Starting phenix.real_space_refine on Tue Feb 11 15:39:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q65_13852/02_2025/7q65_13852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q65_13852/02_2025/7q65_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_13852/02_2025/7q65_13852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q65_13852/02_2025/7q65_13852.map" model { file = "/net/cci-nas-00/data/ceres_data/7q65_13852/02_2025/7q65_13852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q65_13852/02_2025/7q65_13852.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 1.90, per 1000 atoms: 0.31 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: 1.58 Conformation dependent library (CDL) restraints added in 913.6 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: 1.07 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: 1.67 Time building geometry restraints manager: 1.69 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: 0.01 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 15.490 Find NCS groups from input model: 0.270 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- 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= 1.048 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 : 0.624 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: 0.8627 (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: 0.8289 (t0) REVERT: L 124 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.9024 (p) REVERT: M 115 THR cc_start: 0.8610 (p) cc_final: 0.8185 (m) REVERT: N 104 SER cc_start: 0.8834 (m) cc_final: 0.8615 (m) REVERT: N 112 ASN cc_start: 0.8251 (t0) cc_final: 0.7984 (t0) REVERT: O 115 THR cc_start: 0.8657 (p) cc_final: 0.8405 (m) REVERT: R 87 THR cc_start: 0.9106 (t) cc_final: 0.8904 (m) REVERT: S 89 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8672 (p0) REVERT: U 89 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8521 (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: 0.1418 time to fit residues: 50.1272 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 : 0.665 ------------------------------------------------------------------------------- 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 74 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.093136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.078545 restraints weight = 10207.996| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.23 r_work: 0.3207 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6314 Z= 0.203 Angle : 0.663 6.644 8558 Z= 0.349 Chirality : 0.033 0.136 990 Planarity : 0.004 0.025 1144 Dihedral : 8.867 57.384 917 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 8.79 % Allowed : 11.06 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.66 (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 0.032 0.001 PHE V 117 *********************** 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 255 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 197 time to evaluate : 0.715 Fit side-chains REVERT: A 96 SER cc_start: 0.8879 (m) cc_final: 0.8673 (m) REVERT: A 112 ASN cc_start: 0.8444 (t0) cc_final: 0.8108 (t0) REVERT: A 113 LYS cc_start: 0.9074 (ptpt) cc_final: 0.7524 (mmmt) REVERT: E 115 THR cc_start: 0.8770 (t) cc_final: 0.8489 (m) REVERT: H 124 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8753 (p) REVERT: K 113 LYS cc_start: 0.8968 (ptpp) cc_final: 0.8703 (mttm) REVERT: L 117 PHE cc_start: 0.7350 (m-80) cc_final: 0.7110 (m-80) REVERT: L 124 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8565 (p) REVERT: M 87 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7985 (t) REVERT: N 104 SER cc_start: 0.8796 (m) cc_final: 0.8590 (m) outliers start: 58 outliers final: 35 residues processed: 228 average time/residue: 0.1311 time to fit residues: 42.6329 Evaluate side-chains 188 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 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 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** 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 105 GLN ** 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 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 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN P 111 GLN ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 GLN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN 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 = 0.3413 r_free = 0.3413 target = 0.085948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.069854 restraints weight = 10457.113| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.35 r_work: 0.3048 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 6314 Z= 0.454 Angle : 0.765 7.685 8558 Z= 0.401 Chirality : 0.038 0.196 990 Planarity : 0.003 0.019 1144 Dihedral : 8.063 56.821 893 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 12.12 % Allowed : 12.58 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.61 (0.14), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE V 117 *********************** 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 233 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 153 time to evaluate : 0.687 Fit side-chains REVERT: A 96 SER cc_start: 0.8982 (m) cc_final: 0.8762 (m) REVERT: A 113 LYS cc_start: 0.9274 (ptpt) cc_final: 0.7710 (mmmt) REVERT: C 91 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9129 (tp) REVERT: G 113 LYS cc_start: 0.9041 (ptpp) cc_final: 0.8750 (mttp) REVERT: I 91 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8787 (tp) REVERT: K 91 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8946 (tp) REVERT: M 91 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8778 (pp) REVERT: N 112 ASN cc_start: 0.8108 (t0) cc_final: 0.7775 (t0) REVERT: R 87 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8222 (m) REVERT: R 106 ASN cc_start: 0.8500 (p0) cc_final: 0.8241 (p0) REVERT: U 91 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8699 (tp) outliers start: 80 outliers final: 64 residues processed: 200 average time/residue: 0.1281 time to fit residues: 37.4152 Evaluate side-chains 209 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 139 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 B residue 124 THR Chi-restraints excluded: chain C residue 87 THR 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 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 91 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 104 SER 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 I residue 90 THR Chi-restraints excluded: chain I residue 91 LEU 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 106 ASN 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 91 LEU 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 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 P residue 124 THR Chi-restraints excluded: chain Q residue 89 ASN 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 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 107 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 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 6 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** 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 105 GLN ** 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 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** K 89 ASN ** 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** S 89 ASN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 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 = 0.3350 r_free = 0.3350 target = 0.081217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064906 restraints weight = 10960.245| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.34 r_work: 0.2977 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.048 6314 Z= 0.570 Angle : 0.795 7.787 8558 Z= 0.419 Chirality : 0.040 0.154 990 Planarity : 0.003 0.017 1144 Dihedral : 7.425 48.759 885 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 14.55 % Allowed : 12.42 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.41 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.002 PHE V 117 *********************** 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 243 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 147 time to evaluate : 0.767 Fit side-chains REVERT: A 96 SER cc_start: 0.8995 (m) cc_final: 0.8767 (m) REVERT: A 113 LYS cc_start: 0.9278 (ptpt) cc_final: 0.7718 (mmmt) REVERT: B 117 PHE cc_start: 0.7615 (m-80) cc_final: 0.7396 (m-80) REVERT: C 91 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9140 (tp) REVERT: G 113 LYS cc_start: 0.9115 (ptpp) cc_final: 0.8834 (mttp) REVERT: I 91 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8782 (tp) REVERT: L 106 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8693 (p0) REVERT: M 91 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8920 (pp) REVERT: N 112 ASN cc_start: 0.8182 (t0) cc_final: 0.7920 (t0) REVERT: R 87 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8185 (m) outliers start: 96 outliers final: 79 residues processed: 201 average time/residue: 0.1345 time to fit residues: 38.4674 Evaluate side-chains 217 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 133 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 B residue 124 THR Chi-restraints excluded: chain C residue 87 THR 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 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 85 THR Chi-restraints excluded: chain F residue 104 SER 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 90 THR Chi-restraints excluded: chain I residue 91 LEU 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 106 ASN 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 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 94 THR 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 91 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 123 SER Chi-restraints excluded: chain O residue 124 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 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 101 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain T residue 85 THR Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 107 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 106 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 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 ** 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 = 0.3526 r_free = 0.3526 target = 0.089841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.074467 restraints weight = 10332.219| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.37 r_work: 0.3154 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3268 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= 0.194 Angle : 0.636 6.887 8558 Z= 0.326 Chirality : 0.032 0.136 990 Planarity : 0.003 0.018 1144 Dihedral : 6.286 45.454 881 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 10.30 % Allowed : 16.67 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.47 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE V 117 *********************** 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 231 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 163 time to evaluate : 0.523 Fit side-chains REVERT: A 96 SER cc_start: 0.8671 (m) cc_final: 0.8285 (p) REVERT: A 113 LYS cc_start: 0.9147 (ptpt) cc_final: 0.7532 (mmmt) REVERT: D 106 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8420 (p0) REVERT: E 113 LYS cc_start: 0.8980 (ptpp) cc_final: 0.8772 (mttm) REVERT: G 105 GLN cc_start: 0.8549 (mt0) cc_final: 0.8319 (mt0) REVERT: G 113 LYS cc_start: 0.9033 (ptpp) cc_final: 0.8830 (mttp) REVERT: J 112 ASN cc_start: 0.8448 (t0) cc_final: 0.7833 (t0) REVERT: K 115 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8605 (m) REVERT: N 112 ASN cc_start: 0.8163 (t0) cc_final: 0.7929 (t0) REVERT: R 87 THR cc_start: 0.8377 (t) cc_final: 0.8128 (m) outliers start: 68 outliers final: 53 residues processed: 197 average time/residue: 0.1271 time to fit residues: 35.8651 Evaluate side-chains 201 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 124 THR Chi-restraints excluded: chain C residue 87 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 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 123 SER 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 87 THR Chi-restraints excluded: chain K residue 90 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 123 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 90 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 3 optimal weight: 0.0170 chunk 85 optimal weight: 0.0050 chunk 14 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 overall best weight: 2.0036 ------------------------------------------------------------------------------- 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** ** 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** ** 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN O 89 ASN R 111 GLN S 89 ASN ** T 107 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.088949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073502 restraints weight = 10148.911| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.37 r_work: 0.3130 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6314 Z= 0.282 Angle : 0.648 8.338 8558 Z= 0.334 Chirality : 0.033 0.117 990 Planarity : 0.003 0.016 1144 Dihedral : 5.954 48.680 875 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 11.21 % Allowed : 16.21 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.41 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE V 117 *********************** 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 225 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 151 time to evaluate : 0.608 Fit side-chains REVERT: A 96 SER cc_start: 0.8655 (m) cc_final: 0.8232 (p) REVERT: A 113 LYS cc_start: 0.9210 (ptpt) cc_final: 0.7574 (mmmt) REVERT: B 111 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: B 117 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7007 (t80) REVERT: G 113 LYS cc_start: 0.9066 (ptpp) cc_final: 0.8859 (mttp) REVERT: L 106 ASN cc_start: 0.8986 (OUTLIER) cc_final: 0.8751 (p0) REVERT: N 112 ASN cc_start: 0.8200 (t0) cc_final: 0.7931 (t0) REVERT: R 87 THR cc_start: 0.8343 (t) cc_final: 0.8108 (m) outliers start: 74 outliers final: 62 residues processed: 187 average time/residue: 0.1266 time to fit residues: 34.1598 Evaluate side-chains 208 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 143 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 B residue 124 THR 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 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 123 SER 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 106 ASN 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 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 104 SER Chi-restraints excluded: chain M residue 123 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 90 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 Q residue 123 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 20 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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** ** E 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN S 89 ASN ** T 107 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 = 0.3492 r_free = 0.3492 target = 0.087529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072137 restraints weight = 10357.410| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.36 r_work: 0.3116 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6314 Z= 0.314 Angle : 0.657 8.378 8558 Z= 0.340 Chirality : 0.034 0.117 990 Planarity : 0.003 0.016 1144 Dihedral : 5.961 50.949 874 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 11.06 % Allowed : 15.76 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.33 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.001 PHE V 117 *********************** 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 220 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 147 time to evaluate : 0.634 Fit side-chains REVERT: A 96 SER cc_start: 0.8692 (m) cc_final: 0.8459 (m) REVERT: A 113 LYS cc_start: 0.9232 (ptpt) cc_final: 0.7578 (mmmt) REVERT: B 117 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7244 (t80) REVERT: L 106 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8752 (p0) REVERT: N 112 ASN cc_start: 0.8237 (t0) cc_final: 0.7980 (t0) REVERT: P 111 GLN cc_start: 0.8622 (mt0) cc_final: 0.8208 (mt0) REVERT: T 104 SER cc_start: 0.8986 (m) cc_final: 0.8659 (p) outliers start: 73 outliers final: 64 residues processed: 183 average time/residue: 0.1253 time to fit residues: 33.2588 Evaluate side-chains 208 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 142 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 117 PHE Chi-restraints excluded: chain B residue 124 THR 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 124 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 123 SER 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 106 ASN 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 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 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 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 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 104 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 69 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN S 89 ASN ** T 107 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 = 0.3563 r_free = 0.3563 target = 0.091685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076049 restraints weight = 10161.549| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.33 r_work: 0.3214 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3657 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= 0.191 Angle : 0.606 7.667 8558 Z= 0.308 Chirality : 0.031 0.110 990 Planarity : 0.002 0.017 1144 Dihedral : 5.569 55.547 874 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 9.09 % Allowed : 18.33 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.39 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.11), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.001 PHE V 117 *********************** 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 211 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 0.717 Fit side-chains REVERT: A 96 SER cc_start: 0.8600 (m) cc_final: 0.8154 (p) REVERT: A 113 LYS cc_start: 0.9123 (ptpt) cc_final: 0.7486 (mmmt) REVERT: B 111 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: B 117 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7179 (t80) REVERT: D 106 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8374 (p0) REVERT: K 113 LYS cc_start: 0.8981 (ptpp) cc_final: 0.8778 (mttp) REVERT: K 115 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8568 (m) REVERT: L 106 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8675 (p0) outliers start: 60 outliers final: 52 residues processed: 180 average time/residue: 0.1217 time to fit residues: 32.0082 Evaluate side-chains 194 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 137 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR 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 106 ASN 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 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 104 SER Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain N residue 104 SER 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 97 THR Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q 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 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 104 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 62 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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** ** 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** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN K 105 GLN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3470 r_free = 0.3470 target = 0.084809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.069041 restraints weight = 10921.755| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.37 r_work: 0.3090 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3509 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= 0.332 Angle : 0.654 7.798 8558 Z= 0.340 Chirality : 0.034 0.117 990 Planarity : 0.003 0.023 1144 Dihedral : 5.856 54.077 871 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 9.70 % Allowed : 18.33 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.26 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.001 PHE V 117 *********************** 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 204 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 0.689 Fit side-chains REVERT: A 96 SER cc_start: 0.8756 (m) cc_final: 0.8526 (m) REVERT: A 113 LYS cc_start: 0.9239 (ptpt) cc_final: 0.7587 (mmmt) REVERT: K 113 LYS cc_start: 0.9029 (ptpp) cc_final: 0.8788 (mttp) REVERT: L 106 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8794 (p0) REVERT: T 104 SER cc_start: 0.9064 (m) cc_final: 0.8776 (p) outliers start: 64 outliers final: 59 residues processed: 173 average time/residue: 0.1223 time to fit residues: 31.1201 Evaluate side-chains 198 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 138 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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 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 106 ASN 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 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 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 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 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 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 104 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 64 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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** ** 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** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** P 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 GLN ** 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 = 0.3459 r_free = 0.3459 target = 0.084289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.068523 restraints weight = 10997.992| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.37 r_work: 0.3074 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.006 0.039 6314 Z= 0.375 Angle : 0.669 7.655 8558 Z= 0.349 Chirality : 0.035 0.124 990 Planarity : 0.003 0.020 1144 Dihedral : 5.981 50.521 871 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 10.00 % Allowed : 18.33 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.16), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.001 PHE V 117 ********************** 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 205 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 139 time to evaluate : 0.520 Fit side-chains REVERT: A 96 SER cc_start: 0.8735 (m) cc_final: 0.8482 (m) REVERT: A 113 LYS cc_start: 0.9259 (ptpt) cc_final: 0.7660 (mmmt) REVERT: B 117 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7106 (t80) REVERT: J 112 ASN cc_start: 0.8451 (t0) cc_final: 0.7876 (t0) REVERT: L 106 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8808 (p0) REVERT: T 111 GLN cc_start: 0.8481 (mt0) cc_final: 0.8216 (mt0) outliers start: 66 outliers final: 62 residues processed: 170 average time/residue: 0.1258 time to fit residues: 30.8930 Evaluate side-chains 197 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 133 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 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 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 106 ASN 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 90 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 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 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 106 ASN 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 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 104 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain V residue 104 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 38 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 0.0030 chunk 47 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.086122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.070453 restraints weight = 10969.262| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.34 r_work: 0.3132 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6314 Z= 0.256 Angle : 0.625 7.250 8558 Z= 0.320 Chirality : 0.033 0.111 990 Planarity : 0.002 0.017 1144 Dihedral : 5.717 55.260 871 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 9.85 % Allowed : 18.94 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.15), residues: 836 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.12), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.001 PHE V 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3048.59 seconds wall clock time: 56 minutes 20.57 seconds (3380.57 seconds total)