Starting phenix.real_space_refine on Fri Jun 13 03:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5flu_3222/06_2025/5flu_3222.cif Found real_map, /net/cci-nas-00/data/ceres_data/5flu_3222/06_2025/5flu_3222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5flu_3222/06_2025/5flu_3222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5flu_3222/06_2025/5flu_3222.map" model { file = "/net/cci-nas-00/data/ceres_data/5flu_3222/06_2025/5flu_3222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5flu_3222/06_2025/5flu_3222.cif" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.582 sd= 0.540 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 9399 2.51 5 N 2548 2.21 5 O 3146 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-5710/modules/chem_data/mon_lib" Total number of atoms: 15132 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1164 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L Time building chain proxies: 4.11, per 1000 atoms: 0.27 Number of scatterers: 15132 At special positions: 0 Unit cell: (95.7, 94.6, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 3146 8.00 N 2548 7.00 C 9399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 61 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 61 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 61 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 61 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 61 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 61 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 61 " distance=2.03 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: 3.56 Conformation dependent library (CDL) restraints added in 2.1 seconds 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 39 sheets defined 11.8% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 63 through 70 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 63 through 70 Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 63 through 70 Processing helix chain 'E' and resid 25 through 29 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 63 through 70 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 63 through 70 Processing helix chain 'G' and resid 25 through 29 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 63 through 70 Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 63 through 70 Processing helix chain 'I' and resid 25 through 29 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 63 through 70 Processing helix chain 'J' and resid 25 through 29 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 63 through 70 Processing helix chain 'K' and resid 25 through 29 Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 63 through 70 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 63 through 70 Processing helix chain 'M' and resid 25 through 29 Processing helix chain 'M' and resid 40 through 45 Processing helix chain 'M' and resid 63 through 70 Processing sheet with id=HA, first strand: chain 'H' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR A 16 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN H 37 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 18 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER H 39 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AB, first strand: chain 'A' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR G 16 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN A 37 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL G 18 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER A 39 " --> pdb=" O VAL G 18 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=CA, first strand: chain 'C' and resid 30 through 39 removed outlier: 5.811A pdb=" N THR B 16 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN C 37 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 18 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER C 39 " --> pdb=" O VAL B 18 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=BB, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=BC, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=DA, first strand: chain 'D' and resid 30 through 39 removed outlier: 5.809A pdb=" N THR C 16 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN D 37 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL C 18 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER D 39 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 23 through 24 Processing sheet with id=CC, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=EA, first strand: chain 'E' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR D 16 " --> pdb=" O PHE E 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN E 37 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 18 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER E 39 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing sheet with id=DB, first strand: chain 'D' and resid 23 through 24 Processing sheet with id=DC, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=FA, first strand: chain 'F' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR E 16 " --> pdb=" O PHE F 35 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN F 37 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 18 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER F 39 " --> pdb=" O VAL E 18 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 23 through 24 Processing sheet with id=EC, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=GA, first strand: chain 'G' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR F 16 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN G 37 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL F 18 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER G 39 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing sheet with id=FB, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=FC, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=GB, first strand: chain 'G' and resid 23 through 24 Processing sheet with id=GC, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=IA, first strand: chain 'I' and resid 30 through 39 removed outlier: 5.809A pdb=" N THR H 16 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN I 37 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL H 18 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER I 39 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=HB, first strand: chain 'H' and resid 23 through 24 Processing sheet with id=HC, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=JA, first strand: chain 'J' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR I 16 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN J 37 " --> pdb=" O THR I 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL I 18 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER J 39 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Processing sheet with id=IB, first strand: chain 'I' and resid 23 through 24 Processing sheet with id=IC, first strand: chain 'I' and resid 52 through 53 Processing sheet with id=KA, first strand: chain 'K' and resid 30 through 39 removed outlier: 5.809A pdb=" N THR J 16 " --> pdb=" O PHE K 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN K 37 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL J 18 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER K 39 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id=JB, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=JC, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=LA, first strand: chain 'L' and resid 30 through 39 removed outlier: 5.809A pdb=" N THR K 16 " --> pdb=" O PHE L 35 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN L 37 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL K 18 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER L 39 " --> pdb=" O VAL K 18 " (cutoff:3.500A) Processing sheet with id=KB, first strand: chain 'K' and resid 23 through 24 Processing sheet with id=KC, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=MA, first strand: chain 'M' and resid 30 through 39 removed outlier: 5.810A pdb=" N THR L 16 " --> pdb=" O PHE M 35 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN M 37 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL L 18 " --> pdb=" O GLN M 37 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER M 39 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=LB, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=LC, first strand: chain 'L' and resid 52 through 53 Processing sheet with id=MB, first strand: chain 'M' and resid 23 through 24 Processing sheet with id=MC, first strand: chain 'M' and resid 52 through 53 561 hydrogen bonds defined for protein. 1407 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: 4.73 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2962 1.32 - 1.44: 3421 1.44 - 1.57: 8905 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 15340 Sorted by residual: bond pdb=" CG ASP D 19 " pdb=" OD2 ASP D 19 " ideal model delta sigma weight residual 1.249 1.205 0.044 1.90e-02 2.77e+03 5.35e+00 bond pdb=" CD GLU A 118 " pdb=" OE1 GLU A 118 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.17e+00 bond pdb=" CG ASP M 19 " pdb=" OD2 ASP M 19 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.13e+00 bond pdb=" CG ASP E 19 " pdb=" OD2 ASP E 19 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.12e+00 bond pdb=" CG ASP B 19 " pdb=" OD2 ASP B 19 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.10e+00 ... (remaining 15335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 17682 1.27 - 2.53: 2619 2.53 - 3.80: 382 3.80 - 5.06: 78 5.06 - 6.33: 26 Bond angle restraints: 20787 Sorted by residual: angle pdb=" C ALA C 108 " pdb=" CA ALA C 108 " pdb=" CB ALA C 108 " ideal model delta sigma weight residual 116.54 110.21 6.33 1.15e+00 7.56e-01 3.03e+01 angle pdb=" C ALA K 108 " pdb=" CA ALA K 108 " pdb=" CB ALA K 108 " ideal model delta sigma weight residual 116.54 110.22 6.32 1.15e+00 7.56e-01 3.02e+01 angle pdb=" C ALA G 108 " pdb=" CA ALA G 108 " pdb=" CB ALA G 108 " ideal model delta sigma weight residual 116.54 110.23 6.31 1.15e+00 7.56e-01 3.01e+01 angle pdb=" C ALA J 108 " pdb=" CA ALA J 108 " pdb=" CB ALA J 108 " ideal model delta sigma weight residual 116.54 110.25 6.29 1.15e+00 7.56e-01 2.99e+01 angle pdb=" C ALA D 108 " pdb=" CA ALA D 108 " pdb=" CB ALA D 108 " ideal model delta sigma weight residual 116.54 110.25 6.29 1.15e+00 7.56e-01 2.99e+01 ... (remaining 20782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 8639 16.78 - 33.56: 279 33.56 - 50.34: 26 50.34 - 67.12: 52 67.12 - 83.89: 65 Dihedral angle restraints: 9061 sinusoidal: 3263 harmonic: 5798 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 61 " pdb=" CB CYS E 61 " ideal model delta sinusoidal sigma weight residual -86.00 -54.93 -31.07 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 61 " pdb=" CB CYS J 61 " ideal model delta sinusoidal sigma weight residual -86.00 -54.94 -31.06 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 61 " pdb=" CB CYS M 61 " ideal model delta sinusoidal sigma weight residual -86.00 -54.96 -31.04 1 1.00e+01 1.00e-02 1.37e+01 ... (remaining 9058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1790 0.025 - 0.049: 110 0.049 - 0.074: 102 0.074 - 0.099: 205 0.099 - 0.123: 224 Chirality restraints: 2431 Sorted by residual: chirality pdb=" CA VAL M 112 " pdb=" N VAL M 112 " pdb=" C VAL M 112 " pdb=" CB VAL M 112 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA VAL G 112 " pdb=" N VAL G 112 " pdb=" C VAL G 112 " pdb=" CB VAL G 112 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 2428 not shown) Planarity restraints: 2782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 1 " -0.063 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO J 2 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO J 2 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO J 2 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 1 " 0.062 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO I 2 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO I 2 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO I 2 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 1 " -0.062 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 2 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 2 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 2 " -0.050 5.00e-02 4.00e+02 ... (remaining 2779 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1545 2.75 - 3.29: 16056 3.29 - 3.83: 25346 3.83 - 4.36: 31495 4.36 - 4.90: 52126 Nonbonded interactions: 126568 Sorted by model distance: nonbonded pdb=" O HIS M 89 " pdb=" OG SER M 90 " model vdw 2.213 3.040 nonbonded pdb=" O HIS K 89 " pdb=" OG SER K 90 " model vdw 2.213 3.040 nonbonded pdb=" O HIS F 89 " pdb=" OG SER F 90 " model vdw 2.213 3.040 nonbonded pdb=" O HIS C 89 " pdb=" OG SER C 90 " model vdw 2.213 3.040 nonbonded pdb=" O HIS D 89 " pdb=" OG SER D 90 " model vdw 2.214 3.040 ... (remaining 126563 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.620 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 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 : 0.009 0.044 15353 Z= 0.491 Angle : 0.953 6.325 20813 Z= 0.641 Chirality : 0.045 0.123 2431 Planarity : 0.007 0.096 2782 Dihedral : 12.312 83.894 5356 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 1.24 % Allowed : 8.70 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -2.36 (0.15), residues: 2093 helix: -3.87 (0.19), residues: 260 sheet: 0.11 (0.18), residues: 611 loop : -2.01 (0.13), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 89 PHE 0.002 0.000 PHE B 66 TYR 0.001 0.000 TYR E 162 Details of bonding type rmsd hydrogen bonds : bond 0.18688 ( 561) hydrogen bonds : angle 9.87816 ( 1407) SS BOND : bond 0.00380 ( 13) SS BOND : angle 5.41484 ( 26) covalent geometry : bond 0.00871 (15340) covalent geometry : angle 0.93455 (20787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.7822 (mm) cc_final: 0.7597 (mm) REVERT: C 53 ASP cc_start: 0.7610 (m-30) cc_final: 0.7305 (m-30) REVERT: C 91 ASP cc_start: 0.6961 (p0) cc_final: 0.6640 (p0) REVERT: C 101 THR cc_start: 0.7957 (p) cc_final: 0.7095 (t) REVERT: E 59 VAL cc_start: 0.7181 (m) cc_final: 0.6957 (p) REVERT: F 53 ASP cc_start: 0.7699 (m-30) cc_final: 0.7455 (m-30) REVERT: F 101 THR cc_start: 0.6753 (p) cc_final: 0.6329 (t) REVERT: G 52 MET cc_start: 0.7140 (mmm) cc_final: 0.6757 (tpp) REVERT: G 94 ASP cc_start: 0.7943 (t0) cc_final: 0.7741 (t70) REVERT: H 59 VAL cc_start: 0.8635 (m) cc_final: 0.8354 (p) REVERT: L 33 ILE cc_start: 0.7964 (mm) cc_final: 0.7614 (mm) REVERT: L 101 THR cc_start: 0.7563 (p) cc_final: 0.7345 (t) REVERT: L 126 ASP cc_start: 0.7016 (m-30) cc_final: 0.6755 (t70) REVERT: M 94 ASP cc_start: 0.7469 (t0) cc_final: 0.7062 (t0) outliers start: 0 outliers final: 0 residues processed: 595 average time/residue: 0.2814 time to fit residues: 240.7970 Evaluate side-chains 252 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 121 optimal weight: 50.0000 chunk 188 optimal weight: 30.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN E 70 ASN H 87 ASN I 31 GLN J 70 ASN M 70 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.063308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.053364 restraints weight = 69313.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054867 restraints weight = 40378.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.055857 restraints weight = 27176.815| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15353 Z= 0.182 Angle : 0.693 10.336 20813 Z= 0.359 Chirality : 0.046 0.169 2431 Planarity : 0.004 0.036 2782 Dihedral : 6.747 77.822 2145 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.65 % Allowed : 13.34 % Favored : 82.01 % 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: -1.29 (0.16), residues: 2093 helix: -2.07 (0.25), residues: 260 sheet: 0.15 (0.19), residues: 585 loop : -1.08 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 132 PHE 0.029 0.002 PHE H 158 TYR 0.015 0.002 TYR A 162 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 561) hydrogen bonds : angle 7.28717 ( 1407) SS BOND : bond 0.01224 ( 13) SS BOND : angle 1.31314 ( 26) covalent geometry : bond 0.00406 (15340) covalent geometry : angle 0.69174 (20787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 273 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8702 (mm) cc_final: 0.8234 (mm) REVERT: A 52 MET cc_start: 0.7291 (mmm) cc_final: 0.6937 (mtp) REVERT: B 85 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7826 (mt) REVERT: C 162 TYR cc_start: 0.7034 (m-80) cc_final: 0.6181 (m-10) REVERT: E 52 MET cc_start: 0.7451 (mmm) cc_final: 0.7094 (mtp) REVERT: E 57 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7469 (tm-30) REVERT: E 85 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8613 (mt) REVERT: E 93 LEU cc_start: 0.8037 (tp) cc_final: 0.7631 (tp) REVERT: E 106 GLN cc_start: 0.7085 (mm110) cc_final: 0.6820 (mm-40) REVERT: F 106 GLN cc_start: 0.7397 (mp10) cc_final: 0.7161 (mp-120) REVERT: G 52 MET cc_start: 0.7464 (mmm) cc_final: 0.7030 (mmm) REVERT: H 13 PHE cc_start: 0.8236 (m-80) cc_final: 0.7968 (m-80) REVERT: J 52 MET cc_start: 0.7011 (mmm) cc_final: 0.6805 (mmm) REVERT: J 74 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7746 (mptt) REVERT: L 33 ILE cc_start: 0.8714 (mm) cc_final: 0.8507 (mm) REVERT: L 40 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8359 (tttp) REVERT: M 126 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6617 (t70) REVERT: M 148 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.7921 (p) outliers start: 75 outliers final: 37 residues processed: 322 average time/residue: 0.2641 time to fit residues: 124.9962 Evaluate side-chains 252 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 49 SER Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 126 ASP Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 201 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 146 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 197 optimal weight: 30.0000 chunk 49 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 195 optimal weight: 30.0000 chunk 203 optimal weight: 0.9980 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 GLN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051398 restraints weight = 70817.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052882 restraints weight = 41524.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.053801 restraints weight = 27880.539| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.8711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15353 Z= 0.183 Angle : 0.663 9.853 20813 Z= 0.346 Chirality : 0.044 0.183 2431 Planarity : 0.003 0.021 2782 Dihedral : 6.808 85.811 2145 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.09 % Allowed : 15.69 % Favored : 80.21 % 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: -0.51 (0.17), residues: 2093 helix: -1.22 (0.29), residues: 260 sheet: 0.59 (0.21), residues: 572 loop : -0.55 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 132 PHE 0.030 0.002 PHE E 158 TYR 0.017 0.002 TYR H 162 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 561) hydrogen bonds : angle 6.75457 ( 1407) SS BOND : bond 0.00200 ( 13) SS BOND : angle 1.15104 ( 26) covalent geometry : bond 0.00409 (15340) covalent geometry : angle 0.66244 (20787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 248 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: B 85 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7893 (mt) REVERT: B 106 GLN cc_start: 0.8545 (mp10) cc_final: 0.8325 (mp10) REVERT: C 8 GLN cc_start: 0.7639 (mt0) cc_final: 0.7371 (mt0) REVERT: C 50 LYS cc_start: 0.8857 (mmmt) cc_final: 0.8639 (mmtt) REVERT: C 74 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7343 (mptt) REVERT: D 27 LYS cc_start: 0.7240 (mmtp) cc_final: 0.6941 (mmmm) REVERT: D 50 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8388 (ptpp) REVERT: D 52 MET cc_start: 0.7624 (mmm) cc_final: 0.7158 (mtp) REVERT: D 128 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6851 (pm20) REVERT: F 106 GLN cc_start: 0.7845 (mp10) cc_final: 0.7520 (mp10) REVERT: G 8 GLN cc_start: 0.8229 (mt0) cc_final: 0.7571 (mt0) REVERT: G 27 LYS cc_start: 0.7268 (mmmt) cc_final: 0.6644 (mmmm) REVERT: G 52 MET cc_start: 0.8040 (mmm) cc_final: 0.7790 (mmt) REVERT: G 133 TYR cc_start: 0.9225 (m-80) cc_final: 0.9018 (m-80) REVERT: H 13 PHE cc_start: 0.8508 (m-80) cc_final: 0.8058 (m-80) REVERT: H 33 ILE cc_start: 0.9310 (mp) cc_final: 0.9107 (mm) REVERT: H 52 MET cc_start: 0.7471 (mtp) cc_final: 0.7064 (mtt) REVERT: I 27 LYS cc_start: 0.7618 (mmtt) cc_final: 0.6807 (mmmm) REVERT: I 52 MET cc_start: 0.7479 (mpp) cc_final: 0.7148 (mpp) REVERT: I 54 LEU cc_start: 0.8837 (mm) cc_final: 0.8589 (mm) REVERT: J 74 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7412 (mptt) REVERT: J 128 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7578 (mm-30) REVERT: K 73 LYS cc_start: 0.6447 (mttt) cc_final: 0.6134 (mttt) REVERT: L 40 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8119 (ttmt) REVERT: L 52 MET cc_start: 0.7655 (mpp) cc_final: 0.7296 (mmm) REVERT: M 148 THR cc_start: 0.8743 (m) cc_final: 0.8340 (p) outliers start: 66 outliers final: 30 residues processed: 290 average time/residue: 0.2616 time to fit residues: 111.8283 Evaluate side-chains 210 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 30.0000 chunk 91 optimal weight: 50.0000 chunk 44 optimal weight: 50.0000 chunk 41 optimal weight: 20.0000 chunk 177 optimal weight: 40.0000 chunk 152 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 105 optimal weight: 30.0000 chunk 168 optimal weight: 20.0000 chunk 150 optimal weight: 50.0000 chunk 151 optimal weight: 30.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.049073 restraints weight = 72043.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.050439 restraints weight = 41962.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.051333 restraints weight = 28176.957| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 1.0343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 15353 Z= 0.297 Angle : 0.747 9.999 20813 Z= 0.386 Chirality : 0.046 0.167 2431 Planarity : 0.004 0.027 2782 Dihedral : 7.040 72.628 2145 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.96 % Allowed : 15.57 % Favored : 79.47 % 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: -0.75 (0.17), residues: 2093 helix: -1.25 (0.32), residues: 182 sheet: 0.31 (0.21), residues: 585 loop : -0.76 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 132 PHE 0.024 0.002 PHE E 158 TYR 0.015 0.002 TYR F 133 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 561) hydrogen bonds : angle 7.13128 ( 1407) SS BOND : bond 0.00249 ( 13) SS BOND : angle 1.41022 ( 26) covalent geometry : bond 0.00664 (15340) covalent geometry : angle 0.74618 (20787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 150 time to evaluate : 1.567 Fit side-chains REVERT: A 52 MET cc_start: 0.7821 (mmm) cc_final: 0.7212 (mtp) REVERT: B 57 GLU cc_start: 0.8727 (tt0) cc_final: 0.7948 (tm-30) REVERT: B 58 LEU cc_start: 0.8640 (mt) cc_final: 0.8305 (mm) REVERT: B 85 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7852 (mt) REVERT: B 148 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8546 (p) REVERT: C 8 GLN cc_start: 0.8013 (mt0) cc_final: 0.7611 (mt0) REVERT: C 52 MET cc_start: 0.7786 (mpp) cc_final: 0.7227 (mpp) REVERT: C 74 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7358 (mtmm) REVERT: F 106 GLN cc_start: 0.7899 (mp10) cc_final: 0.7618 (mp10) REVERT: G 52 MET cc_start: 0.8154 (mmm) cc_final: 0.7905 (mmt) REVERT: G 54 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8321 (mm) REVERT: I 40 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7912 (ttmp) REVERT: I 52 MET cc_start: 0.7623 (mpp) cc_final: 0.7235 (mpp) REVERT: J 128 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7456 (mm-30) REVERT: J 149 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6428 (tm-30) REVERT: K 73 LYS cc_start: 0.5994 (mttt) cc_final: 0.5516 (mttt) outliers start: 80 outliers final: 50 residues processed: 214 average time/residue: 0.2272 time to fit residues: 75.7019 Evaluate side-chains 181 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 147 optimal weight: 7.9990 chunk 148 optimal weight: 30.0000 chunk 145 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 170 optimal weight: 30.0000 chunk 150 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 59 optimal weight: 0.9990 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.059185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.049453 restraints weight = 71686.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.050881 restraints weight = 42200.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.051808 restraints weight = 28655.360| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 1.0560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15353 Z= 0.164 Angle : 0.613 11.353 20813 Z= 0.308 Chirality : 0.044 0.161 2431 Planarity : 0.003 0.027 2782 Dihedral : 6.427 73.289 2145 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.03 % Allowed : 17.31 % Favored : 78.66 % 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: -0.64 (0.17), residues: 2093 helix: -1.29 (0.33), residues: 182 sheet: 0.42 (0.21), residues: 585 loop : -0.68 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 89 PHE 0.023 0.002 PHE E 158 TYR 0.009 0.001 TYR L 162 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 561) hydrogen bonds : angle 6.53630 ( 1407) SS BOND : bond 0.00075 ( 13) SS BOND : angle 0.80498 ( 26) covalent geometry : bond 0.00369 (15340) covalent geometry : angle 0.61236 (20787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 152 time to evaluate : 1.802 Fit side-chains REVERT: B 85 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7759 (mt) REVERT: C 8 GLN cc_start: 0.7878 (mt0) cc_final: 0.7476 (mt0) REVERT: C 74 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7375 (mtmm) REVERT: F 106 GLN cc_start: 0.7850 (mp10) cc_final: 0.7517 (mp10) REVERT: G 52 MET cc_start: 0.8050 (mmm) cc_final: 0.7753 (mmt) REVERT: G 54 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8268 (mm) REVERT: H 40 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8624 (tttm) REVERT: I 52 MET cc_start: 0.7441 (mpp) cc_final: 0.7102 (mpp) REVERT: I 54 LEU cc_start: 0.8818 (mm) cc_final: 0.8504 (mm) REVERT: J 128 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7424 (mm-30) REVERT: J 149 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6627 (tm-30) REVERT: K 70 ASN cc_start: 0.5634 (t0) cc_final: 0.5334 (t0) REVERT: K 73 LYS cc_start: 0.6529 (mttt) cc_final: 0.5943 (mttt) REVERT: L 43 LEU cc_start: 0.9226 (mm) cc_final: 0.9018 (mm) REVERT: L 44 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8244 (tp30) outliers start: 65 outliers final: 42 residues processed: 200 average time/residue: 0.2569 time to fit residues: 80.1662 Evaluate side-chains 174 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 62 optimal weight: 50.0000 chunk 90 optimal weight: 50.0000 chunk 92 optimal weight: 20.0000 chunk 103 optimal weight: 40.0000 chunk 133 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 79 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 chunk 9 optimal weight: 40.0000 chunk 74 optimal weight: 40.0000 chunk 169 optimal weight: 50.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.048523 restraints weight = 72858.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.049877 restraints weight = 43595.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.050761 restraints weight = 30006.356| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 1.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15353 Z= 0.237 Angle : 0.678 12.220 20813 Z= 0.343 Chirality : 0.044 0.139 2431 Planarity : 0.003 0.029 2782 Dihedral : 6.600 68.897 2145 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.96 % Allowed : 17.62 % Favored : 77.42 % 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: -0.79 (0.17), residues: 2093 helix: -1.51 (0.32), residues: 182 sheet: 0.35 (0.22), residues: 585 loop : -0.78 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 89 PHE 0.021 0.002 PHE E 158 TYR 0.010 0.002 TYR F 133 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 561) hydrogen bonds : angle 6.77671 ( 1407) SS BOND : bond 0.00180 ( 13) SS BOND : angle 1.09253 ( 26) covalent geometry : bond 0.00533 (15340) covalent geometry : angle 0.67721 (20787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 136 time to evaluate : 1.876 Fit side-chains revert: symmetry clash REVERT: B 85 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7670 (mt) REVERT: C 74 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7685 (mptt) REVERT: D 152 PHE cc_start: 0.6403 (OUTLIER) cc_final: 0.5164 (m-80) REVERT: F 106 GLN cc_start: 0.7983 (mp10) cc_final: 0.7665 (mp10) REVERT: G 52 MET cc_start: 0.8047 (mmm) cc_final: 0.7725 (mmt) REVERT: G 54 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8332 (mm) REVERT: H 40 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8639 (tttm) REVERT: I 40 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7862 (ttmp) REVERT: I 52 MET cc_start: 0.7544 (mpp) cc_final: 0.7174 (mpp) REVERT: I 54 LEU cc_start: 0.8852 (mm) cc_final: 0.8569 (mm) REVERT: J 73 LYS cc_start: 0.7023 (mtpt) cc_final: 0.6756 (mtmm) REVERT: J 128 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7450 (mm-30) REVERT: J 149 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6817 (tm-30) REVERT: L 44 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8317 (tp30) REVERT: M 52 MET cc_start: 0.7579 (mmm) cc_final: 0.6690 (mtt) outliers start: 80 outliers final: 57 residues processed: 201 average time/residue: 0.2195 time to fit residues: 70.0190 Evaluate side-chains 186 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 122 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 154 optimal weight: 50.0000 chunk 66 optimal weight: 6.9990 chunk 95 optimal weight: 40.0000 chunk 128 optimal weight: 40.0000 chunk 116 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 chunk 195 optimal weight: 10.0000 chunk 109 optimal weight: 50.0000 chunk 13 optimal weight: 8.9990 chunk 39 optimal weight: 50.0000 chunk 12 optimal weight: 10.0000 overall best weight: 13.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.049073 restraints weight = 72540.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.050464 restraints weight = 42680.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.051347 restraints weight = 28800.120| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 1.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15353 Z= 0.206 Angle : 0.648 12.003 20813 Z= 0.326 Chirality : 0.044 0.138 2431 Planarity : 0.003 0.027 2782 Dihedral : 6.329 67.374 2145 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.90 % Allowed : 17.80 % Favored : 77.30 % 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: -0.82 (0.17), residues: 2093 helix: -1.52 (0.32), residues: 182 sheet: 0.33 (0.22), residues: 585 loop : -0.81 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 132 PHE 0.020 0.002 PHE E 158 TYR 0.008 0.001 TYR F 133 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 561) hydrogen bonds : angle 6.59754 ( 1407) SS BOND : bond 0.00192 ( 13) SS BOND : angle 0.94559 ( 26) covalent geometry : bond 0.00464 (15340) covalent geometry : angle 0.64708 (20787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 121 time to evaluate : 1.759 Fit side-chains REVERT: B 85 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7653 (mt) REVERT: C 30 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7830 (p0) REVERT: C 52 MET cc_start: 0.7747 (mpp) cc_final: 0.7504 (mmt) REVERT: C 74 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7670 (mtmm) REVERT: D 152 PHE cc_start: 0.6272 (OUTLIER) cc_final: 0.4987 (m-80) REVERT: F 106 GLN cc_start: 0.7958 (mp10) cc_final: 0.7534 (mp10) REVERT: G 52 MET cc_start: 0.8031 (mmm) cc_final: 0.7702 (mmt) REVERT: G 54 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8290 (mm) REVERT: H 40 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8591 (tttm) REVERT: I 40 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7864 (ttmp) REVERT: I 52 MET cc_start: 0.7472 (mpp) cc_final: 0.7098 (mpp) REVERT: I 54 LEU cc_start: 0.8829 (mm) cc_final: 0.8532 (mm) REVERT: J 73 LYS cc_start: 0.6967 (mtpt) cc_final: 0.6668 (mtmm) REVERT: J 128 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7391 (mm-30) REVERT: J 149 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6955 (tm-30) REVERT: L 44 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: M 52 MET cc_start: 0.7597 (mmm) cc_final: 0.6820 (mtt) outliers start: 79 outliers final: 60 residues processed: 187 average time/residue: 0.2213 time to fit residues: 65.5514 Evaluate side-chains 180 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 112 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 40 LYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 78 LYS Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 21 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 201 optimal weight: 30.0000 chunk 25 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.050411 restraints weight = 71695.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.051854 restraints weight = 42185.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.052711 restraints weight = 28318.554| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 1.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15353 Z= 0.119 Angle : 0.589 13.571 20813 Z= 0.289 Chirality : 0.043 0.130 2431 Planarity : 0.003 0.024 2782 Dihedral : 5.865 69.902 2145 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.41 % Allowed : 19.48 % Favored : 77.11 % 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: -0.51 (0.17), residues: 2093 helix: -1.12 (0.28), residues: 260 sheet: 0.46 (0.22), residues: 585 loop : -0.51 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 132 PHE 0.019 0.001 PHE E 158 TYR 0.008 0.001 TYR L 162 Details of bonding type rmsd hydrogen bonds : bond 0.02650 ( 561) hydrogen bonds : angle 6.16255 ( 1407) SS BOND : bond 0.00089 ( 13) SS BOND : angle 0.65483 ( 26) covalent geometry : bond 0.00272 (15340) covalent geometry : angle 0.58849 (20787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 143 time to evaluate : 1.751 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8483 (tp) cc_final: 0.8274 (tt) REVERT: B 85 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7641 (mt) REVERT: C 8 GLN cc_start: 0.7968 (mt0) cc_final: 0.7539 (mt0) REVERT: C 74 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7938 (mtmm) REVERT: D 152 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.5004 (m-80) REVERT: F 106 GLN cc_start: 0.7831 (mp10) cc_final: 0.7495 (mp10) REVERT: G 54 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8138 (mm) REVERT: I 52 MET cc_start: 0.7364 (mpp) cc_final: 0.7117 (mpp) REVERT: I 54 LEU cc_start: 0.8777 (mm) cc_final: 0.8421 (mm) REVERT: J 128 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7444 (mm-30) REVERT: L 44 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8247 (tp30) REVERT: M 52 MET cc_start: 0.7479 (mmm) cc_final: 0.6714 (mtt) outliers start: 55 outliers final: 43 residues processed: 187 average time/residue: 0.2278 time to fit residues: 67.5479 Evaluate side-chains 170 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 118 GLU Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 181 optimal weight: 30.0000 chunk 126 optimal weight: 10.0000 chunk 133 optimal weight: 30.0000 chunk 145 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 50.0000 chunk 165 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 186 optimal weight: 50.0000 chunk 79 optimal weight: 7.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.058913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049832 restraints weight = 71605.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.051245 restraints weight = 41753.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.052106 restraints weight = 28003.049| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 1.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15353 Z= 0.154 Angle : 0.614 13.575 20813 Z= 0.302 Chirality : 0.043 0.130 2431 Planarity : 0.003 0.024 2782 Dihedral : 5.936 70.543 2145 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.54 % Allowed : 19.42 % Favored : 77.05 % 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: -0.40 (0.18), residues: 2093 helix: -1.13 (0.29), residues: 260 sheet: 0.61 (0.21), residues: 637 loop : -0.51 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 132 PHE 0.021 0.002 PHE M 158 TYR 0.008 0.001 TYR L 162 Details of bonding type rmsd hydrogen bonds : bond 0.02830 ( 561) hydrogen bonds : angle 6.26510 ( 1407) SS BOND : bond 0.00127 ( 13) SS BOND : angle 0.80113 ( 26) covalent geometry : bond 0.00352 (15340) covalent geometry : angle 0.61341 (20787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 116 time to evaluate : 1.712 Fit side-chains REVERT: B 85 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7685 (mt) REVERT: C 74 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7770 (mtmm) REVERT: D 152 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.4877 (m-80) REVERT: F 106 GLN cc_start: 0.7870 (mp10) cc_final: 0.7549 (mp10) REVERT: G 54 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8130 (mm) REVERT: I 52 MET cc_start: 0.7425 (mpp) cc_final: 0.7146 (mpp) REVERT: J 128 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7483 (mm-30) REVERT: M 52 MET cc_start: 0.7628 (mmm) cc_final: 0.6828 (mtt) outliers start: 57 outliers final: 48 residues processed: 162 average time/residue: 0.2363 time to fit residues: 62.4173 Evaluate side-chains 163 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 111 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 118 GLU Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 108 optimal weight: 30.0000 chunk 126 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 33 optimal weight: 40.0000 chunk 103 optimal weight: 50.0000 chunk 75 optimal weight: 30.0000 chunk 14 optimal weight: 40.0000 chunk 119 optimal weight: 30.0000 chunk 106 optimal weight: 50.0000 chunk 109 optimal weight: 8.9990 overall best weight: 10.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.058986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.049628 restraints weight = 71666.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051036 restraints weight = 42446.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051901 restraints weight = 28863.317| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 1.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15353 Z= 0.180 Angle : 0.645 18.577 20813 Z= 0.317 Chirality : 0.044 0.164 2431 Planarity : 0.003 0.029 2782 Dihedral : 6.016 67.393 2145 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.47 % Allowed : 19.79 % Favored : 76.74 % 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: -0.37 (0.17), residues: 2093 helix: -1.16 (0.29), residues: 260 sheet: 0.83 (0.21), residues: 611 loop : -0.57 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 89 PHE 0.025 0.002 PHE M 158 TYR 0.008 0.001 TYR L 162 Details of bonding type rmsd hydrogen bonds : bond 0.02973 ( 561) hydrogen bonds : angle 6.39708 ( 1407) SS BOND : bond 0.00164 ( 13) SS BOND : angle 0.87862 ( 26) covalent geometry : bond 0.00410 (15340) covalent geometry : angle 0.64503 (20787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4186 Ramachandran restraints generated. 2093 Oldfield, 0 Emsley, 2093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 113 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7664 (mt) REVERT: C 30 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7912 (p0) REVERT: D 152 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5066 (m-80) REVERT: F 106 GLN cc_start: 0.7958 (mp10) cc_final: 0.7572 (mp10) REVERT: G 54 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8163 (mm) REVERT: I 52 MET cc_start: 0.7432 (mpp) cc_final: 0.7144 (mpp) REVERT: J 128 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7496 (mm-30) REVERT: M 52 MET cc_start: 0.7681 (mmm) cc_final: 0.6891 (mtt) outliers start: 56 outliers final: 49 residues processed: 159 average time/residue: 0.2005 time to fit residues: 52.2002 Evaluate side-chains 162 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 106 GLN Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 152 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 152 PHE Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 152 PHE Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 118 GLU Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 82 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 152 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 11 optimal weight: 50.0000 chunk 202 optimal weight: 40.0000 chunk 1 optimal weight: 8.9990 chunk 170 optimal weight: 40.0000 chunk 22 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 40.0000 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 50.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 ASN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.051392 restraints weight = 71175.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.052828 restraints weight = 41683.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053735 restraints weight = 27964.193| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 1.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15353 Z= 0.104 Angle : 0.601 16.661 20813 Z= 0.290 Chirality : 0.043 0.127 2431 Planarity : 0.003 0.028 2782 Dihedral : 5.482 66.451 2145 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.79 % Allowed : 20.41 % Favored : 76.80 % 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: -0.31 (0.18), residues: 2093 helix: -1.31 (0.29), residues: 260 sheet: 0.70 (0.21), residues: 637 loop : -0.40 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 132 PHE 0.028 0.001 PHE M 158 TYR 0.007 0.001 TYR B 162 Details of bonding type rmsd hydrogen bonds : bond 0.02431 ( 561) hydrogen bonds : angle 5.97858 ( 1407) SS BOND : bond 0.00093 ( 13) SS BOND : angle 0.62885 ( 26) covalent geometry : bond 0.00239 (15340) covalent geometry : angle 0.60099 (20787) =============================================================================== Job complete usr+sys time: 3931.90 seconds wall clock time: 70 minutes 26.82 seconds (4226.82 seconds total)