Starting phenix.real_space_refine on Wed Mar 4 06:17:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lmw_0922/03_2026/6lmw_0922.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lmw_0922/03_2026/6lmw_0922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lmw_0922/03_2026/6lmw_0922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lmw_0922/03_2026/6lmw_0922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lmw_0922/03_2026/6lmw_0922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lmw_0922/03_2026/6lmw_0922.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 7608 2.51 5 N 1888 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11624 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 1.50, per 1000 atoms: 0.13 Number of scatterers: 11624 At special positions: 0 Unit cell: (125.823, 125.823, 87.6519, 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 136 16.00 O 1992 8.00 N 1888 7.00 C 7608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 160 " distance=2.02 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 160 " distance=2.02 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 160 " distance=2.02 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 160 " distance=2.02 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 160 " distance=2.02 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 160 " distance=2.02 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 160 " distance=2.02 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 160 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 526.1 milliseconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 77.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 21 through 37 Processing helix chain 'A' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.809A pdb=" N LEU A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE A 137 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 166 through 203 Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 73 through 83 removed outlier: 3.808A pdb=" N LEU B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.671A pdb=" N PHE B 137 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 166 through 203 Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 73 through 83 removed outlier: 3.809A pdb=" N LEU C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 166 through 203 Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 73 through 83 removed outlier: 3.809A pdb=" N LEU D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE D 137 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 166 through 203 Processing helix chain 'E' and resid 22 through 37 Processing helix chain 'E' and resid 47 through 70 removed outlier: 3.628A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 73 through 83 removed outlier: 3.810A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG E 83 " --> pdb=" O GLU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE E 137 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 166 through 203 Processing helix chain 'F' and resid 22 through 37 Processing helix chain 'F' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU F 56 " --> pdb=" O GLY F 52 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 73 through 83 removed outlier: 3.809A pdb=" N LEU F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE F 137 " --> pdb=" O ILE F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 166 through 203 Processing helix chain 'G' and resid 22 through 37 Processing helix chain 'G' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 73 through 83 removed outlier: 3.810A pdb=" N LEU G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 121 Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE G 137 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 166 through 203 Processing helix chain 'H' and resid 22 through 37 Processing helix chain 'H' and resid 47 through 70 removed outlier: 3.629A pdb=" N LEU H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.808A pdb=" N LEU H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG H 83 " --> pdb=" O GLU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 106 removed outlier: 3.859A pdb=" N LEU H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 121 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 133 through 137 removed outlier: 3.670A pdb=" N PHE H 137 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 156 Processing helix chain 'H' and resid 166 through 203 793 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3484 1.34 - 1.46: 2594 1.46 - 1.58: 5618 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 11904 Sorted by residual: bond pdb=" CB THR B 117 " pdb=" CG2 THR B 117 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB THR H 117 " pdb=" CG2 THR H 117 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB THR D 117 " pdb=" CG2 THR D 117 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB THR F 117 " pdb=" CG2 THR F 117 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" CB THR A 117 " pdb=" CG2 THR A 117 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 ... (remaining 11899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 15604 2.13 - 4.26: 420 4.26 - 6.39: 56 6.39 - 8.52: 16 8.52 - 10.66: 24 Bond angle restraints: 16120 Sorted by residual: angle pdb=" CA PRO E 59 " pdb=" C PRO E 59 " pdb=" N PRO E 60 " ideal model delta sigma weight residual 117.93 121.93 -4.00 1.20e+00 6.94e-01 1.11e+01 angle pdb=" CA PRO C 59 " pdb=" C PRO C 59 " pdb=" N PRO C 60 " ideal model delta sigma weight residual 117.93 121.93 -4.00 1.20e+00 6.94e-01 1.11e+01 angle pdb=" CA PRO A 59 " pdb=" C PRO A 59 " pdb=" N PRO A 60 " ideal model delta sigma weight residual 117.93 121.93 -4.00 1.20e+00 6.94e-01 1.11e+01 angle pdb=" CA PRO G 59 " pdb=" C PRO G 59 " pdb=" N PRO G 60 " ideal model delta sigma weight residual 117.93 121.93 -4.00 1.20e+00 6.94e-01 1.11e+01 angle pdb=" CA PRO B 59 " pdb=" C PRO B 59 " pdb=" N PRO B 60 " ideal model delta sigma weight residual 117.93 121.92 -3.99 1.20e+00 6.94e-01 1.11e+01 ... (remaining 16115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 6287 17.18 - 34.37: 729 34.37 - 51.55: 112 51.55 - 68.73: 16 68.73 - 85.91: 24 Dihedral angle restraints: 7168 sinusoidal: 2872 harmonic: 4296 Sorted by residual: dihedral pdb=" CB CYS F 43 " pdb=" SG CYS F 43 " pdb=" SG CYS F 160 " pdb=" CB CYS F 160 " ideal model delta sinusoidal sigma weight residual 93.00 120.01 -27.01 1 1.00e+01 1.00e-02 1.05e+01 dihedral pdb=" CB CYS H 43 " pdb=" SG CYS H 43 " pdb=" SG CYS H 160 " pdb=" CB CYS H 160 " ideal model delta sinusoidal sigma weight residual 93.00 120.01 -27.01 1 1.00e+01 1.00e-02 1.05e+01 dihedral pdb=" CB CYS A 43 " pdb=" SG CYS A 43 " pdb=" SG CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sinusoidal sigma weight residual 93.00 120.00 -27.00 1 1.00e+01 1.00e-02 1.05e+01 ... (remaining 7165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 861 0.030 - 0.060: 674 0.060 - 0.090: 201 0.090 - 0.120: 60 0.120 - 0.150: 44 Chirality restraints: 1840 Sorted by residual: chirality pdb=" CB VAL G 74 " pdb=" CA VAL G 74 " pdb=" CG1 VAL G 74 " pdb=" CG2 VAL G 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CB VAL A 74 " pdb=" CA VAL A 74 " pdb=" CG1 VAL A 74 " pdb=" CG2 VAL A 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CB VAL D 74 " pdb=" CA VAL D 74 " pdb=" CG1 VAL D 74 " pdb=" CG2 VAL D 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1837 not shown) Planarity restraints: 1984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 59 " -0.052 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO D 60 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 59 " -0.052 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO F 60 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 59 " 0.052 5.00e-02 4.00e+02 7.69e-02 9.45e+00 pdb=" N PRO B 60 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 60 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 60 " 0.044 5.00e-02 4.00e+02 ... (remaining 1981 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3467 2.81 - 3.33: 10472 3.33 - 3.86: 18446 3.86 - 4.38: 21314 4.38 - 4.90: 37158 Nonbonded interactions: 90857 Sorted by model distance: nonbonded pdb=" O LEU D 118 " pdb=" OG SER D 181 " model vdw 2.292 3.040 nonbonded pdb=" O LEU F 118 " pdb=" OG SER F 181 " model vdw 2.292 3.040 nonbonded pdb=" O LEU A 118 " pdb=" OG SER A 181 " model vdw 2.292 3.040 nonbonded pdb=" O LEU C 118 " pdb=" OG SER C 181 " model vdw 2.292 3.040 nonbonded pdb=" O LEU H 118 " pdb=" OG SER H 181 " model vdw 2.292 3.040 ... (remaining 90852 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.930 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 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 : 0.007 0.081 11920 Z= 0.260 Angle : 0.914 10.656 16152 Z= 0.480 Chirality : 0.047 0.150 1840 Planarity : 0.008 0.077 1984 Dihedral : 15.334 85.915 4336 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.63 % Allowed : 6.92 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.34 (0.13), residues: 1456 helix: -3.84 (0.07), residues: 992 sheet: None (None), residues: 0 loop : -2.24 (0.22), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 87 TYR 0.008 0.002 TYR D 34 PHE 0.009 0.002 PHE A 68 TRP 0.012 0.002 TRP F 62 Details of bonding type rmsd covalent geometry : bond 0.00663 (11904) covalent geometry : angle 0.91239 (16120) SS BOND : bond 0.00663 ( 16) SS BOND : angle 1.52383 ( 32) hydrogen bonds : bond 0.19676 ( 793) hydrogen bonds : angle 8.36568 ( 2355) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 236 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7967 (ttt) cc_final: 0.7718 (ttt) REVERT: A 192 MET cc_start: 0.6774 (ttp) cc_final: 0.6414 (ttt) REVERT: B 49 TYR cc_start: 0.8213 (t80) cc_final: 0.7986 (t80) REVERT: B 153 LYS cc_start: 0.8610 (mttt) cc_final: 0.7897 (mtpp) REVERT: B 176 TYR cc_start: 0.8062 (t80) cc_final: 0.7750 (t80) REVERT: B 192 MET cc_start: 0.6397 (ttp) cc_final: 0.6118 (ttt) REVERT: C 33 MET cc_start: 0.7967 (ttt) cc_final: 0.7694 (ttt) REVERT: C 192 MET cc_start: 0.6779 (ttp) cc_final: 0.6420 (ttt) REVERT: D 49 TYR cc_start: 0.8212 (t80) cc_final: 0.7988 (t80) REVERT: D 153 LYS cc_start: 0.8608 (mttt) cc_final: 0.7897 (mtpp) REVERT: D 176 TYR cc_start: 0.8068 (t80) cc_final: 0.7754 (t80) REVERT: D 192 MET cc_start: 0.6397 (ttp) cc_final: 0.6119 (ttt) REVERT: E 33 MET cc_start: 0.7968 (ttt) cc_final: 0.7693 (ttt) REVERT: E 192 MET cc_start: 0.6777 (ttp) cc_final: 0.6416 (ttt) REVERT: F 49 TYR cc_start: 0.8209 (t80) cc_final: 0.7986 (t80) REVERT: F 153 LYS cc_start: 0.8610 (mttt) cc_final: 0.7897 (mtpp) REVERT: F 176 TYR cc_start: 0.8073 (t80) cc_final: 0.7760 (t80) REVERT: F 192 MET cc_start: 0.6403 (ttp) cc_final: 0.6112 (ttt) REVERT: G 33 MET cc_start: 0.7968 (ttt) cc_final: 0.7720 (ttt) REVERT: G 192 MET cc_start: 0.6770 (ttp) cc_final: 0.6411 (ttt) REVERT: H 49 TYR cc_start: 0.8207 (t80) cc_final: 0.7984 (t80) REVERT: H 153 LYS cc_start: 0.8608 (mttt) cc_final: 0.7897 (mtpp) REVERT: H 176 TYR cc_start: 0.8064 (t80) cc_final: 0.7752 (t80) REVERT: H 192 MET cc_start: 0.6403 (ttp) cc_final: 0.6110 (ttt) outliers start: 8 outliers final: 8 residues processed: 244 average time/residue: 0.0913 time to fit residues: 33.5183 Evaluate side-chains 216 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN B 131 ASN C 71 ASN D 71 ASN D 131 ASN E 71 ASN F 71 ASN F 131 ASN G 71 ASN H 71 ASN H 131 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.186891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.138435 restraints weight = 12834.663| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.73 r_work: 0.3306 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11920 Z= 0.130 Angle : 0.614 7.780 16152 Z= 0.301 Chirality : 0.037 0.110 1840 Planarity : 0.006 0.058 1984 Dihedral : 4.342 15.865 1600 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.89 % Allowed : 12.11 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.19), residues: 1456 helix: -0.73 (0.14), residues: 1024 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 83 TYR 0.013 0.001 TYR B 34 PHE 0.010 0.001 PHE B 68 TRP 0.008 0.001 TRP C 62 Details of bonding type rmsd covalent geometry : bond 0.00294 (11904) covalent geometry : angle 0.61353 (16120) SS BOND : bond 0.00343 ( 16) SS BOND : angle 0.88344 ( 32) hydrogen bonds : bond 0.04077 ( 793) hydrogen bonds : angle 4.29585 ( 2355) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 0.416 Fit side-chains REVERT: A 48 ASN cc_start: 0.8335 (m-40) cc_final: 0.7993 (m110) REVERT: A 157 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7539 (mtp85) REVERT: A 187 MET cc_start: 0.8790 (mmp) cc_final: 0.8525 (mmt) REVERT: A 192 MET cc_start: 0.7880 (ttp) cc_final: 0.7529 (ttt) REVERT: B 104 GLN cc_start: 0.8097 (mp10) cc_final: 0.7734 (mp10) REVERT: B 153 LYS cc_start: 0.8917 (mttt) cc_final: 0.8263 (mtpp) REVERT: B 192 MET cc_start: 0.7641 (ttp) cc_final: 0.7243 (ttt) REVERT: C 48 ASN cc_start: 0.8335 (m-40) cc_final: 0.7989 (m110) REVERT: C 157 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7546 (mtp85) REVERT: C 187 MET cc_start: 0.8808 (mmp) cc_final: 0.8545 (mmt) REVERT: C 192 MET cc_start: 0.7904 (ttp) cc_final: 0.7553 (ttt) REVERT: D 104 GLN cc_start: 0.8108 (mp10) cc_final: 0.7749 (mp10) REVERT: D 153 LYS cc_start: 0.8930 (mttt) cc_final: 0.8286 (mtpp) REVERT: D 192 MET cc_start: 0.7639 (ttp) cc_final: 0.7238 (ttt) REVERT: E 48 ASN cc_start: 0.8346 (m-40) cc_final: 0.8001 (m110) REVERT: E 157 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7546 (mtp85) REVERT: E 187 MET cc_start: 0.8804 (mmp) cc_final: 0.8539 (mmt) REVERT: E 192 MET cc_start: 0.7887 (ttp) cc_final: 0.7544 (ttt) REVERT: F 104 GLN cc_start: 0.8113 (mp10) cc_final: 0.7753 (mp10) REVERT: F 153 LYS cc_start: 0.8933 (mttt) cc_final: 0.8290 (mtpp) REVERT: F 192 MET cc_start: 0.7651 (ttp) cc_final: 0.7251 (ttt) REVERT: G 48 ASN cc_start: 0.8337 (m-40) cc_final: 0.7993 (m110) REVERT: G 157 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7553 (mtp85) REVERT: G 187 MET cc_start: 0.8798 (mmp) cc_final: 0.8533 (mmt) REVERT: G 192 MET cc_start: 0.7892 (ttp) cc_final: 0.7544 (ttt) REVERT: H 104 GLN cc_start: 0.8102 (mp10) cc_final: 0.7740 (mp10) REVERT: H 153 LYS cc_start: 0.8916 (mttt) cc_final: 0.8266 (mtpp) REVERT: H 192 MET cc_start: 0.7659 (ttp) cc_final: 0.7262 (ttt) outliers start: 24 outliers final: 10 residues processed: 232 average time/residue: 0.1068 time to fit residues: 35.1036 Evaluate side-chains 222 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 199 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.187975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139876 restraints weight = 12868.192| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.73 r_work: 0.3308 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11920 Z= 0.112 Angle : 0.578 7.711 16152 Z= 0.272 Chirality : 0.036 0.112 1840 Planarity : 0.005 0.054 1984 Dihedral : 3.794 12.531 1592 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.77 % Allowed : 12.03 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1456 helix: 0.97 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -1.18 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 83 TYR 0.011 0.001 TYR B 34 PHE 0.005 0.001 PHE E 68 TRP 0.006 0.001 TRP F 62 Details of bonding type rmsd covalent geometry : bond 0.00259 (11904) covalent geometry : angle 0.57852 (16120) SS BOND : bond 0.00265 ( 16) SS BOND : angle 0.56274 ( 32) hydrogen bonds : bond 0.03437 ( 793) hydrogen bonds : angle 3.65966 ( 2355) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.413 Fit side-chains REVERT: A 150 GLU cc_start: 0.8843 (mp0) cc_final: 0.8467 (mp0) REVERT: A 187 MET cc_start: 0.8796 (mmp) cc_final: 0.8570 (mmt) REVERT: A 192 MET cc_start: 0.7946 (ttp) cc_final: 0.7622 (ttt) REVERT: B 153 LYS cc_start: 0.8943 (mttt) cc_final: 0.8316 (mtpp) REVERT: B 192 MET cc_start: 0.7637 (ttp) cc_final: 0.7293 (ttt) REVERT: C 150 GLU cc_start: 0.8824 (mp0) cc_final: 0.8456 (mp0) REVERT: C 187 MET cc_start: 0.8807 (mmp) cc_final: 0.8582 (mmt) REVERT: C 192 MET cc_start: 0.7974 (ttp) cc_final: 0.7645 (ttt) REVERT: D 107 LEU cc_start: 0.8547 (mt) cc_final: 0.8336 (mp) REVERT: D 153 LYS cc_start: 0.8948 (mttt) cc_final: 0.8328 (mtpp) REVERT: D 192 MET cc_start: 0.7613 (ttp) cc_final: 0.7267 (ttt) REVERT: E 46 GLU cc_start: 0.8348 (mp0) cc_final: 0.8110 (mp0) REVERT: E 150 GLU cc_start: 0.8847 (mp0) cc_final: 0.8466 (mp0) REVERT: E 187 MET cc_start: 0.8820 (mmp) cc_final: 0.8595 (mmt) REVERT: E 192 MET cc_start: 0.7968 (ttp) cc_final: 0.7649 (ttt) REVERT: F 107 LEU cc_start: 0.8557 (mt) cc_final: 0.8348 (mp) REVERT: F 153 LYS cc_start: 0.8958 (mttt) cc_final: 0.8340 (mtpp) REVERT: F 192 MET cc_start: 0.7641 (ttp) cc_final: 0.7296 (ttt) REVERT: G 46 GLU cc_start: 0.8346 (mp0) cc_final: 0.8106 (mp0) REVERT: G 150 GLU cc_start: 0.8840 (mp0) cc_final: 0.8462 (mp0) REVERT: G 187 MET cc_start: 0.8806 (mmp) cc_final: 0.8579 (mmt) REVERT: G 192 MET cc_start: 0.7955 (ttp) cc_final: 0.7634 (ttt) REVERT: H 107 LEU cc_start: 0.8543 (mt) cc_final: 0.8338 (mp) REVERT: H 153 LYS cc_start: 0.8938 (mttt) cc_final: 0.8315 (mtpp) REVERT: H 192 MET cc_start: 0.7659 (ttp) cc_final: 0.7317 (ttt) outliers start: 48 outliers final: 17 residues processed: 236 average time/residue: 0.1044 time to fit residues: 35.3449 Evaluate side-chains 217 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 169 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.188783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.138592 restraints weight = 12818.299| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.80 r_work: 0.3289 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11920 Z= 0.107 Angle : 0.564 7.628 16152 Z= 0.263 Chirality : 0.036 0.112 1840 Planarity : 0.005 0.053 1984 Dihedral : 3.630 11.250 1592 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.22 % Allowed : 13.60 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.22), residues: 1456 helix: 1.65 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -1.03 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 87 TYR 0.010 0.001 TYR B 34 PHE 0.005 0.001 PHE E 64 TRP 0.005 0.001 TRP D 62 Details of bonding type rmsd covalent geometry : bond 0.00253 (11904) covalent geometry : angle 0.56376 (16120) SS BOND : bond 0.00263 ( 16) SS BOND : angle 0.61130 ( 32) hydrogen bonds : bond 0.03230 ( 793) hydrogen bonds : angle 3.45773 ( 2355) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.267 Fit side-chains REVERT: A 46 GLU cc_start: 0.8332 (mp0) cc_final: 0.8083 (mp0) REVERT: A 55 LEU cc_start: 0.8607 (tp) cc_final: 0.8292 (tp) REVERT: A 150 GLU cc_start: 0.8854 (mp0) cc_final: 0.8484 (mp0) REVERT: A 192 MET cc_start: 0.7835 (ttp) cc_final: 0.7530 (ttt) REVERT: B 152 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8864 (mm) REVERT: B 153 LYS cc_start: 0.8836 (mttt) cc_final: 0.8200 (mtpp) REVERT: B 192 MET cc_start: 0.7529 (ttp) cc_final: 0.7220 (ttt) REVERT: C 46 GLU cc_start: 0.8326 (mp0) cc_final: 0.8079 (mp0) REVERT: C 55 LEU cc_start: 0.8615 (tp) cc_final: 0.8299 (tp) REVERT: C 150 GLU cc_start: 0.8827 (mp0) cc_final: 0.8462 (mp0) REVERT: C 192 MET cc_start: 0.7857 (ttp) cc_final: 0.7556 (ttt) REVERT: D 152 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8877 (mm) REVERT: D 153 LYS cc_start: 0.8845 (mttt) cc_final: 0.8214 (mtpp) REVERT: D 192 MET cc_start: 0.7501 (ttp) cc_final: 0.7189 (ttt) REVERT: E 46 GLU cc_start: 0.8434 (mp0) cc_final: 0.8134 (mp0) REVERT: E 55 LEU cc_start: 0.8610 (tp) cc_final: 0.8295 (tp) REVERT: E 107 LEU cc_start: 0.8563 (mt) cc_final: 0.8356 (mp) REVERT: E 150 GLU cc_start: 0.8853 (mp0) cc_final: 0.8469 (mp0) REVERT: E 192 MET cc_start: 0.7854 (ttp) cc_final: 0.7556 (ttt) REVERT: F 152 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8883 (mm) REVERT: F 153 LYS cc_start: 0.8852 (mttt) cc_final: 0.8222 (mtpp) REVERT: F 192 MET cc_start: 0.7513 (ttp) cc_final: 0.7199 (ttt) REVERT: G 46 GLU cc_start: 0.8434 (mp0) cc_final: 0.8136 (mp0) REVERT: G 55 LEU cc_start: 0.8609 (tp) cc_final: 0.8292 (tp) REVERT: G 107 LEU cc_start: 0.8555 (mt) cc_final: 0.8352 (mp) REVERT: G 150 GLU cc_start: 0.8869 (mp0) cc_final: 0.8482 (mp0) REVERT: G 192 MET cc_start: 0.7834 (ttp) cc_final: 0.7533 (ttt) REVERT: H 107 LEU cc_start: 0.8439 (mt) cc_final: 0.8214 (mp) REVERT: H 152 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8870 (mm) REVERT: H 153 LYS cc_start: 0.8840 (mttt) cc_final: 0.8208 (mtpp) REVERT: H 192 MET cc_start: 0.7547 (ttp) cc_final: 0.7232 (ttt) outliers start: 41 outliers final: 24 residues processed: 239 average time/residue: 0.0962 time to fit residues: 32.7399 Evaluate side-chains 228 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 169 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 124 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.186968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.137278 restraints weight = 12800.606| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.76 r_work: 0.3272 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11920 Z= 0.126 Angle : 0.591 7.556 16152 Z= 0.275 Chirality : 0.037 0.114 1840 Planarity : 0.005 0.052 1984 Dihedral : 3.643 11.559 1592 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.25 % Allowed : 14.15 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.22), residues: 1456 helix: 1.96 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.02 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 157 TYR 0.012 0.001 TYR B 34 PHE 0.006 0.001 PHE A 63 TRP 0.005 0.001 TRP A 186 Details of bonding type rmsd covalent geometry : bond 0.00308 (11904) covalent geometry : angle 0.59053 (16120) SS BOND : bond 0.00313 ( 16) SS BOND : angle 0.68677 ( 32) hydrogen bonds : bond 0.03283 ( 793) hydrogen bonds : angle 3.41896 ( 2355) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.403 Fit side-chains REVERT: A 150 GLU cc_start: 0.8862 (mp0) cc_final: 0.8459 (mp0) REVERT: A 192 MET cc_start: 0.7819 (ttp) cc_final: 0.7490 (ttt) REVERT: B 38 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: B 192 MET cc_start: 0.7478 (ttp) cc_final: 0.7176 (ttt) REVERT: C 150 GLU cc_start: 0.8844 (mp0) cc_final: 0.8439 (mp0) REVERT: C 192 MET cc_start: 0.7842 (ttp) cc_final: 0.7513 (ttt) REVERT: D 38 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: D 192 MET cc_start: 0.7453 (ttp) cc_final: 0.7150 (ttt) REVERT: E 46 GLU cc_start: 0.8435 (mp0) cc_final: 0.8124 (mp0) REVERT: E 150 GLU cc_start: 0.8860 (mp0) cc_final: 0.8446 (mp0) REVERT: E 192 MET cc_start: 0.7839 (ttp) cc_final: 0.7518 (ttt) REVERT: F 38 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: F 192 MET cc_start: 0.7457 (ttp) cc_final: 0.7155 (ttt) REVERT: G 46 GLU cc_start: 0.8430 (mp0) cc_final: 0.8119 (mp0) REVERT: G 150 GLU cc_start: 0.8863 (mp0) cc_final: 0.8450 (mp0) REVERT: G 192 MET cc_start: 0.7811 (ttp) cc_final: 0.7490 (ttt) REVERT: H 38 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: H 192 MET cc_start: 0.7498 (ttp) cc_final: 0.7198 (ttt) outliers start: 54 outliers final: 34 residues processed: 238 average time/residue: 0.1001 time to fit residues: 34.2411 Evaluate side-chains 235 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 169 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.193531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.143562 restraints weight = 12736.401| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.82 r_work: 0.3383 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11920 Z= 0.106 Angle : 0.571 7.546 16152 Z= 0.264 Chirality : 0.036 0.112 1840 Planarity : 0.005 0.052 1984 Dihedral : 3.522 11.031 1592 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.91 % Allowed : 15.80 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.22), residues: 1456 helix: 2.12 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -0.92 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 157 TYR 0.008 0.001 TYR A 34 PHE 0.004 0.001 PHE A 197 TRP 0.005 0.001 TRP D 62 Details of bonding type rmsd covalent geometry : bond 0.00251 (11904) covalent geometry : angle 0.57082 (16120) SS BOND : bond 0.00262 ( 16) SS BOND : angle 0.56819 ( 32) hydrogen bonds : bond 0.03062 ( 793) hydrogen bonds : angle 3.33456 ( 2355) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.371 Fit side-chains REVERT: A 46 GLU cc_start: 0.8328 (mp0) cc_final: 0.8093 (mp0) REVERT: A 55 LEU cc_start: 0.8522 (tp) cc_final: 0.8206 (tp) REVERT: A 150 GLU cc_start: 0.8779 (mp0) cc_final: 0.8513 (mp0) REVERT: A 192 MET cc_start: 0.7879 (ttp) cc_final: 0.7553 (ttt) REVERT: B 38 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: B 104 GLN cc_start: 0.8148 (mp10) cc_final: 0.7750 (mp10) REVERT: B 152 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8922 (mm) REVERT: B 157 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7415 (mtp85) REVERT: B 192 MET cc_start: 0.7488 (ttp) cc_final: 0.7178 (ttt) REVERT: C 46 GLU cc_start: 0.8330 (mp0) cc_final: 0.8088 (mp0) REVERT: C 55 LEU cc_start: 0.8522 (tp) cc_final: 0.8206 (tp) REVERT: C 150 GLU cc_start: 0.8771 (mp0) cc_final: 0.8509 (mp0) REVERT: C 192 MET cc_start: 0.7888 (ttp) cc_final: 0.7563 (ttt) REVERT: D 38 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: D 104 GLN cc_start: 0.8038 (mp10) cc_final: 0.7646 (mp10) REVERT: D 152 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8942 (mm) REVERT: D 157 ARG cc_start: 0.7793 (mtm-85) cc_final: 0.7426 (mtp85) REVERT: D 192 MET cc_start: 0.7469 (ttp) cc_final: 0.7158 (ttt) REVERT: E 46 GLU cc_start: 0.8457 (mp0) cc_final: 0.8158 (mp0) REVERT: E 55 LEU cc_start: 0.8523 (tp) cc_final: 0.8207 (tp) REVERT: E 150 GLU cc_start: 0.8772 (mp0) cc_final: 0.8498 (mp0) REVERT: E 192 MET cc_start: 0.7874 (ttp) cc_final: 0.7563 (ttt) REVERT: F 38 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: F 104 GLN cc_start: 0.8049 (mp10) cc_final: 0.7654 (mp10) REVERT: F 152 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8945 (mm) REVERT: F 157 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7439 (mtp85) REVERT: F 192 MET cc_start: 0.7467 (ttp) cc_final: 0.7158 (ttt) REVERT: G 46 GLU cc_start: 0.8451 (mp0) cc_final: 0.8151 (mp0) REVERT: G 55 LEU cc_start: 0.8525 (tp) cc_final: 0.8208 (tp) REVERT: G 150 GLU cc_start: 0.8782 (mp0) cc_final: 0.8507 (mp0) REVERT: G 192 MET cc_start: 0.7858 (ttp) cc_final: 0.7545 (ttt) REVERT: H 104 GLN cc_start: 0.8022 (mp10) cc_final: 0.7629 (mp10) REVERT: H 152 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8937 (mm) REVERT: H 157 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7422 (mtp85) REVERT: H 192 MET cc_start: 0.7504 (ttp) cc_final: 0.7194 (ttt) outliers start: 37 outliers final: 25 residues processed: 231 average time/residue: 0.1038 time to fit residues: 34.6041 Evaluate side-chains 230 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 169 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 80 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.193179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.143573 restraints weight = 12702.884| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.19 r_work: 0.3233 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11920 Z= 0.178 Angle : 0.636 7.507 16152 Z= 0.301 Chirality : 0.039 0.124 1840 Planarity : 0.005 0.054 1984 Dihedral : 3.776 12.215 1592 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 5.19 % Allowed : 15.33 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.22), residues: 1456 helix: 2.16 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -0.83 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 157 TYR 0.015 0.002 TYR H 34 PHE 0.007 0.001 PHE E 63 TRP 0.007 0.002 TRP A 186 Details of bonding type rmsd covalent geometry : bond 0.00450 (11904) covalent geometry : angle 0.63522 (16120) SS BOND : bond 0.00472 ( 16) SS BOND : angle 0.96026 ( 32) hydrogen bonds : bond 0.03535 ( 793) hydrogen bonds : angle 3.51385 ( 2355) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 0.449 Fit side-chains REVERT: A 46 GLU cc_start: 0.8149 (mp0) cc_final: 0.7918 (mp0) REVERT: A 150 GLU cc_start: 0.8785 (mp0) cc_final: 0.8287 (mp0) REVERT: A 192 MET cc_start: 0.7745 (ttp) cc_final: 0.7378 (ttt) REVERT: B 192 MET cc_start: 0.7374 (ttp) cc_final: 0.7024 (ttt) REVERT: C 46 GLU cc_start: 0.8157 (mp0) cc_final: 0.7916 (mp0) REVERT: C 150 GLU cc_start: 0.8772 (mp0) cc_final: 0.8275 (mp0) REVERT: C 192 MET cc_start: 0.7740 (ttp) cc_final: 0.7372 (ttt) REVERT: D 192 MET cc_start: 0.7374 (ttp) cc_final: 0.7022 (ttt) REVERT: E 46 GLU cc_start: 0.8282 (mp0) cc_final: 0.7990 (mp0) REVERT: E 150 GLU cc_start: 0.8770 (mp0) cc_final: 0.8281 (mp0) REVERT: E 192 MET cc_start: 0.7732 (ttp) cc_final: 0.7369 (ttt) REVERT: F 192 MET cc_start: 0.7367 (ttp) cc_final: 0.7018 (ttt) REVERT: G 46 GLU cc_start: 0.8275 (mp0) cc_final: 0.7988 (mp0) REVERT: G 150 GLU cc_start: 0.8796 (mp0) cc_final: 0.8293 (mp0) REVERT: G 192 MET cc_start: 0.7728 (ttp) cc_final: 0.7365 (ttt) REVERT: H 192 MET cc_start: 0.7407 (ttp) cc_final: 0.7058 (ttt) outliers start: 66 outliers final: 49 residues processed: 247 average time/residue: 0.1070 time to fit residues: 38.5440 Evaluate side-chains 240 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 CYS Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 49 optimal weight: 0.0170 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.199706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.151695 restraints weight = 12558.060| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.72 r_work: 0.3380 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11920 Z= 0.100 Angle : 0.569 7.526 16152 Z= 0.263 Chirality : 0.036 0.108 1840 Planarity : 0.005 0.051 1984 Dihedral : 3.538 11.403 1592 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.75 % Allowed : 17.22 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.22), residues: 1456 helix: 2.29 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -0.89 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 157 TYR 0.008 0.001 TYR A 34 PHE 0.005 0.001 PHE F 154 TRP 0.007 0.001 TRP C 62 Details of bonding type rmsd covalent geometry : bond 0.00227 (11904) covalent geometry : angle 0.56871 (16120) SS BOND : bond 0.00228 ( 16) SS BOND : angle 0.45828 ( 32) hydrogen bonds : bond 0.03051 ( 793) hydrogen bonds : angle 3.32808 ( 2355) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.466 Fit side-chains REVERT: A 46 GLU cc_start: 0.8171 (mp0) cc_final: 0.7949 (mp0) REVERT: A 192 MET cc_start: 0.7666 (ttp) cc_final: 0.7318 (ttt) REVERT: B 38 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: B 104 GLN cc_start: 0.7896 (mp10) cc_final: 0.7601 (mp10) REVERT: B 192 MET cc_start: 0.7243 (ttp) cc_final: 0.6914 (ttt) REVERT: C 46 GLU cc_start: 0.8167 (mp0) cc_final: 0.7937 (mp0) REVERT: C 192 MET cc_start: 0.7682 (ttp) cc_final: 0.7337 (ttt) REVERT: D 38 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: D 104 GLN cc_start: 0.7844 (mp10) cc_final: 0.7540 (mp10) REVERT: D 192 MET cc_start: 0.7235 (ttp) cc_final: 0.6920 (ttt) REVERT: E 46 GLU cc_start: 0.8305 (mp0) cc_final: 0.8031 (mp0) REVERT: E 192 MET cc_start: 0.7676 (ttp) cc_final: 0.7333 (ttt) REVERT: F 38 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: F 104 GLN cc_start: 0.7847 (mp10) cc_final: 0.7542 (mp10) REVERT: F 192 MET cc_start: 0.7223 (ttp) cc_final: 0.6909 (ttt) REVERT: G 46 GLU cc_start: 0.8304 (mp0) cc_final: 0.8029 (mp0) REVERT: G 192 MET cc_start: 0.7654 (ttp) cc_final: 0.7310 (ttt) REVERT: H 104 GLN cc_start: 0.7843 (mp10) cc_final: 0.7540 (mp10) REVERT: H 192 MET cc_start: 0.7249 (ttp) cc_final: 0.6930 (ttt) outliers start: 35 outliers final: 27 residues processed: 223 average time/residue: 0.0970 time to fit residues: 32.1231 Evaluate side-chains 227 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 169 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 101 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.189236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.137370 restraints weight = 12643.000| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.83 r_work: 0.3278 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11920 Z= 0.114 Angle : 0.583 7.513 16152 Z= 0.272 Chirality : 0.037 0.112 1840 Planarity : 0.005 0.053 1984 Dihedral : 3.586 14.590 1592 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.62 % Allowed : 16.59 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.22), residues: 1456 helix: 2.18 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -0.87 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 170 TYR 0.014 0.001 TYR C 49 PHE 0.005 0.001 PHE A 154 TRP 0.005 0.001 TRP E 186 Details of bonding type rmsd covalent geometry : bond 0.00273 (11904) covalent geometry : angle 0.58298 (16120) SS BOND : bond 0.00284 ( 16) SS BOND : angle 0.59421 ( 32) hydrogen bonds : bond 0.03104 ( 793) hydrogen bonds : angle 3.32769 ( 2355) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.511 Fit side-chains REVERT: A 46 GLU cc_start: 0.8330 (mp0) cc_final: 0.8071 (mp0) REVERT: A 192 MET cc_start: 0.7803 (ttp) cc_final: 0.7478 (ttt) REVERT: B 38 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: B 104 GLN cc_start: 0.7942 (mp10) cc_final: 0.7571 (mp10) REVERT: B 192 MET cc_start: 0.7420 (ttp) cc_final: 0.7098 (ttt) REVERT: C 46 GLU cc_start: 0.8325 (mp0) cc_final: 0.8061 (mp0) REVERT: C 192 MET cc_start: 0.7818 (ttp) cc_final: 0.7494 (ttt) REVERT: D 38 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: D 104 GLN cc_start: 0.7809 (mp10) cc_final: 0.7445 (mp10) REVERT: D 157 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7358 (mtp85) REVERT: D 192 MET cc_start: 0.7408 (ttp) cc_final: 0.7084 (ttt) REVERT: E 46 GLU cc_start: 0.8468 (mp0) cc_final: 0.8161 (mp0) REVERT: E 192 MET cc_start: 0.7811 (ttp) cc_final: 0.7492 (ttt) REVERT: F 38 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: F 104 GLN cc_start: 0.7825 (mp10) cc_final: 0.7460 (mp10) REVERT: F 157 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7365 (mtp85) REVERT: F 192 MET cc_start: 0.7423 (ttp) cc_final: 0.7096 (ttt) REVERT: G 46 GLU cc_start: 0.8462 (mp0) cc_final: 0.8153 (mp0) REVERT: G 192 MET cc_start: 0.7794 (ttp) cc_final: 0.7471 (ttt) REVERT: H 104 GLN cc_start: 0.7801 (mp10) cc_final: 0.7438 (mp10) REVERT: H 192 MET cc_start: 0.7459 (ttp) cc_final: 0.7135 (ttt) outliers start: 46 outliers final: 38 residues processed: 230 average time/residue: 0.1053 time to fit residues: 35.0037 Evaluate side-chains 239 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 125 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.197033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.153733 restraints weight = 12670.839| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.83 r_work: 0.3293 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11920 Z= 0.113 Angle : 0.595 7.531 16152 Z= 0.275 Chirality : 0.036 0.111 1840 Planarity : 0.005 0.052 1984 Dihedral : 3.564 10.893 1592 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.17 % Allowed : 16.04 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.22), residues: 1456 helix: 2.20 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -0.80 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 157 TYR 0.009 0.001 TYR H 34 PHE 0.005 0.001 PHE E 154 TRP 0.005 0.001 TRP C 62 Details of bonding type rmsd covalent geometry : bond 0.00272 (11904) covalent geometry : angle 0.59489 (16120) SS BOND : bond 0.00267 ( 16) SS BOND : angle 0.56665 ( 32) hydrogen bonds : bond 0.03058 ( 793) hydrogen bonds : angle 3.31780 ( 2355) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.433 Fit side-chains REVERT: A 46 GLU cc_start: 0.8315 (mp0) cc_final: 0.8090 (mp0) REVERT: A 192 MET cc_start: 0.7877 (ttp) cc_final: 0.7527 (ttt) REVERT: B 38 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: B 104 GLN cc_start: 0.8042 (mp10) cc_final: 0.7569 (mp10) REVERT: B 107 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7706 (mp) REVERT: B 192 MET cc_start: 0.7504 (ttp) cc_final: 0.7167 (ttt) REVERT: C 46 GLU cc_start: 0.8343 (mp0) cc_final: 0.8119 (mp0) REVERT: C 192 MET cc_start: 0.7918 (ttp) cc_final: 0.7572 (ttt) REVERT: D 38 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: D 157 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7463 (mtp85) REVERT: D 192 MET cc_start: 0.7487 (ttp) cc_final: 0.7144 (ttt) REVERT: E 46 GLU cc_start: 0.8445 (mp0) cc_final: 0.8164 (mp0) REVERT: E 192 MET cc_start: 0.7901 (ttp) cc_final: 0.7555 (ttt) REVERT: F 38 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: F 157 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7476 (mtp85) REVERT: F 192 MET cc_start: 0.7500 (ttp) cc_final: 0.7160 (ttt) REVERT: G 46 GLU cc_start: 0.8445 (mp0) cc_final: 0.8162 (mp0) REVERT: G 192 MET cc_start: 0.7884 (ttp) cc_final: 0.7536 (ttt) REVERT: H 192 MET cc_start: 0.7535 (ttp) cc_final: 0.7195 (ttt) outliers start: 53 outliers final: 44 residues processed: 229 average time/residue: 0.0921 time to fit residues: 31.9924 Evaluate side-chains 244 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 31 optimal weight: 0.0870 chunk 110 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.0030 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.201961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.154517 restraints weight = 12511.275| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.73 r_work: 0.3368 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11920 Z= 0.097 Angle : 0.574 7.467 16152 Z= 0.263 Chirality : 0.036 0.108 1840 Planarity : 0.005 0.051 1984 Dihedral : 3.411 10.452 1592 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.62 % Allowed : 16.98 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.23), residues: 1456 helix: 2.26 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -0.67 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 157 TYR 0.008 0.001 TYR A 176 PHE 0.004 0.001 PHE G 164 TRP 0.005 0.001 TRP F 62 Details of bonding type rmsd covalent geometry : bond 0.00217 (11904) covalent geometry : angle 0.57475 (16120) SS BOND : bond 0.00188 ( 16) SS BOND : angle 0.37832 ( 32) hydrogen bonds : bond 0.02844 ( 793) hydrogen bonds : angle 3.22775 ( 2355) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2802.50 seconds wall clock time: 48 minutes 42.60 seconds (2922.60 seconds total)