 (m) REVERT: H 124 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8756 (p) REVERT: K 113 LYS cc_start: 0.8964 (ptpp) cc_final: 0.8701 (mttm) REVERT: L 117 PHE cc_start: 0.7350 (m-80) cc_final: 0.7110 (m-80) REVERT: L 124 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8560 (p) REVERT: M 87 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8000 (t) REVERT: N 104 SER cc_start: 0.8805 (m) cc_final: 0.8596 (m) outliers start: 60 outliers final: 38 residues processed: 228 average time/residue: 0.0541 time to fit residues: 17.8831 Evaluate side-chains 193 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.091352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.076048 restraints weight = 10278.166| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.37 r_work: 0.3186 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6314 Z= 0.161 Angle : 0.643 6.766 8558 Z= 0.336 Chirality : 0.033 0.187 990 Planarity : 0.003 0.021 1144 Dihedral : 8.120 59.957 893 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 10.76 % Allowed : 13.33 % Favored : 75.91 % 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: -5.69 (0.13), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.33 (0.10), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE O 102 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6314) covalent geometry : angle 0.64256 ( 8558) hydrogen bonds : bond 0.02686 ( 60) hydrogen bonds : angle 4.20057 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 153 time to evaluate : 0.212 Fit side-chains REVERT: A 112 ASN cc_start: 0.8484 (t0) cc_final: 0.8121 (t0) REVERT: A 113 LYS cc_start: 0.9129 (ptpt) cc_final: 0.7518 (mmmt) REVERT: D 112 ASN cc_start: 0.8159 (t0) cc_final: 0.7919 (t0) REVERT: G 91 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8755 (tp) REVERT: H 124 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8774 (p) REVERT: K 115 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8604 (m) REVERT: L 124 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8563 (p) REVERT: N 111 GLN cc_start: 0.8709 (mt0) cc_final: 0.8402 (mt0) REVERT: R 87 THR cc_start: 0.8535 (t) cc_final: 0.8242 (m) REVERT: R 106 ASN cc_start: 0.8352 (p0) cc_final: 0.8103 (p0) outliers start: 71 outliers final: 51 residues processed: 192 average time/residue: 0.0514 time to fit residues: 14.8237 Evaluate side-chains 187 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 132 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.0770 chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.0870 chunk 66 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072696 restraints weight = 10334.511| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.35 r_work: 0.3121 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6314 Z= 0.223 Angle : 0.666 6.994 8558 Z= 0.348 Chirality : 0.034 0.175 990 Planarity : 0.003 0.017 1144 Dihedral : 7.156 58.258 885 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 11.67 % Allowed : 13.64 % Favored : 74.70 % 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: -5.56 (0.14), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE V 117 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 6314) covalent geometry : angle 0.66628 ( 8558) hydrogen bonds : bond 0.02227 ( 60) hydrogen bonds : angle 4.60375 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 142 time to evaluate : 0.194 Fit side-chains REVERT: A 113 LYS cc_start: 0.9233 (ptpt) cc_final: 0.7655 (mmmt) REVERT: D 112 ASN cc_start: 0.8355 (t0) cc_final: 0.8153 (t0) REVERT: E 113 LYS cc_start: 0.9004 (ptpp) cc_final: 0.8792 (mttm) REVERT: K 91 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8953 (tt) REVERT: M 91 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8704 (pp) REVERT: O 89 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8298 (m-40) REVERT: R 87 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8144 (m) REVERT: R 106 ASN cc_start: 0.8425 (p0) cc_final: 0.8158 (p0) outliers start: 77 outliers final: 65 residues processed: 185 average time/residue: 0.0468 time to fit residues: 13.0998 Evaluate side-chains 203 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 134 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 75 optimal weight: 0.4980 chunk 7 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 111 GLN P 112 ASN ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.088232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072810 restraints weight = 10591.570| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.37 r_work: 0.3117 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6314 Z= 0.222 Angle : 0.659 6.813 8558 Z= 0.342 Chirality : 0.034 0.114 990 Planarity : 0.003 0.018 1144 Dihedral : 6.408 54.924 877 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 11.97 % Allowed : 15.15 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.49 (0.14), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE V 117 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 6314) covalent geometry : angle 0.65912 ( 8558) hydrogen bonds : bond 0.02127 ( 60) hydrogen bonds : angle 4.67997 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 140 time to evaluate : 0.214 Fit side-chains REVERT: A 113 LYS cc_start: 0.9251 (ptpt) cc_final: 0.7660 (mmmt) REVERT: E 113 LYS cc_start: 0.9021 (ptpp) cc_final: 0.8819 (mttm) REVERT: L 106 ASN cc_start: 0.9016 (p0) cc_final: 0.8551 (p0) REVERT: M 91 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8750 (pp) REVERT: R 87 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8146 (m) outliers start: 79 outliers final: 71 residues processed: 182 average time/residue: 0.0517 time to fit residues: 14.0331 Evaluate side-chains 201 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 128 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 42 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 81 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 112 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 107 ASN T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.091100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.075383 restraints weight = 10265.438| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.35 r_work: 0.3205 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6314 Z= 0.138 Angle : 0.610 6.785 8558 Z= 0.311 Chirality : 0.031 0.103 990 Planarity : 0.002 0.019 1144 Dihedral : 5.784 59.540 873 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 11.21 % Allowed : 16.52 % Favored : 72.27 % 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: -5.48 (0.14), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE V 117 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6314) covalent geometry : angle 0.60996 ( 8558) hydrogen bonds : bond 0.01592 ( 60) hydrogen bonds : angle 4.33240 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 144 time to evaluate : 0.240 Fit side-chains REVERT: A 113 LYS cc_start: 0.9159 (ptpt) cc_final: 0.7556 (mmmt) REVERT: B 117 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7198 (t80) REVERT: E 113 LYS cc_start: 0.9025 (ptpp) cc_final: 0.8811 (mttm) REVERT: K 113 LYS cc_start: 0.8999 (ptpp) cc_final: 0.8792 (mttp) REVERT: K 115 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8560 (m) REVERT: M 91 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8653 (pp) REVERT: P 111 GLN cc_start: 0.8577 (mt0) cc_final: 0.8309 (mt0) REVERT: R 87 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8163 (m) REVERT: R 106 ASN cc_start: 0.8332 (p0) cc_final: 0.8079 (p0) REVERT: R 112 ASN cc_start: 0.8180 (t0) cc_final: 0.7915 (t0) outliers start: 74 outliers final: 61 residues processed: 182 average time/residue: 0.0525 time to fit residues: 14.1716 Evaluate side-chains 199 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 134 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 19 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.087070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071025 restraints weight = 10298.981| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.36 r_work: 0.3103 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6314 Z= 0.262 Angle : 0.679 7.234 8558 Z= 0.353 Chirality : 0.035 0.114 990 Planarity : 0.003 0.016 1144 Dihedral : 6.129 56.489 873 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 11.67 % Allowed : 15.00 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.36 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE V 117 Details of bonding type rmsd covalent geometry : bond 0.00576 ( 6314) covalent geometry : angle 0.67866 ( 8558) hydrogen bonds : bond 0.02005 ( 60) hydrogen bonds : angle 4.81383 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 136 time to evaluate : 0.221 Fit side-chains REVERT: A 113 LYS cc_start: 0.9249 (ptpt) cc_final: 0.7654 (mmmt) REVERT: B 117 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7231 (t80) REVERT: E 113 LYS cc_start: 0.9038 (ptpp) cc_final: 0.8838 (mttm) REVERT: M 91 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8738 (pp) REVERT: P 111 GLN cc_start: 0.8618 (mt0) cc_final: 0.8220 (mt0) REVERT: R 87 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8120 (m) REVERT: R 112 ASN cc_start: 0.8179 (t0) cc_final: 0.7935 (t0) outliers start: 77 outliers final: 71 residues processed: 177 average time/residue: 0.0503 time to fit residues: 13.2738 Evaluate side-chains 204 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 130 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN R 111 GLN S 89 ASN ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.087958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.071874 restraints weight = 10461.679| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.37 r_work: 0.3124 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6314 Z= 0.216 Angle : 0.654 7.259 8558 Z= 0.339 Chirality : 0.034 0.110 990 Planarity : 0.003 0.017 1144 Dihedral : 6.039 57.335 873 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 11.36 % Allowed : 15.91 % Favored : 72.73 % 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: -5.31 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE V 117 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 6314) covalent geometry : angle 0.65355 ( 8558) hydrogen bonds : bond 0.02126 ( 60) hydrogen bonds : angle 4.69772 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 140 time to evaluate : 0.266 Fit side-chains REVERT: A 113 LYS cc_start: 0.9240 (ptpt) cc_final: 0.7655 (mmmt) REVERT: B 117 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7135 (t80) REVERT: L 106 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8690 (p0) REVERT: M 91 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8666 (pp) REVERT: R 87 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8116 (m) REVERT: R 112 ASN cc_start: 0.8094 (t0) cc_final: 0.7887 (t0) REVERT: T 111 GLN cc_start: 0.8607 (mt0) cc_final: 0.8353 (mt0) outliers start: 75 outliers final: 67 residues processed: 181 average time/residue: 0.0495 time to fit residues: 13.5684 Evaluate side-chains 205 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 134 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 106 ASN Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070530 restraints weight = 10481.260| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.38 r_work: 0.3092 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6314 Z= 0.270 Angle : 0.679 7.432 8558 Z= 0.354 Chirality : 0.036 0.114 990 Planarity : 0.003 0.016 1144 Dihedral : 6.169 55.744 873 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 11.82 % Allowed : 15.91 % Favored : 72.27 % 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: -5.23 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE V 117 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 6314) covalent geometry : angle 0.67936 ( 8558) hydrogen bonds : bond 0.02102 ( 60) hydrogen bonds : angle 4.90081 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 129 time to evaluate : 0.203 Fit side-chains REVERT: A 113 LYS cc_start: 0.9257 (ptpt) cc_final: 0.7678 (mmmt) REVERT: B 117 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7127 (t80) REVERT: L 106 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8708 (p0) REVERT: M 91 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8721 (pp) REVERT: R 87 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8087 (m) REVERT: R 112 ASN cc_start: 0.8110 (t0) cc_final: 0.7899 (t0) outliers start: 78 outliers final: 69 residues processed: 173 average time/residue: 0.0524 time to fit residues: 13.4803 Evaluate side-chains 198 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 125 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 106 ASN Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 70 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.089278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.073223 restraints weight = 10340.759| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.38 r_work: 0.3166 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6314 Z= 0.154 Angle : 0.623 7.311 8558 Z= 0.319 Chirality : 0.032 0.104 990 Planarity : 0.003 0.019 1144 Dihedral : 5.853 59.551 873 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 10.30 % Allowed : 17.58 % Favored : 72.12 % 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: -5.23 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE V 117 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6314) covalent geometry : angle 0.62338 ( 8558) hydrogen bonds : bond 0.02085 ( 60) hydrogen bonds : angle 4.46241 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 133 time to evaluate : 0.203 Fit side-chains REVERT: A 113 LYS cc_start: 0.9220 (ptpt) cc_final: 0.7628 (mmmt) REVERT: B 117 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7058 (t80) REVERT: L 106 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8708 (p0) REVERT: M 91 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8633 (pp) REVERT: R 87 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8089 (m) REVERT: T 111 GLN cc_start: 0.8554 (mt0) cc_final: 0.8276 (mt0) outliers start: 68 outliers final: 62 residues processed: 172 average time/residue: 0.0468 time to fit residues: 12.1526 Evaluate side-chains 194 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 128 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 106 ASN Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 104 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 85 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 106 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 112 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 = 0.3493 r_free = 0.3493 target = 0.087936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.071932 restraints weight = 10312.796| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.36 r_work: 0.3134 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6314 Z= 0.213 Angle : 0.647 7.871 8558 Z= 0.333 Chirality : 0.033 0.107 990 Planarity : 0.003 0.017 1144 Dihedral : 5.926 59.909 871 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 10.76 % Allowed : 17.12 % Favored : 72.12 % 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: -5.20 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE V 117 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 6314) covalent geometry : angle 0.64732 ( 8558) hydrogen bonds : bond 0.02029 ( 60) hydrogen bonds : angle 4.63159 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1431.74 seconds wall clock time: 26 minutes 9.09 seconds (1569.09 seconds total)