Starting phenix.real_space_refine on Tue Jul 29 15:29:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lmw_0922/07_2025/6lmw_0922.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lmw_0922/07_2025/6lmw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6lmw_0922/07_2025/6lmw_0922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lmw_0922/07_2025/6lmw_0922.map" model { file = "/net/cci-nas-00/data/ceres_data/6lmw_0922/07_2025/6lmw_0922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lmw_0922/07_2025/6lmw_0922.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D, G, F, H Time building chain proxies: 3.99, per 1000 atoms: 0.34 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 C 41 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.04 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 160 " distance=2.02 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 160 " distance=2.02 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 160 " distance=2.02 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 160 " distance=2.02 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 160 " distance=2.02 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 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: 3.21 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.64 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: 4.74 Time building geometry restraints manager: 3.28 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain '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: 112.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 28.500 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (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 TRP 0.012 0.002 TRP F 62 PHE 0.009 0.002 PHE A 68 TYR 0.008 0.002 TYR D 34 ARG 0.008 0.001 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.19676 ( 793) hydrogen bonds : angle 8.36568 ( 2355) SS BOND : bond 0.00663 ( 16) SS BOND : angle 1.52383 ( 32) covalent geometry : bond 0.00663 (11904) covalent geometry : angle 0.91239 (16120) *********************** 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 : 2.475 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: 0.7719 (ttt) REVERT: A 192 MET cc_start: 0.6773 (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: 0.7985 (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: 0.7751 (t80) REVERT: H 192 MET cc_start: 0.6403 (ttp) cc_final: 0.6109 (ttt) outliers start: 8 outliers final: 8 residues processed: 244 average time/residue: 0.3271 time to fit residues: 120.9707 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 : 1.326 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.0370 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.187343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.138908 restraints weight = 12790.064| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.74 r_work: 0.3304 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11920 Z= 0.116 Angle : 0.605 7.815 16152 Z= 0.294 Chirality : 0.036 0.105 1840 Planarity : 0.006 0.057 1984 Dihedral : 4.286 15.706 1600 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.89 % Allowed : 11.08 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.19), residues: 1456 helix: -0.66 (0.14), residues: 1024 sheet: None (None), residues: 0 loop : -1.40 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 62 PHE 0.010 0.001 PHE D 68 TYR 0.012 0.001 TYR B 34 ARG 0.002 0.000 ARG G 83 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 793) hydrogen bonds : angle 4.27373 ( 2355) SS BOND : bond 0.00274 ( 16) SS BOND : angle 0.84578 ( 32) covalent geometry : bond 0.00257 (11904) covalent geometry : angle 0.60412 (16120) *********************** 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 : 1.147 Fit side-chains REVERT: A 46 GLU cc_start: 0.8340 (mp0) cc_final: 0.8002 (mp0) REVERT: A 48 ASN cc_start: 0.8267 (m-40) cc_final: 0.7962 (m110) REVERT: A 157 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7584 (mtp85) REVERT: A 187 MET cc_start: 0.8756 (mmp) cc_final: 0.8495 (mmt) REVERT: A 192 MET cc_start: 0.7907 (ttp) cc_final: 0.7568 (ttt) REVERT: B 104 GLN cc_start: 0.8105 (mp10) cc_final: 0.7746 (mp10) REVERT: B 153 LYS cc_start: 0.8936 (mttt) cc_final: 0.8289 (mtpp) REVERT: B 157 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7380 (mtp85) REVERT: B 192 MET cc_start: 0.7654 (ttp) cc_final: 0.7262 (ttt) REVERT: C 46 GLU cc_start: 0.8330 (mp0) cc_final: 0.7994 (mp0) REVERT: C 48 ASN cc_start: 0.8262 (m-40) cc_final: 0.7951 (m110) REVERT: C 157 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7590 (mtp85) REVERT: C 187 MET cc_start: 0.8772 (mmp) cc_final: 0.8511 (mmt) REVERT: C 192 MET cc_start: 0.7916 (ttp) cc_final: 0.7580 (ttt) REVERT: D 104 GLN cc_start: 0.8113 (mp10) cc_final: 0.7757 (mp10) REVERT: D 153 LYS cc_start: 0.8949 (mttt) cc_final: 0.8315 (mtpp) REVERT: D 157 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7371 (mtp85) REVERT: D 192 MET cc_start: 0.7639 (ttp) cc_final: 0.7244 (ttt) REVERT: E 46 GLU cc_start: 0.8332 (mp0) cc_final: 0.7996 (mp0) REVERT: E 48 ASN cc_start: 0.8270 (m-40) cc_final: 0.7963 (m110) REVERT: E 157 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7591 (mtp85) REVERT: E 187 MET cc_start: 0.8775 (mmp) cc_final: 0.8513 (mmt) REVERT: E 192 MET cc_start: 0.7900 (ttp) cc_final: 0.7568 (ttt) REVERT: F 104 GLN cc_start: 0.8115 (mp10) cc_final: 0.7758 (mp10) REVERT: F 153 LYS cc_start: 0.8944 (mttt) cc_final: 0.8307 (mtpp) REVERT: F 157 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7374 (mtp85) REVERT: F 192 MET cc_start: 0.7658 (ttp) cc_final: 0.7265 (ttt) REVERT: G 46 GLU cc_start: 0.8328 (mp0) cc_final: 0.7996 (mp0) REVERT: G 48 ASN cc_start: 0.8262 (m-40) cc_final: 0.7958 (m110) REVERT: G 157 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7599 (mtp85) REVERT: G 187 MET cc_start: 0.8770 (mmp) cc_final: 0.8508 (mmt) REVERT: G 192 MET cc_start: 0.7895 (ttp) cc_final: 0.7559 (ttt) REVERT: H 104 GLN cc_start: 0.8102 (mp10) cc_final: 0.7743 (mp10) REVERT: H 153 LYS cc_start: 0.8927 (mttt) cc_final: 0.8281 (mtpp) REVERT: H 157 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7371 (mtp85) REVERT: H 192 MET cc_start: 0.7672 (ttp) cc_final: 0.7280 (ttt) outliers start: 24 outliers final: 14 residues processed: 232 average time/residue: 0.3136 time to fit residues: 102.5433 Evaluate side-chains 225 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 119 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 119 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain G residue 119 MET 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 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 66 optimal weight: 0.0020 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 72 optimal weight: 10.0000 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.200695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.154377 restraints weight = 12586.384| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.69 r_work: 0.3378 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11920 Z= 0.105 Angle : 0.571 7.756 16152 Z= 0.269 Chirality : 0.035 0.110 1840 Planarity : 0.005 0.054 1984 Dihedral : 3.815 12.539 1592 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.46 % Allowed : 11.71 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1456 helix: 0.97 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.01 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 186 PHE 0.005 0.001 PHE E 68 TYR 0.012 0.001 TYR A 34 ARG 0.001 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 793) hydrogen bonds : angle 3.66201 ( 2355) SS BOND : bond 0.00240 ( 16) SS BOND : angle 0.56874 ( 32) covalent geometry : bond 0.00237 (11904) covalent geometry : angle 0.57052 (16120) *********************** 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 260 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 1.293 Fit side-chains REVERT: A 46 GLU cc_start: 0.8322 (mp0) cc_final: 0.7989 (mp0) REVERT: A 150 GLU cc_start: 0.8765 (mp0) cc_final: 0.8465 (mp0) REVERT: A 187 MET cc_start: 0.8717 (mmp) cc_final: 0.8502 (mmt) REVERT: A 192 MET cc_start: 0.7912 (ttp) cc_final: 0.7578 (ttt) REVERT: B 153 LYS cc_start: 0.8934 (mttt) cc_final: 0.8705 (mttm) REVERT: B 192 MET cc_start: 0.7748 (ttp) cc_final: 0.7407 (ttt) REVERT: C 46 GLU cc_start: 0.8322 (mp0) cc_final: 0.7994 (mp0) REVERT: C 150 GLU cc_start: 0.8772 (mp0) cc_final: 0.8472 (mp0) REVERT: C 187 MET cc_start: 0.8730 (mmp) cc_final: 0.8516 (mmt) REVERT: C 192 MET cc_start: 0.7938 (ttp) cc_final: 0.7601 (ttt) REVERT: D 153 LYS cc_start: 0.8938 (mttt) cc_final: 0.8712 (mttm) REVERT: D 192 MET cc_start: 0.7754 (ttp) cc_final: 0.7412 (ttt) REVERT: E 46 GLU cc_start: 0.8336 (mp0) cc_final: 0.8001 (mp0) REVERT: E 150 GLU cc_start: 0.8798 (mp0) cc_final: 0.8483 (mp0) REVERT: E 187 MET cc_start: 0.8793 (mmp) cc_final: 0.8584 (mmt) REVERT: E 192 MET cc_start: 0.7937 (ttp) cc_final: 0.7613 (ttt) REVERT: F 153 LYS cc_start: 0.8942 (mttt) cc_final: 0.8719 (mttm) REVERT: F 192 MET cc_start: 0.7760 (ttp) cc_final: 0.7419 (ttt) REVERT: G 46 GLU cc_start: 0.8323 (mp0) cc_final: 0.7983 (mp0) REVERT: G 150 GLU cc_start: 0.8775 (mp0) cc_final: 0.8480 (mp0) REVERT: G 187 MET cc_start: 0.8720 (mmp) cc_final: 0.8507 (mmt) REVERT: G 192 MET cc_start: 0.7951 (ttp) cc_final: 0.7622 (ttt) REVERT: H 153 LYS cc_start: 0.8968 (mttt) cc_final: 0.8736 (mttm) REVERT: H 192 MET cc_start: 0.7764 (ttp) cc_final: 0.7424 (ttt) outliers start: 44 outliers final: 14 residues processed: 236 average time/residue: 0.2391 time to fit residues: 80.1854 Evaluate side-chains 215 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 65 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 65 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 65 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 48 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 84 optimal weight: 0.0970 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.200870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.152968 restraints weight = 12491.936| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.17 r_work: 0.3429 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11920 Z= 0.101 Angle : 0.556 7.629 16152 Z= 0.259 Chirality : 0.036 0.109 1840 Planarity : 0.005 0.051 1984 Dihedral : 3.609 11.015 1592 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.46 % Allowed : 12.81 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.22), residues: 1456 helix: 1.60 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -1.02 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 62 PHE 0.004 0.001 PHE E 64 TYR 0.010 0.001 TYR B 34 ARG 0.001 0.000 ARG G 157 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 793) hydrogen bonds : angle 3.43390 ( 2355) SS BOND : bond 0.00233 ( 16) SS BOND : angle 0.54985 ( 32) covalent geometry : bond 0.00231 (11904) covalent geometry : angle 0.55591 (16120) *********************** 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 264 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 1.335 Fit side-chains REVERT: A 46 GLU cc_start: 0.8205 (mp0) cc_final: 0.7901 (mp0) REVERT: A 55 LEU cc_start: 0.8460 (tp) cc_final: 0.8136 (tp) REVERT: A 192 MET cc_start: 0.7667 (ttp) cc_final: 0.7389 (ttt) REVERT: B 152 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8958 (mm) REVERT: B 192 MET cc_start: 0.7306 (ttp) cc_final: 0.6968 (ttt) REVERT: C 46 GLU cc_start: 0.8197 (mp0) cc_final: 0.7877 (mp0) REVERT: C 55 LEU cc_start: 0.8465 (tp) cc_final: 0.8141 (tp) REVERT: C 192 MET cc_start: 0.7666 (ttp) cc_final: 0.7385 (ttt) REVERT: D 152 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8973 (mm) REVERT: D 192 MET cc_start: 0.7296 (ttp) cc_final: 0.6955 (ttt) REVERT: E 46 GLU cc_start: 0.8215 (mp0) cc_final: 0.7893 (mp0) REVERT: E 55 LEU cc_start: 0.8472 (tp) cc_final: 0.8155 (tp) REVERT: E 192 MET cc_start: 0.7690 (ttp) cc_final: 0.7418 (ttt) REVERT: F 152 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8975 (mm) REVERT: F 192 MET cc_start: 0.7324 (ttp) cc_final: 0.6985 (ttt) REVERT: G 46 GLU cc_start: 0.8204 (mp0) cc_final: 0.7890 (mp0) REVERT: G 55 LEU cc_start: 0.8461 (tp) cc_final: 0.8142 (tp) REVERT: G 192 MET cc_start: 0.7681 (ttp) cc_final: 0.7405 (ttt) REVERT: H 152 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8948 (mm) REVERT: H 153 LYS cc_start: 0.8880 (mttt) cc_final: 0.8299 (mtpp) REVERT: H 192 MET cc_start: 0.7312 (ttp) cc_final: 0.6977 (ttt) outliers start: 44 outliers final: 26 residues processed: 238 average time/residue: 0.2673 time to fit residues: 89.8728 Evaluate side-chains 233 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain B residue 65 LEU 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 169 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain D residue 65 LEU 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 65 LEU 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 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 65 LEU 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 141 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 135 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 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 = 0.4169 r_free = 0.4169 target = 0.200841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.155366 restraints weight = 12428.049| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.73 r_work: 0.3343 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2383 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= 0.112 Angle : 0.575 7.585 16152 Z= 0.267 Chirality : 0.036 0.112 1840 Planarity : 0.005 0.052 1984 Dihedral : 3.584 11.729 1592 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.40 % Allowed : 12.11 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.22), residues: 1456 helix: 1.82 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -1.05 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 62 PHE 0.005 0.001 PHE E 64 TYR 0.010 0.001 TYR B 34 ARG 0.005 0.000 ARG G 157 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 793) hydrogen bonds : angle 3.39519 ( 2355) SS BOND : bond 0.00267 ( 16) SS BOND : angle 0.60785 ( 32) covalent geometry : bond 0.00268 (11904) covalent geometry : angle 0.57501 (16120) *********************** 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 264 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 1.170 Fit side-chains REVERT: A 46 GLU cc_start: 0.8391 (mp0) cc_final: 0.8059 (mp0) REVERT: A 55 LEU cc_start: 0.8428 (tp) cc_final: 0.8114 (tp) REVERT: A 192 MET cc_start: 0.7934 (ttp) cc_final: 0.7618 (ttt) REVERT: B 152 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9009 (mm) REVERT: B 157 ARG cc_start: 0.7874 (mtp85) cc_final: 0.7495 (mtm-85) REVERT: B 192 MET cc_start: 0.7611 (ttp) cc_final: 0.7265 (ttt) REVERT: C 46 GLU cc_start: 0.8384 (mp0) cc_final: 0.8054 (mp0) REVERT: C 55 LEU cc_start: 0.8436 (tp) cc_final: 0.8119 (tp) REVERT: C 192 MET cc_start: 0.7972 (ttp) cc_final: 0.7653 (ttt) REVERT: D 152 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9025 (mm) REVERT: D 157 ARG cc_start: 0.7874 (mtp85) cc_final: 0.7511 (mtm-85) REVERT: D 192 MET cc_start: 0.7581 (ttp) cc_final: 0.7236 (ttt) REVERT: E 46 GLU cc_start: 0.8389 (mp0) cc_final: 0.8049 (mp0) REVERT: E 55 LEU cc_start: 0.8432 (tp) cc_final: 0.8117 (tp) REVERT: E 192 MET cc_start: 0.7990 (ttp) cc_final: 0.7668 (ttt) REVERT: F 152 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9001 (mm) REVERT: F 157 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7512 (mtm-85) REVERT: F 192 MET cc_start: 0.7585 (ttp) cc_final: 0.7240 (ttt) REVERT: G 46 GLU cc_start: 0.8401 (mp0) cc_final: 0.8073 (mp0) REVERT: G 55 LEU cc_start: 0.8442 (tp) cc_final: 0.8123 (tp) REVERT: G 192 MET cc_start: 0.7965 (ttp) cc_final: 0.7638 (ttt) REVERT: H 152 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8956 (mm) REVERT: H 157 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7501 (mtp85) REVERT: H 192 MET cc_start: 0.7649 (ttp) cc_final: 0.7303 (ttt) outliers start: 56 outliers final: 36 residues processed: 234 average time/residue: 0.2272 time to fit residues: 75.9353 Evaluate side-chains 244 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 119 MET 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 65 LEU Chi-restraints excluded: chain B residue 152 LEU 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 119 MET 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 65 LEU Chi-restraints excluded: chain D residue 152 LEU 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 119 MET 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 65 LEU Chi-restraints excluded: chain F residue 152 LEU 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 119 MET 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 65 LEU Chi-restraints excluded: chain H residue 152 LEU 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 25 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 111 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.189593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.138267 restraints weight = 12924.745| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.10 r_work: 0.3297 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11920 Z= 0.120 Angle : 0.580 7.523 16152 Z= 0.270 Chirality : 0.037 0.114 1840 Planarity : 0.005 0.052 1984 Dihedral : 3.581 12.176 1592 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.30 % Allowed : 15.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.22), residues: 1456 helix: 1.94 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -0.96 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 186 PHE 0.005 0.001 PHE G 63 TYR 0.011 0.001 TYR B 34 ARG 0.005 0.000 ARG G 157 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 793) hydrogen bonds : angle 3.38107 ( 2355) SS BOND : bond 0.00318 ( 16) SS BOND : angle 0.67242 ( 32) covalent geometry : bond 0.00293 (11904) covalent geometry : angle 0.58002 (16120) *********************** 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 251 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 1.144 Fit side-chains REVERT: A 46 GLU cc_start: 0.8457 (mp0) cc_final: 0.8063 (mp0) REVERT: A 55 LEU cc_start: 0.8569 (tp) cc_final: 0.8238 (tp) REVERT: A 192 MET cc_start: 0.7880 (ttp) cc_final: 0.7542 (ttt) REVERT: B 104 GLN cc_start: 0.8113 (mp10) cc_final: 0.7704 (mp10) REVERT: B 157 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7395 (mtm-85) REVERT: B 192 MET cc_start: 0.7547 (ttp) cc_final: 0.7211 (ttt) REVERT: C 46 GLU cc_start: 0.8458 (mp0) cc_final: 0.8061 (mp0) REVERT: C 55 LEU cc_start: 0.8574 (tp) cc_final: 0.8239 (tp) REVERT: C 146 MET cc_start: 0.5087 (OUTLIER) cc_final: 0.4581 (mtp) REVERT: C 192 MET cc_start: 0.7896 (ttp) cc_final: 0.7554 (ttt) REVERT: D 46 GLU cc_start: 0.8414 (mp0) cc_final: 0.8211 (mp0) REVERT: D 104 GLN cc_start: 0.8135 (mp10) cc_final: 0.7729 (mp10) REVERT: D 157 ARG cc_start: 0.7858 (mtp85) cc_final: 0.7403 (mtm-85) REVERT: D 192 MET cc_start: 0.7514 (ttp) cc_final: 0.7178 (ttt) REVERT: E 46 GLU cc_start: 0.8439 (mp0) cc_final: 0.8034 (mp0) REVERT: E 55 LEU cc_start: 0.8573 (tp) cc_final: 0.8240 (tp) REVERT: E 146 MET cc_start: 0.5081 (OUTLIER) cc_final: 0.4573 (mtp) REVERT: E 192 MET cc_start: 0.7888 (ttp) cc_final: 0.7553 (ttt) REVERT: F 104 GLN cc_start: 0.8143 (mp10) cc_final: 0.7736 (mp10) REVERT: F 157 ARG cc_start: 0.7873 (mtp85) cc_final: 0.7420 (mtm-85) REVERT: F 192 MET cc_start: 0.7500 (ttp) cc_final: 0.7162 (ttt) REVERT: G 46 GLU cc_start: 0.8433 (mp0) cc_final: 0.8020 (mp0) REVERT: G 55 LEU cc_start: 0.8574 (tp) cc_final: 0.8242 (tp) REVERT: G 192 MET cc_start: 0.7871 (ttp) cc_final: 0.7534 (ttt) REVERT: H 46 GLU cc_start: 0.8445 (mp0) cc_final: 0.8240 (mp0) REVERT: H 104 GLN cc_start: 0.8130 (mp10) cc_final: 0.7722 (mp10) REVERT: H 192 MET cc_start: 0.7575 (ttp) cc_final: 0.7239 (ttt) outliers start: 42 outliers final: 38 residues processed: 227 average time/residue: 0.2280 time to fit residues: 73.8850 Evaluate side-chains 245 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 119 MET 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 65 LEU 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 119 MET Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 146 MET 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 65 LEU 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 119 MET Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 146 MET 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 65 LEU 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 119 MET 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 65 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 50 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 6 optimal weight: 0.0370 chunk 37 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.201472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.155069 restraints weight = 12616.128| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.66 r_work: 0.3451 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2587 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= 0.103 Angle : 0.567 7.549 16152 Z= 0.262 Chirality : 0.036 0.110 1840 Planarity : 0.005 0.051 1984 Dihedral : 3.494 12.098 1592 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.40 % Allowed : 15.64 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.22), residues: 1456 helix: 2.04 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -0.96 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 62 PHE 0.004 0.001 PHE H 154 TYR 0.008 0.001 TYR D 34 ARG 0.005 0.000 ARG G 157 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 793) hydrogen bonds : angle 3.32858 ( 2355) SS BOND : bond 0.00248 ( 16) SS BOND : angle 0.53747 ( 32) covalent geometry : bond 0.00243 (11904) covalent geometry : angle 0.56680 (16120) *********************** 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 270 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 1.888 Fit side-chains REVERT: A 46 GLU cc_start: 0.8168 (mp0) cc_final: 0.7891 (mp0) REVERT: A 55 LEU cc_start: 0.8344 (tp) cc_final: 0.8048 (tp) REVERT: A 146 MET cc_start: 0.5005 (OUTLIER) cc_final: 0.4494 (mtp) REVERT: A 192 MET cc_start: 0.7641 (ttp) cc_final: 0.7322 (ttt) REVERT: B 157 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7442 (mtm-85) REVERT: B 192 MET cc_start: 0.7519 (ttp) cc_final: 0.7202 (ttt) REVERT: C 46 GLU cc_start: 0.8166 (mp0) cc_final: 0.7884 (mp0) REVERT: C 55 LEU cc_start: 0.8341 (tp) cc_final: 0.8046 (tp) REVERT: C 146 MET cc_start: 0.4865 (OUTLIER) cc_final: 0.4329 (mtp) REVERT: C 192 MET cc_start: 0.7696 (ttp) cc_final: 0.7376 (ttt) REVERT: D 157 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7454 (mtm-85) REVERT: D 192 MET cc_start: 0.7472 (ttp) cc_final: 0.7165 (ttt) REVERT: E 46 GLU cc_start: 0.8174 (mp0) cc_final: 0.7871 (mp0) REVERT: E 55 LEU cc_start: 0.8338 (tp) cc_final: 0.8042 (tp) REVERT: E 146 MET cc_start: 0.4866 (OUTLIER) cc_final: 0.4325 (mtp) REVERT: E 192 MET cc_start: 0.7693 (ttp) cc_final: 0.7369 (ttt) REVERT: F 157 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7467 (mtm-85) REVERT: F 192 MET cc_start: 0.7446 (ttp) cc_final: 0.7133 (ttt) REVERT: G 46 GLU cc_start: 0.8170 (mp0) cc_final: 0.7870 (mp0) REVERT: G 55 LEU cc_start: 0.8344 (tp) cc_final: 0.8046 (tp) REVERT: G 146 MET cc_start: 0.5022 (OUTLIER) cc_final: 0.4523 (mtp) REVERT: G 192 MET cc_start: 0.7659 (ttp) cc_final: 0.7336 (ttt) REVERT: H 192 MET cc_start: 0.7508 (ttp) cc_final: 0.7193 (ttt) outliers start: 56 outliers final: 35 residues processed: 242 average time/residue: 0.2965 time to fit residues: 104.9667 Evaluate side-chains 253 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 146 MET 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 65 LEU 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 146 MET 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 65 LEU 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 146 MET 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 65 LEU 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 119 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 146 MET 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 65 LEU 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 51 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.201503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.160408 restraints weight = 12540.781| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.40 r_work: 0.3409 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2656 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= 0.107 Angle : 0.574 7.520 16152 Z= 0.266 Chirality : 0.036 0.111 1840 Planarity : 0.005 0.051 1984 Dihedral : 3.483 11.417 1592 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.62 % Allowed : 16.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.22), residues: 1456 helix: 2.06 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -0.93 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 62 PHE 0.005 0.001 PHE B 154 TYR 0.009 0.001 TYR F 34 ARG 0.005 0.000 ARG C 157 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 793) hydrogen bonds : angle 3.32427 ( 2355) SS BOND : bond 0.00255 ( 16) SS BOND : angle 0.55879 ( 32) covalent geometry : bond 0.00254 (11904) covalent geometry : angle 0.57446 (16120) *********************** 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 265 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 1.322 Fit side-chains REVERT: A 46 GLU cc_start: 0.8211 (mp0) cc_final: 0.7876 (mp0) REVERT: A 55 LEU cc_start: 0.8382 (tp) cc_final: 0.8079 (tp) REVERT: A 146 MET cc_start: 0.5056 (OUTLIER) cc_final: 0.4538 (mtp) REVERT: A 192 MET cc_start: 0.7831 (ttp) cc_final: 0.7493 (ttt) REVERT: B 104 GLN cc_start: 0.7933 (mp10) cc_final: 0.7627 (mp10) REVERT: B 157 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7448 (mtm-85) REVERT: B 192 MET cc_start: 0.7499 (ttp) cc_final: 0.7161 (ttt) REVERT: C 46 GLU cc_start: 0.8209 (mp0) cc_final: 0.7870 (mp0) REVERT: C 55 LEU cc_start: 0.8383 (tp) cc_final: 0.8079 (tp) REVERT: C 146 MET cc_start: 0.4963 (OUTLIER) cc_final: 0.4409 (mtp) REVERT: C 192 MET cc_start: 0.7869 (ttp) cc_final: 0.7529 (ttt) REVERT: D 104 GLN cc_start: 0.7944 (mp10) cc_final: 0.7641 (mp10) REVERT: D 157 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7455 (mtm-85) REVERT: D 192 MET cc_start: 0.7465 (ttp) cc_final: 0.7126 (ttt) REVERT: E 46 GLU cc_start: 0.8152 (mp0) cc_final: 0.7833 (mp0) REVERT: E 55 LEU cc_start: 0.8383 (tp) cc_final: 0.8084 (tp) REVERT: E 146 MET cc_start: 0.4956 (OUTLIER) cc_final: 0.4393 (mtp) REVERT: E 192 MET cc_start: 0.7846 (ttp) cc_final: 0.7515 (ttt) REVERT: F 104 GLN cc_start: 0.7956 (mp10) cc_final: 0.7656 (mp10) REVERT: F 157 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7465 (mtm-85) REVERT: F 192 MET cc_start: 0.7431 (ttp) cc_final: 0.7103 (ttt) REVERT: G 46 GLU cc_start: 0.8148 (mp0) cc_final: 0.7828 (mp0) REVERT: G 55 LEU cc_start: 0.8387 (tp) cc_final: 0.8082 (tp) REVERT: G 146 MET cc_start: 0.5096 (OUTLIER) cc_final: 0.4583 (mtp) REVERT: G 192 MET cc_start: 0.7841 (ttp) cc_final: 0.7506 (ttt) REVERT: H 104 GLN cc_start: 0.7949 (mp10) cc_final: 0.7649 (mp10) REVERT: H 192 MET cc_start: 0.7501 (ttp) cc_final: 0.7171 (ttt) outliers start: 46 outliers final: 37 residues processed: 237 average time/residue: 0.2211 time to fit residues: 75.7183 Evaluate side-chains 259 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 146 MET 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 65 LEU 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 146 MET 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 65 LEU 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 146 MET 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 65 LEU 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 146 MET 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 65 LEU 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 62 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 134 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.200708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.152171 restraints weight = 12626.486| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.74 r_work: 0.3332 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2715 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= 0.106 Angle : 0.574 7.514 16152 Z= 0.266 Chirality : 0.036 0.111 1840 Planarity : 0.005 0.051 1984 Dihedral : 3.464 10.917 1592 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.69 % Allowed : 15.96 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.22), residues: 1456 helix: 2.10 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -0.92 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 62 PHE 0.004 0.001 PHE E 154 TYR 0.009 0.001 TYR D 34 ARG 0.005 0.000 ARG G 157 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 793) hydrogen bonds : angle 3.31625 ( 2355) SS BOND : bond 0.00251 ( 16) SS BOND : angle 0.56597 ( 32) covalent geometry : bond 0.00253 (11904) covalent geometry : angle 0.57412 (16120) *********************** 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 263 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 1.291 Fit side-chains REVERT: A 46 GLU cc_start: 0.8274 (mp0) cc_final: 0.7928 (mp0) REVERT: A 55 LEU cc_start: 0.8430 (tp) cc_final: 0.8124 (tp) REVERT: A 146 MET cc_start: 0.5121 (OUTLIER) cc_final: 0.4591 (mtp) REVERT: A 192 MET cc_start: 0.7945 (ttp) cc_final: 0.7600 (ttt) REVERT: B 104 GLN cc_start: 0.7968 (mp10) cc_final: 0.7622 (mp10) REVERT: B 157 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7472 (mtm-85) REVERT: B 192 MET cc_start: 0.7742 (ttp) cc_final: 0.7405 (ttt) REVERT: C 46 GLU cc_start: 0.8281 (mp0) cc_final: 0.7929 (mp0) REVERT: C 55 LEU cc_start: 0.8432 (tp) cc_final: 0.8125 (tp) REVERT: C 146 MET cc_start: 0.5049 (OUTLIER) cc_final: 0.4458 (mtp) REVERT: C 192 MET cc_start: 0.7981 (ttp) cc_final: 0.7635 (ttt) REVERT: D 104 GLN cc_start: 0.7978 (mp10) cc_final: 0.7631 (mp10) REVERT: D 157 ARG cc_start: 0.7899 (mtp85) cc_final: 0.7479 (mtm-85) REVERT: D 192 MET cc_start: 0.7741 (ttp) cc_final: 0.7407 (ttt) REVERT: E 46 GLU cc_start: 0.8278 (mp0) cc_final: 0.7990 (mp0) REVERT: E 55 LEU cc_start: 0.8434 (tp) cc_final: 0.8126 (tp) REVERT: E 146 MET cc_start: 0.5030 (OUTLIER) cc_final: 0.4455 (mtp) REVERT: E 192 MET cc_start: 0.7974 (ttp) cc_final: 0.7634 (ttt) REVERT: F 104 GLN cc_start: 0.8094 (mp10) cc_final: 0.7733 (mp10) REVERT: F 157 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7486 (mtm-85) REVERT: F 192 MET cc_start: 0.7731 (ttp) cc_final: 0.7387 (ttt) REVERT: G 46 GLU cc_start: 0.8276 (mp0) cc_final: 0.7985 (mp0) REVERT: G 55 LEU cc_start: 0.8433 (tp) cc_final: 0.8129 (tp) REVERT: G 146 MET cc_start: 0.5142 (OUTLIER) cc_final: 0.4619 (mtp) REVERT: G 192 MET cc_start: 0.7959 (ttp) cc_final: 0.7616 (ttt) REVERT: H 104 GLN cc_start: 0.8091 (mp10) cc_final: 0.7730 (mp10) REVERT: H 192 MET cc_start: 0.7777 (ttp) cc_final: 0.7439 (ttt) outliers start: 47 outliers final: 34 residues processed: 238 average time/residue: 0.2228 time to fit residues: 76.5512 Evaluate side-chains 254 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 146 MET 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 65 LEU 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 130 ILE Chi-restraints excluded: chain C residue 146 MET 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 65 LEU 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 130 ILE Chi-restraints excluded: chain E residue 146 MET 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 65 LEU 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 130 ILE Chi-restraints excluded: chain G residue 146 MET 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 65 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 106 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.199616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.154067 restraints weight = 12505.428| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.99 r_work: 0.3304 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11920 Z= 0.120 Angle : 0.601 7.500 16152 Z= 0.278 Chirality : 0.037 0.114 1840 Planarity : 0.005 0.052 1984 Dihedral : 3.522 10.121 1592 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.22), residues: 1456 helix: 2.07 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -0.91 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 186 PHE 0.005 0.001 PHE B 154 TYR 0.011 0.001 TYR D 49 ARG 0.001 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 793) hydrogen bonds : angle 3.34765 ( 2355) SS BOND : bond 0.00286 ( 16) SS BOND : angle 0.66513 ( 32) covalent geometry : bond 0.00297 (11904) covalent geometry : angle 0.60076 (16120) ********************** 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 257 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 1.154 Fit side-chains REVERT: A 55 LEU cc_start: 0.8486 (tp) cc_final: 0.8166 (tp) REVERT: A 146 MET cc_start: 0.5158 (OUTLIER) cc_final: 0.4651 (mtp) REVERT: A 192 MET cc_start: 0.7849 (ttp) cc_final: 0.7542 (ttt) REVERT: B 157 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7445 (mtm-85) REVERT: B 192 MET cc_start: 0.7547 (ttp) cc_final: 0.7190 (ttt) REVERT: C 55 LEU cc_start: 0.8494 (tp) cc_final: 0.8172 (tp) REVERT: C 146 MET cc_start: 0.5225 (OUTLIER) cc_final: 0.4779 (mtp) REVERT: C 192 MET cc_start: 0.7890 (ttp) cc_final: 0.7582 (ttt) REVERT: D 157 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7452 (mtm-85) REVERT: D 192 MET cc_start: 0.7523 (ttp) cc_final: 0.7168 (ttt) REVERT: E 46 GLU cc_start: 0.8254 (mp0) cc_final: 0.7945 (mp0) REVERT: E 55 LEU cc_start: 0.8486 (tp) cc_final: 0.8166 (tp) REVERT: E 146 MET cc_start: 0.5227 (OUTLIER) cc_final: 0.4785 (mtp) REVERT: E 192 MET cc_start: 0.7873 (ttp) cc_final: 0.7571 (ttt) REVERT: F 157 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7462 (mtm-85) REVERT: F 192 MET cc_start: 0.7505 (ttp) cc_final: 0.7151 (ttt) REVERT: G 46 GLU cc_start: 0.8260 (mp0) cc_final: 0.7941 (mp0) REVERT: G 55 LEU cc_start: 0.8487 (tp) cc_final: 0.8163 (tp) REVERT: G 146 MET cc_start: 0.5175 (OUTLIER) cc_final: 0.4665 (mtp) REVERT: G 192 MET cc_start: 0.7853 (ttp) cc_final: 0.7554 (ttt) REVERT: H 157 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7249 (mtp85) REVERT: H 192 MET cc_start: 0.7572 (ttp) cc_final: 0.7219 (ttt) outliers start: 46 outliers final: 36 residues processed: 235 average time/residue: 0.2210 time to fit residues: 73.9707 Evaluate side-chains 243 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 146 MET 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 65 LEU 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 146 MET 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 65 LEU 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 130 ILE Chi-restraints excluded: chain E residue 146 MET 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 65 LEU 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 130 ILE Chi-restraints excluded: chain G residue 146 MET 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 65 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 162 ASP 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 92 optimal weight: 0.0980 chunk 75 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 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 = 0.4170 r_free = 0.4170 target = 0.200729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.151936 restraints weight = 12506.453| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.17 r_work: 0.3310 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2791 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= 0.109 Angle : 0.594 7.508 16152 Z= 0.274 Chirality : 0.036 0.116 1840 Planarity : 0.005 0.051 1984 Dihedral : 3.479 9.952 1592 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.62 % Allowed : 16.12 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.22), residues: 1456 helix: 2.15 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -0.86 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 62 PHE 0.005 0.001 PHE H 154 TYR 0.012 0.001 TYR H 49 ARG 0.007 0.000 ARG E 157 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 793) hydrogen bonds : angle 3.32482 ( 2355) SS BOND : bond 0.00242 ( 16) SS BOND : angle 0.55801 ( 32) covalent geometry : bond 0.00262 (11904) covalent geometry : angle 0.59360 (16120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6630.02 seconds wall clock time: 119 minutes 4.21 seconds (7144.21 seconds total)