Starting phenix.real_space_refine on Sat Aug 23 09:40:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqc_34023/08_2025/7yqc_34023.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqc_34023/08_2025/7yqc_34023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yqc_34023/08_2025/7yqc_34023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqc_34023/08_2025/7yqc_34023.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqc_34023/08_2025/7yqc_34023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqc_34023/08_2025/7yqc_34023.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.056 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 28 5.16 5 C 7287 2.51 5 N 1939 2.21 5 O 2142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11396 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.99, per 1000 atoms: 0.26 Number of scatterers: 11396 At special positions: 0 Unit cell: (110.24, 112.32, 79.04, 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 28 16.00 O 2142 8.00 N 1939 7.00 C 7287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 396.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2744 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 45 removed outlier: 4.305A pdb=" N PHE A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 46 through 51 removed outlier: 6.514A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 142 removed outlier: 3.521A pdb=" N ILE A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 152 through 196 removed outlier: 3.515A pdb=" N LEU A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 238 removed outlier: 3.509A pdb=" N VAL A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'B' and resid 8 through 32 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.693A pdb=" N ILE B 58 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 142 removed outlier: 3.587A pdb=" N ILE B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 152 through 196 removed outlier: 3.545A pdb=" N TYR B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 238 removed outlier: 3.531A pdb=" N VAL B 206 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.531A pdb=" N LEU C 50 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 112 through 142 Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 152 through 196 removed outlier: 3.542A pdb=" N TYR C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 238 removed outlier: 3.545A pdb=" N ARG C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 206 " --> pdb=" O TYR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 54 through 58 Processing helix chain 'D' and resid 112 through 142 removed outlier: 3.540A pdb=" N ILE D 118 " --> pdb=" O GLN D 114 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 152 through 196 removed outlier: 3.538A pdb=" N TYR D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 238 removed outlier: 3.648A pdb=" N ARG D 204 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 206 " --> pdb=" O TYR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'E' and resid 8 through 45 removed outlier: 4.349A pdb=" N PHE E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix Processing helix chain 'E' and resid 46 through 51 removed outlier: 6.566A pdb=" N ILE E 49 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 142 removed outlier: 3.507A pdb=" N ASP E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 152 through 196 removed outlier: 3.529A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 238 removed outlier: 3.527A pdb=" N ARG E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL E 206 " --> pdb=" O TYR E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 244 Processing helix chain 'F' and resid 8 through 32 Processing helix chain 'F' and resid 32 through 45 Processing helix chain 'F' and resid 46 through 51 removed outlier: 6.598A pdb=" N ILE F 49 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 59 removed outlier: 3.720A pdb=" N HIS F 59 " --> pdb=" O THR F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 142 removed outlier: 3.587A pdb=" N ILE F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 152 through 196 removed outlier: 3.505A pdb=" N TYR F 183 " --> pdb=" O ILE F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 238 removed outlier: 3.571A pdb=" N VAL F 206 " --> pdb=" O TYR F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 244 Processing helix chain 'G' and resid 8 through 32 Processing helix chain 'G' and resid 32 through 45 Processing helix chain 'G' and resid 46 through 51 removed outlier: 6.624A pdb=" N ILE G 49 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 142 removed outlier: 3.537A pdb=" N LYS G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 152 through 196 removed outlier: 3.608A pdb=" N TYR G 183 " --> pdb=" O ILE G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 238 removed outlier: 3.547A pdb=" N VAL G 206 " --> pdb=" O TYR G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 244 932 hydrogen bonds defined for protein. 2733 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1946 1.31 - 1.43: 2639 1.43 - 1.56: 6916 1.56 - 1.68: 0 1.68 - 1.81: 49 Bond restraints: 11550 Sorted by residual: bond pdb=" C PRO F 35 " pdb=" O PRO F 35 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.26e-02 6.30e+03 2.08e+01 bond pdb=" C PRO E 35 " pdb=" O PRO E 35 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.26e-02 6.30e+03 1.76e+01 bond pdb=" CA ALA B 26 " pdb=" CB ALA B 26 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.55e+01 bond pdb=" CA ALA D 26 " pdb=" CB ALA D 26 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.53e+01 bond pdb=" C PRO E 245 " pdb=" O PRO E 245 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.26e-02 6.30e+03 1.53e+01 ... (remaining 11545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 12159 2.26 - 4.51: 3186 4.51 - 6.77: 184 6.77 - 9.02: 18 9.02 - 11.28: 21 Bond angle restraints: 15568 Sorted by residual: angle pdb=" N LYS C 110 " pdb=" CA LYS C 110 " pdb=" C LYS C 110 " ideal model delta sigma weight residual 110.43 120.87 -10.44 1.31e+00 5.83e-01 6.35e+01 angle pdb=" N LYS B 110 " pdb=" CA LYS B 110 " pdb=" C LYS B 110 " ideal model delta sigma weight residual 110.35 120.77 -10.42 1.36e+00 5.41e-01 5.88e+01 angle pdb=" N LYS G 110 " pdb=" CA LYS G 110 " pdb=" C LYS G 110 " ideal model delta sigma weight residual 110.35 120.71 -10.36 1.36e+00 5.41e-01 5.81e+01 angle pdb=" N LYS A 110 " pdb=" CA LYS A 110 " pdb=" C LYS A 110 " ideal model delta sigma weight residual 110.35 120.49 -10.14 1.36e+00 5.41e-01 5.56e+01 angle pdb=" N LYS F 110 " pdb=" CA LYS F 110 " pdb=" C LYS F 110 " ideal model delta sigma weight residual 110.35 119.95 -9.60 1.36e+00 5.41e-01 4.98e+01 ... (remaining 15563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 6258 17.28 - 34.56: 733 34.56 - 51.84: 210 51.84 - 69.12: 67 69.12 - 86.40: 5 Dihedral angle restraints: 7273 sinusoidal: 3108 harmonic: 4165 Sorted by residual: dihedral pdb=" C THR G 135 " pdb=" N THR G 135 " pdb=" CA THR G 135 " pdb=" CB THR G 135 " ideal model delta harmonic sigma weight residual -122.00 -136.46 14.46 0 2.50e+00 1.60e-01 3.34e+01 dihedral pdb=" C THR F 135 " pdb=" N THR F 135 " pdb=" CA THR F 135 " pdb=" CB THR F 135 " ideal model delta harmonic sigma weight residual -122.00 -135.76 13.76 0 2.50e+00 1.60e-01 3.03e+01 dihedral pdb=" C LEU A 109 " pdb=" N LEU A 109 " pdb=" CA LEU A 109 " pdb=" CB LEU A 109 " ideal model delta harmonic sigma weight residual -122.60 -135.76 13.16 0 2.50e+00 1.60e-01 2.77e+01 ... (remaining 7270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1073 0.106 - 0.212: 620 0.212 - 0.317: 124 0.317 - 0.423: 18 0.423 - 0.529: 13 Chirality restraints: 1848 Sorted by residual: chirality pdb=" CA LEU A 109 " pdb=" N LEU A 109 " pdb=" C LEU A 109 " pdb=" CB LEU A 109 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" CA LEU G 109 " pdb=" N LEU G 109 " pdb=" C LEU G 109 " pdb=" CB LEU G 109 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CA LEU E 109 " pdb=" N LEU E 109 " pdb=" C LEU E 109 " pdb=" CB LEU E 109 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.94e+00 ... (remaining 1845 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 241 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LYS D 241 " 0.058 2.00e-02 2.50e+03 pdb=" O LYS D 241 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE D 242 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 241 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C LYS E 241 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS E 241 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE E 242 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 241 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C LYS A 241 " 0.051 2.00e-02 2.50e+03 pdb=" O LYS A 241 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE A 242 " -0.017 2.00e-02 2.50e+03 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4801 2.98 - 3.46: 11707 3.46 - 3.94: 19805 3.94 - 4.42: 22196 4.42 - 4.90: 36558 Nonbonded interactions: 95067 Sorted by model distance: nonbonded pdb=" O ASP D 201 " pdb=" OG1 THR D 205 " model vdw 2.497 3.040 nonbonded pdb=" O PHE D 153 " pdb=" OG SER D 156 " model vdw 2.503 3.040 nonbonded pdb=" O PHE G 153 " pdb=" OG SER G 156 " model vdw 2.505 3.040 nonbonded pdb=" C SER B 24 " pdb=" OG SER B 24 " model vdw 2.505 2.616 nonbonded pdb=" O PHE E 153 " pdb=" OG SER E 156 " model vdw 2.516 3.040 ... (remaining 95062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.500 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.013 0.061 11550 Z= 1.019 Angle : 1.865 11.277 15568 Z= 1.424 Chirality : 0.128 0.529 1848 Planarity : 0.007 0.033 1953 Dihedral : 16.597 86.404 4529 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 9.34 % Allowed : 9.81 % Favored : 80.85 % Cbeta Deviations : 1.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.07 (0.18), residues: 1358 helix: 2.74 (0.13), residues: 1015 sheet: None (None), residues: 0 loop : -0.19 (0.26), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 21 TYR 0.021 0.003 TYR B 228 PHE 0.020 0.003 PHE C 33 TRP 0.015 0.003 TRP F 139 HIS 0.009 0.003 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.01346 (11550) covalent geometry : angle 1.86479 (15568) hydrogen bonds : bond 0.25808 ( 932) hydrogen bonds : angle 6.23858 ( 2733) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 132 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7543 (tt0) cc_final: 0.7322 (tt0) REVERT: A 178 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7156 (pt0) REVERT: A 240 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7309 (mp0) REVERT: B 149 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6303 (m-30) REVERT: B 223 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 234 MET cc_start: 0.7337 (tmt) cc_final: 0.7071 (tmm) REVERT: B 240 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7248 (tp30) REVERT: C 38 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7989 (tp) REVERT: C 54 ASP cc_start: 0.7958 (t0) cc_final: 0.7758 (t0) REVERT: C 56 THR cc_start: 0.8805 (m) cc_final: 0.8463 (p) REVERT: D 5 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6701 (mt) REVERT: D 56 THR cc_start: 0.8911 (m) cc_final: 0.8695 (p) REVERT: D 109 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7219 (mm) REVERT: D 178 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6856 (pt0) REVERT: D 204 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7904 (mmt90) REVERT: E 37 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7970 (tptt) REVERT: E 164 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: F 5 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.5836 (pp) REVERT: F 38 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8115 (tp) REVERT: G 5 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6489 (mt) REVERT: G 178 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: G 234 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7213 (ttm) outliers start: 121 outliers final: 50 residues processed: 232 average time/residue: 0.6508 time to fit residues: 161.9180 Evaluate side-chains 177 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 113 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 124 PRO Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 204 ARG Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 124 PRO Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 124 PRO Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 134 ASN B 178 GLN C 134 ASN C 178 GLN D 178 GLN D 198 HIS E 134 ASN E 178 GLN F 134 ASN F 178 GLN G 134 ASN G 178 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.127894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.108422 restraints weight = 11769.935| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.65 r_work: 0.2943 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11550 Z= 0.152 Angle : 0.510 10.305 15568 Z= 0.281 Chirality : 0.039 0.139 1848 Planarity : 0.003 0.032 1953 Dihedral : 10.342 59.652 1650 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 6.33 % Allowed : 14.21 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.81 (0.21), residues: 1358 helix: 3.10 (0.14), residues: 1085 sheet: None (None), residues: 0 loop : -0.00 (0.32), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 204 TYR 0.009 0.001 TYR B 228 PHE 0.007 0.001 PHE C 33 TRP 0.002 0.000 TRP F 139 HIS 0.004 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00298 (11550) covalent geometry : angle 0.51039 (15568) hydrogen bonds : bond 0.06930 ( 932) hydrogen bonds : angle 3.66183 ( 2733) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 139 time to evaluate : 0.350 Fit side-chains REVERT: A 49 ILE cc_start: 0.8353 (tt) cc_final: 0.8111 (tt) REVERT: A 55 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8082 (mp) REVERT: A 138 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8008 (ttm) REVERT: A 164 GLU cc_start: 0.7470 (tt0) cc_final: 0.7012 (tp30) REVERT: A 178 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: A 240 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7162 (mp0) REVERT: B 55 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 138 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8188 (tmm) REVERT: B 240 GLU cc_start: 0.8001 (tm-30) cc_final: 0.6975 (mp0) REVERT: C 37 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8177 (mmtm) REVERT: C 38 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7938 (tp) REVERT: D 138 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7331 (tpp) REVERT: D 240 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7306 (mp0) REVERT: E 138 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8245 (ttm) REVERT: E 160 GLU cc_start: 0.7333 (tt0) cc_final: 0.7047 (mt-10) REVERT: E 164 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7432 (tp30) REVERT: E 240 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7377 (mp0) REVERT: F 5 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5815 (pp) REVERT: F 37 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8349 (mmtm) REVERT: F 38 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7994 (tp) REVERT: F 138 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8173 (ttm) REVERT: F 149 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.6296 (m-30) REVERT: F 240 GLU cc_start: 0.8128 (tm-30) cc_final: 0.6875 (mp0) REVERT: G 28 ASP cc_start: 0.7979 (t70) cc_final: 0.7671 (t0) REVERT: G 42 ASP cc_start: 0.8600 (t0) cc_final: 0.8398 (t70) REVERT: G 49 ILE cc_start: 0.8583 (tt) cc_final: 0.8331 (tt) REVERT: G 138 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8109 (ttm) REVERT: G 178 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7610 (pt0) outliers start: 82 outliers final: 26 residues processed: 203 average time/residue: 0.4940 time to fit residues: 108.3803 Evaluate side-chains 166 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 178 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN C 134 ASN C 178 GLN D 178 GLN E 178 GLN E 198 HIS F 141 GLN F 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.126317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.106615 restraints weight = 12204.489| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.66 r_work: 0.3018 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11550 Z= 0.139 Angle : 0.444 5.040 15568 Z= 0.244 Chirality : 0.038 0.120 1848 Planarity : 0.003 0.024 1953 Dihedral : 7.682 59.339 1570 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 6.25 % Allowed : 15.44 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.76 (0.21), residues: 1358 helix: 3.03 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.00 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 204 TYR 0.007 0.001 TYR B 228 PHE 0.008 0.001 PHE E 33 TRP 0.002 0.000 TRP F 139 HIS 0.007 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00280 (11550) covalent geometry : angle 0.44380 (15568) hydrogen bonds : bond 0.06242 ( 932) hydrogen bonds : angle 3.40119 ( 2733) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 154 time to evaluate : 0.326 Fit side-chains REVERT: A 49 ILE cc_start: 0.8399 (tt) cc_final: 0.8189 (tt) REVERT: A 149 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.6158 (m-30) REVERT: A 178 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: A 223 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8030 (mm-30) REVERT: A 240 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7135 (mp0) REVERT: B 178 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: B 189 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8318 (mp) REVERT: B 223 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 240 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7119 (mp0) REVERT: C 37 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8298 (mmtm) REVERT: C 38 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8023 (tp) REVERT: C 223 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7922 (tp30) REVERT: D 38 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7983 (tp) REVERT: D 109 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6657 (mm) REVERT: E 58 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8190 (pp) REVERT: E 138 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8390 (tmm) REVERT: E 160 GLU cc_start: 0.7448 (tt0) cc_final: 0.7217 (mt-10) REVERT: E 181 ARG cc_start: 0.8227 (mtm-85) cc_final: 0.7884 (ttp-110) REVERT: E 240 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: F 6 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.5811 (mttt) REVERT: F 38 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8117 (tp) REVERT: F 138 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7751 (tpp) REVERT: F 240 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7029 (mp0) REVERT: G 28 ASP cc_start: 0.8202 (t70) cc_final: 0.7833 (t0) REVERT: G 138 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7997 (tpp) REVERT: G 178 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: G 234 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7528 (ttt) outliers start: 81 outliers final: 22 residues processed: 204 average time/residue: 0.5273 time to fit residues: 116.2208 Evaluate side-chains 166 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 0.0470 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 GLN D 178 GLN E 178 GLN F 141 GLN F 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.127195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.107557 restraints weight = 12282.009| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.65 r_work: 0.2933 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11550 Z= 0.128 Angle : 0.428 6.635 15568 Z= 0.231 Chirality : 0.037 0.120 1848 Planarity : 0.003 0.022 1953 Dihedral : 6.153 55.519 1545 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 5.79 % Allowed : 16.14 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.22), residues: 1358 helix: 3.00 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -0.22 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 204 TYR 0.005 0.001 TYR G 228 PHE 0.004 0.001 PHE E 33 TRP 0.003 0.000 TRP D 139 HIS 0.003 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00249 (11550) covalent geometry : angle 0.42786 (15568) hydrogen bonds : bond 0.05845 ( 932) hydrogen bonds : angle 3.31623 ( 2733) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 141 time to evaluate : 0.499 Fit side-chains REVERT: A 49 ILE cc_start: 0.8374 (tt) cc_final: 0.8148 (tt) REVERT: A 55 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8265 (mp) REVERT: A 178 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7724 (pt0) REVERT: A 221 ILE cc_start: 0.8384 (mm) cc_final: 0.8181 (mt) REVERT: A 223 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 240 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: B 178 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7383 (pt0) REVERT: B 189 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8276 (mp) REVERT: B 223 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7959 (mm-30) REVERT: B 240 GLU cc_start: 0.8149 (tm-30) cc_final: 0.6970 (mp0) REVERT: C 37 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8252 (mmtm) REVERT: C 38 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7934 (tp) REVERT: C 223 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7937 (tp30) REVERT: D 38 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7932 (tp) REVERT: D 109 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6396 (mm) REVERT: E 58 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8180 (pp) REVERT: E 160 GLU cc_start: 0.7380 (tt0) cc_final: 0.7177 (mt-10) REVERT: E 240 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: F 38 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7985 (tp) REVERT: F 138 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7621 (tpp) REVERT: F 149 ASP cc_start: 0.6598 (OUTLIER) cc_final: 0.6299 (m-30) REVERT: F 240 GLU cc_start: 0.8178 (tm-30) cc_final: 0.6930 (mp0) REVERT: G 138 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7801 (tpp) REVERT: G 178 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: G 234 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7518 (ttt) REVERT: G 240 GLU cc_start: 0.7318 (mp0) cc_final: 0.6962 (mp0) outliers start: 75 outliers final: 24 residues processed: 183 average time/residue: 0.5712 time to fit residues: 112.6331 Evaluate side-chains 180 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 104 optimal weight: 0.0770 chunk 52 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 114 optimal weight: 0.0570 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN D 178 GLN E 178 GLN F 141 GLN F 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.128405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.108864 restraints weight = 12237.262| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.64 r_work: 0.2976 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11550 Z= 0.121 Angle : 0.411 6.208 15568 Z= 0.222 Chirality : 0.037 0.120 1848 Planarity : 0.003 0.026 1953 Dihedral : 5.728 53.637 1543 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 5.02 % Allowed : 16.14 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (0.22), residues: 1358 helix: 3.01 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : -0.16 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 204 TYR 0.005 0.001 TYR G 228 PHE 0.005 0.001 PHE C 44 TRP 0.003 0.000 TRP E 139 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00230 (11550) covalent geometry : angle 0.41089 (15568) hydrogen bonds : bond 0.05560 ( 932) hydrogen bonds : angle 3.24668 ( 2733) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 148 time to evaluate : 0.479 Fit side-chains REVERT: A 49 ILE cc_start: 0.8375 (tt) cc_final: 0.8143 (tt) REVERT: A 55 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8330 (mp) REVERT: A 58 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8253 (pp) REVERT: A 223 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 240 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: B 160 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7003 (mt-10) REVERT: B 178 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: B 223 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 240 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: C 38 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7979 (tp) REVERT: C 109 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6467 (mm) REVERT: C 223 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7963 (tp30) REVERT: D 38 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7962 (tp) REVERT: D 109 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6290 (mm) REVERT: E 58 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8196 (pp) REVERT: E 135 THR cc_start: 0.8168 (t) cc_final: 0.7875 (m) REVERT: E 240 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: F 6 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.5954 (mttt) REVERT: F 38 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8041 (tp) REVERT: F 138 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7634 (tpp) REVERT: F 149 ASP cc_start: 0.6644 (OUTLIER) cc_final: 0.6333 (m-30) REVERT: F 240 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7022 (mp0) REVERT: G 28 ASP cc_start: 0.8203 (t70) cc_final: 0.7817 (t0) REVERT: G 138 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7810 (tpp) REVERT: G 159 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7414 (mp0) REVERT: G 178 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: G 234 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7507 (ttt) REVERT: G 240 GLU cc_start: 0.7297 (mp0) cc_final: 0.6963 (mp0) outliers start: 65 outliers final: 27 residues processed: 189 average time/residue: 0.5726 time to fit residues: 117.0788 Evaluate side-chains 175 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 178 GLN F 141 GLN F 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.126773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.107199 restraints weight = 12282.646| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.65 r_work: 0.2934 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11550 Z= 0.130 Angle : 0.424 6.696 15568 Z= 0.227 Chirality : 0.037 0.119 1848 Planarity : 0.003 0.021 1953 Dihedral : 5.265 51.783 1532 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.56 % Allowed : 16.83 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.62 (0.22), residues: 1358 helix: 2.96 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -0.24 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 204 TYR 0.005 0.001 TYR B 202 PHE 0.016 0.001 PHE A 44 TRP 0.002 0.000 TRP G 139 HIS 0.003 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00266 (11550) covalent geometry : angle 0.42430 (15568) hydrogen bonds : bond 0.05797 ( 932) hydrogen bonds : angle 3.27445 ( 2733) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 137 time to evaluate : 0.285 Fit side-chains REVERT: A 49 ILE cc_start: 0.8374 (tt) cc_final: 0.8138 (tt) REVERT: A 58 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8224 (pp) REVERT: A 159 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7665 (mp0) REVERT: A 223 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7920 (mm-30) REVERT: A 240 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: B 160 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7017 (mt-10) REVERT: B 178 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: B 223 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7931 (mm-30) REVERT: B 240 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: C 37 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8268 (mmtm) REVERT: C 38 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7997 (tp) REVERT: C 223 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7934 (tp30) REVERT: D 38 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7960 (tp) REVERT: D 109 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6317 (mm) REVERT: E 58 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8156 (pp) REVERT: E 181 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7753 (ttp-110) REVERT: E 240 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: F 38 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7985 (tp) REVERT: F 138 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7635 (tpp) REVERT: F 149 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.6339 (m-30) REVERT: F 240 GLU cc_start: 0.8198 (tm-30) cc_final: 0.6998 (mp0) REVERT: G 28 ASP cc_start: 0.8160 (t70) cc_final: 0.7768 (t0) REVERT: G 138 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7801 (tpp) REVERT: G 159 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7625 (mp0) REVERT: G 234 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7468 (ttt) REVERT: G 240 GLU cc_start: 0.7298 (mp0) cc_final: 0.6953 (mp0) outliers start: 59 outliers final: 30 residues processed: 175 average time/residue: 0.5487 time to fit residues: 103.5828 Evaluate side-chains 174 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 87 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN G 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113004 restraints weight = 12148.538| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.49 r_work: 0.2999 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11550 Z= 0.126 Angle : 0.419 6.169 15568 Z= 0.225 Chirality : 0.037 0.119 1848 Planarity : 0.003 0.021 1953 Dihedral : 4.723 46.819 1525 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.40 % Allowed : 16.91 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.67 (0.22), residues: 1358 helix: 2.96 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : -0.20 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 204 TYR 0.005 0.001 TYR B 202 PHE 0.011 0.001 PHE A 44 TRP 0.002 0.000 TRP D 139 HIS 0.003 0.001 HIS G 198 Details of bonding type rmsd covalent geometry : bond 0.00251 (11550) covalent geometry : angle 0.41863 (15568) hydrogen bonds : bond 0.05653 ( 932) hydrogen bonds : angle 3.25178 ( 2733) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 136 time to evaluate : 0.404 Fit side-chains REVERT: A 49 ILE cc_start: 0.8450 (tt) cc_final: 0.8205 (tt) REVERT: A 58 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8291 (pp) REVERT: A 159 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7726 (mp0) REVERT: A 223 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 240 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: B 160 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7122 (mt-10) REVERT: B 178 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: B 223 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 240 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: C 37 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8388 (mmtm) REVERT: C 38 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8057 (tp) REVERT: C 223 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8018 (tp30) REVERT: D 38 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8084 (tp) REVERT: D 109 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6392 (mm) REVERT: D 178 GLN cc_start: 0.7869 (pt0) cc_final: 0.7419 (pt0) REVERT: D 240 GLU cc_start: 0.7458 (mp0) cc_final: 0.7095 (mp0) REVERT: E 58 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8256 (pp) REVERT: E 181 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7797 (ttp-110) REVERT: E 240 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: F 6 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.5909 (mttt) REVERT: F 38 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8102 (tp) REVERT: F 138 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7765 (tpp) REVERT: F 149 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6399 (m-30) REVERT: F 240 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7116 (mp0) REVERT: G 28 ASP cc_start: 0.8244 (t70) cc_final: 0.7838 (t0) REVERT: G 138 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7917 (tpp) REVERT: G 178 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: G 234 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7584 (ttt) REVERT: G 240 GLU cc_start: 0.7328 (mp0) cc_final: 0.7028 (mp0) outliers start: 57 outliers final: 32 residues processed: 171 average time/residue: 0.5155 time to fit residues: 95.5162 Evaluate side-chains 177 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 108 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.128503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.109907 restraints weight = 12255.818| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.51 r_work: 0.2943 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11550 Z= 0.138 Angle : 0.435 6.171 15568 Z= 0.233 Chirality : 0.038 0.117 1848 Planarity : 0.003 0.024 1953 Dihedral : 4.813 47.594 1525 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.56 % Allowed : 16.99 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.55 (0.22), residues: 1358 helix: 2.90 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -0.23 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 204 TYR 0.004 0.001 TYR B 228 PHE 0.008 0.001 PHE A 44 TRP 0.001 0.000 TRP F 139 HIS 0.003 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00296 (11550) covalent geometry : angle 0.43488 (15568) hydrogen bonds : bond 0.05971 ( 932) hydrogen bonds : angle 3.31146 ( 2733) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 0.365 Fit side-chains REVERT: A 49 ILE cc_start: 0.8517 (tt) cc_final: 0.8272 (tt) REVERT: A 58 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8319 (pp) REVERT: A 159 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7726 (mp0) REVERT: A 223 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8059 (mm-30) REVERT: A 240 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: B 178 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7433 (pt0) REVERT: B 223 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7968 (mm-30) REVERT: B 240 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: C 38 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8083 (tp) REVERT: C 223 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8014 (tp30) REVERT: D 38 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8016 (tp) REVERT: D 109 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6367 (mm) REVERT: D 240 GLU cc_start: 0.7416 (mp0) cc_final: 0.7046 (mp0) REVERT: E 58 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8259 (pp) REVERT: E 181 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7775 (ttp-110) REVERT: E 234 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7525 (tmm) REVERT: E 240 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: F 38 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8117 (tp) REVERT: F 138 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7725 (tpp) REVERT: F 149 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.6403 (m-30) REVERT: F 240 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7110 (mp0) REVERT: G 28 ASP cc_start: 0.8242 (t70) cc_final: 0.7836 (t0) REVERT: G 138 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7891 (tpp) REVERT: G 234 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7534 (ttt) REVERT: G 240 GLU cc_start: 0.7348 (mp0) cc_final: 0.7015 (mp0) outliers start: 59 outliers final: 33 residues processed: 172 average time/residue: 0.5411 time to fit residues: 100.4261 Evaluate side-chains 175 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 115 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 61 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 178 GLN G 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.127764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.108160 restraints weight = 12211.892| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.66 r_work: 0.3158 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11550 Z= 0.125 Angle : 0.416 6.161 15568 Z= 0.225 Chirality : 0.037 0.119 1848 Planarity : 0.003 0.025 1953 Dihedral : 4.715 48.330 1525 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.25 % Allowed : 17.22 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.22), residues: 1358 helix: 2.96 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : -0.18 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 204 TYR 0.004 0.001 TYR B 202 PHE 0.008 0.001 PHE A 44 TRP 0.002 0.000 TRP G 139 HIS 0.003 0.001 HIS G 198 Details of bonding type rmsd covalent geometry : bond 0.00247 (11550) covalent geometry : angle 0.41643 (15568) hydrogen bonds : bond 0.05622 ( 932) hydrogen bonds : angle 3.27569 ( 2733) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 128 time to evaluate : 0.486 Fit side-chains REVERT: A 49 ILE cc_start: 0.8451 (tt) cc_final: 0.8211 (tt) REVERT: A 58 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8210 (pp) REVERT: A 159 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7635 (mp0) REVERT: A 223 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 240 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: B 160 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6926 (mt-10) REVERT: B 178 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7336 (pt0) REVERT: B 223 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7853 (mm-30) REVERT: B 240 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: C 37 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8281 (mmtm) REVERT: C 38 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7957 (tp) REVERT: C 223 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7896 (tp30) REVERT: D 38 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8033 (tp) REVERT: D 109 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6308 (mm) REVERT: D 178 GLN cc_start: 0.7807 (pt0) cc_final: 0.7385 (pt0) REVERT: D 240 GLU cc_start: 0.7335 (mp0) cc_final: 0.6947 (mp0) REVERT: E 58 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8166 (pp) REVERT: E 181 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7695 (ttp-110) REVERT: E 234 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7295 (tmm) REVERT: E 240 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: F 6 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.5872 (mttt) REVERT: F 38 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8037 (tp) REVERT: F 138 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7649 (tpp) REVERT: F 149 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6349 (m-30) REVERT: F 240 GLU cc_start: 0.8177 (tm-30) cc_final: 0.6990 (mp0) REVERT: G 28 ASP cc_start: 0.8189 (t70) cc_final: 0.7820 (t0) REVERT: G 138 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7833 (tpp) REVERT: G 234 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7479 (ttt) REVERT: G 240 GLU cc_start: 0.7294 (mp0) cc_final: 0.6972 (mp0) outliers start: 55 outliers final: 33 residues processed: 163 average time/residue: 0.5766 time to fit residues: 101.3051 Evaluate side-chains 173 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 62 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 123 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.123229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.103504 restraints weight = 12433.522| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.68 r_work: 0.2932 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11550 Z= 0.162 Angle : 0.464 6.126 15568 Z= 0.250 Chirality : 0.039 0.135 1848 Planarity : 0.003 0.029 1953 Dihedral : 4.953 49.321 1525 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.09 % Allowed : 17.37 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.41 (0.22), residues: 1358 helix: 2.78 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -0.20 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 181 TYR 0.007 0.001 TYR G 175 PHE 0.005 0.001 PHE F 153 TRP 0.003 0.001 TRP F 139 HIS 0.004 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00371 (11550) covalent geometry : angle 0.46384 (15568) hydrogen bonds : bond 0.06442 ( 932) hydrogen bonds : angle 3.41044 ( 2733) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 0.493 Fit side-chains REVERT: A 49 ILE cc_start: 0.8482 (tt) cc_final: 0.8238 (tt) REVERT: A 58 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8286 (pp) REVERT: A 164 GLU cc_start: 0.7406 (tt0) cc_final: 0.7001 (tp30) REVERT: A 223 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8018 (mm-30) REVERT: A 240 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: B 160 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7118 (mt-10) REVERT: B 178 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: B 240 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: C 38 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8017 (tp) REVERT: C 223 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7956 (tp30) REVERT: D 109 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6332 (mm) REVERT: D 178 GLN cc_start: 0.7877 (pt0) cc_final: 0.7493 (pt0) REVERT: D 240 GLU cc_start: 0.7405 (mp0) cc_final: 0.7040 (mp0) REVERT: E 159 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7169 (mp0) REVERT: E 234 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7471 (tmm) REVERT: E 240 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: F 6 LYS cc_start: 0.6377 (OUTLIER) cc_final: 0.5735 (mttt) REVERT: F 38 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8061 (tp) REVERT: F 149 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.6319 (m-30) REVERT: F 240 GLU cc_start: 0.8194 (tm-30) cc_final: 0.6963 (mp0) REVERT: G 28 ASP cc_start: 0.8196 (t70) cc_final: 0.7950 (t70) REVERT: G 138 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7911 (tpp) REVERT: G 234 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7472 (ttt) REVERT: G 240 GLU cc_start: 0.7346 (mp0) cc_final: 0.6991 (mp0) outliers start: 53 outliers final: 31 residues processed: 161 average time/residue: 0.5527 time to fit residues: 96.2047 Evaluate side-chains 167 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.0050 chunk 39 optimal weight: 0.9980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN G 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.125088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.105459 restraints weight = 12337.084| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.67 r_work: 0.2942 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11550 Z= 0.139 Angle : 0.436 6.200 15568 Z= 0.236 Chirality : 0.038 0.121 1848 Planarity : 0.003 0.033 1953 Dihedral : 4.796 49.503 1523 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.78 % Allowed : 17.68 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.47 (0.22), residues: 1358 helix: 2.82 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : -0.21 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 181 TYR 0.004 0.001 TYR G 202 PHE 0.007 0.001 PHE A 44 TRP 0.002 0.000 TRP F 139 HIS 0.003 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00298 (11550) covalent geometry : angle 0.43646 (15568) hydrogen bonds : bond 0.06030 ( 932) hydrogen bonds : angle 3.37585 ( 2733) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3159.92 seconds wall clock time: 54 minutes 38.17 seconds (3278.17 seconds total)