Starting phenix.real_space_refine on Tue Jun 10 02:15:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqc_34023/06_2025/7yqc_34023.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqc_34023/06_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_34023/06_2025/7yqc_34023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqc_34023/06_2025/7yqc_34023.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqc_34023/06_2025/7yqc_34023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqc_34023/06_2025/7yqc_34023.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.056 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.64, per 1000 atoms: 0.67 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: 2.34 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.88 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: 3.49 Time building geometry restraints manager: 2.85 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.980 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.015 0.003 TRP F 139 HIS 0.009 0.003 HIS D 232 PHE 0.020 0.003 PHE C 33 TYR 0.021 0.003 TYR B 228 ARG 0.005 0.001 ARG F 21 Details of bonding type rmsd hydrogen bonds : bond 0.25808 ( 932) hydrogen bonds : angle 6.23858 ( 2733) covalent geometry : bond 0.01346 (11550) covalent geometry : angle 1.86479 (15568) *********************** 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 : 1.251 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: 1.2957 time to fit residues: 323.3308 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 : 1.220 ------------------------------------------------------------------------------- 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 112 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN F 134 ASN F 178 GLN G 134 ASN G 178 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.127985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.108558 restraints weight = 11626.745| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.64 r_work: 0.2940 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11550 Z= 0.151 Angle : 0.514 10.415 15568 Z= 0.282 Chirality : 0.039 0.135 1848 Planarity : 0.003 0.032 1953 Dihedral : 10.346 59.675 1650 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 6.33 % Allowed : 14.29 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.21), residues: 1358 helix: 3.10 (0.14), residues: 1085 sheet: None (None), residues: 0 loop : -0.02 (0.32), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 139 HIS 0.005 0.001 HIS B 198 PHE 0.007 0.001 PHE C 33 TYR 0.010 0.001 TYR G 228 ARG 0.005 0.000 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.06834 ( 932) hydrogen bonds : angle 3.65506 ( 2733) covalent geometry : bond 0.00299 (11550) covalent geometry : angle 0.51448 (15568) *********************** 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 224 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 142 time to evaluate : 1.588 Fit side-chains REVERT: A 49 ILE cc_start: 0.8347 (tt) cc_final: 0.8110 (tt) REVERT: A 55 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8075 (mp) REVERT: A 164 GLU cc_start: 0.7467 (tt0) cc_final: 0.7005 (tp30) REVERT: A 178 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7536 (pt0) REVERT: A 240 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7177 (mp0) REVERT: B 55 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8015 (mp) REVERT: B 138 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8223 (tmm) REVERT: B 240 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7008 (mp0) REVERT: C 37 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8165 (mmtm) REVERT: C 38 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7922 (tp) REVERT: D 56 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8536 (p) REVERT: D 138 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8392 (tmm) REVERT: D 240 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7296 (mp0) REVERT: E 138 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8235 (ttm) REVERT: E 160 GLU cc_start: 0.7328 (tt0) cc_final: 0.7040 (mt-10) REVERT: E 164 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: E 240 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7353 (mp0) REVERT: F 5 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5850 (pp) REVERT: F 37 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8328 (mmtm) REVERT: F 38 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7992 (tp) REVERT: F 138 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8165 (ttm) REVERT: F 149 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.6291 (m-30) REVERT: F 240 GLU cc_start: 0.8138 (tm-30) cc_final: 0.6932 (mp0) REVERT: G 28 ASP cc_start: 0.7972 (t70) cc_final: 0.7666 (t0) REVERT: G 42 ASP cc_start: 0.8602 (t0) cc_final: 0.8400 (t70) REVERT: G 49 ILE cc_start: 0.8580 (tt) cc_final: 0.8329 (tt) REVERT: G 138 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8097 (ttm) REVERT: G 178 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7558 (pt0) outliers start: 82 outliers final: 26 residues processed: 205 average time/residue: 1.2927 time to fit residues: 286.5131 Evaluate side-chains 170 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 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 56 THR 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 65 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 178 GLN C 134 ASN C 178 GLN D 178 GLN E 134 ASN E 178 GLN F 141 GLN F 178 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117661 restraints weight = 12032.267| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.36 r_work: 0.2940 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2475 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= 0.155 Angle : 0.466 5.035 15568 Z= 0.256 Chirality : 0.039 0.123 1848 Planarity : 0.003 0.025 1953 Dihedral : 7.835 59.073 1570 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 6.41 % Allowed : 15.21 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.21), residues: 1358 helix: 2.94 (0.14), residues: 1085 sheet: None (None), residues: 0 loop : -0.10 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 139 HIS 0.004 0.001 HIS E 232 PHE 0.007 0.001 PHE E 33 TYR 0.007 0.001 TYR B 228 ARG 0.003 0.000 ARG B 204 Details of bonding type rmsd hydrogen bonds : bond 0.06681 ( 932) hydrogen bonds : angle 3.48233 ( 2733) covalent geometry : bond 0.00332 (11550) covalent geometry : angle 0.46620 (15568) *********************** 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 238 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 155 time to evaluate : 2.942 Fit side-chains REVERT: A 49 ILE cc_start: 0.8242 (tt) cc_final: 0.8021 (tt) REVERT: A 138 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7974 (tmm) REVERT: A 149 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5942 (m-30) REVERT: A 164 GLU cc_start: 0.6999 (tt0) cc_final: 0.6505 (tp30) REVERT: A 178 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: A 223 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 240 GLU cc_start: 0.7912 (tm-30) cc_final: 0.6768 (mp0) REVERT: B 240 GLU cc_start: 0.7897 (tm-30) cc_final: 0.6716 (mp0) REVERT: C 37 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7769 (mmtm) REVERT: C 38 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7595 (tp) REVERT: D 38 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7605 (tp) REVERT: D 56 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8168 (p) REVERT: D 240 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: E 58 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7889 (pp) REVERT: E 138 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7985 (ttm) REVERT: E 160 GLU cc_start: 0.7008 (tt0) cc_final: 0.6718 (mt-10) REVERT: E 164 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7119 (tp30) REVERT: E 181 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7608 (ttp-110) REVERT: E 219 LEU cc_start: 0.7830 (tp) cc_final: 0.7617 (tt) REVERT: E 240 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: F 6 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.5694 (mttt) REVERT: F 38 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7653 (tp) REVERT: F 138 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7851 (ttm) REVERT: F 240 GLU cc_start: 0.7907 (tm-30) cc_final: 0.6619 (mp0) REVERT: G 28 ASP cc_start: 0.7810 (t70) cc_final: 0.7484 (t0) REVERT: G 49 ILE cc_start: 0.8443 (tt) cc_final: 0.8242 (tt) REVERT: G 138 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7807 (ttm) REVERT: G 178 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7394 (pt0) REVERT: G 234 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7129 (ttt) outliers start: 83 outliers final: 23 residues processed: 203 average time/residue: 1.6028 time to fit residues: 349.1377 Evaluate side-chains 187 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 2.853 ------------------------------------------------------------------------------- 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 149 ASP Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 189 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 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 56 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 241 LYS 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 164 GLU 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 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 9 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.106131 restraints weight = 12112.116| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.65 r_work: 0.3001 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11550 Z= 0.142 Angle : 0.445 5.851 15568 Z= 0.243 Chirality : 0.038 0.120 1848 Planarity : 0.003 0.024 1953 Dihedral : 6.636 56.386 1550 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 5.95 % Allowed : 15.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.21), residues: 1358 helix: 2.93 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -0.17 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 139 HIS 0.004 0.001 HIS E 232 PHE 0.004 0.001 PHE E 33 TYR 0.005 0.001 TYR B 228 ARG 0.003 0.000 ARG B 204 Details of bonding type rmsd hydrogen bonds : bond 0.06267 ( 932) hydrogen bonds : angle 3.39761 ( 2733) covalent geometry : bond 0.00301 (11550) covalent geometry : angle 0.44500 (15568) *********************** 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 227 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 150 time to evaluate : 1.429 Fit side-chains REVERT: A 49 ILE cc_start: 0.8391 (tt) cc_final: 0.8170 (tt) REVERT: A 138 MET cc_start: 0.8576 (ttm) cc_final: 0.8362 (tmm) REVERT: A 164 GLU cc_start: 0.7346 (tt0) cc_final: 0.6927 (tp30) REVERT: A 178 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7717 (pt0) REVERT: A 223 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 240 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: B 58 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8141 (pp) REVERT: B 110 LYS cc_start: 0.8395 (mmmt) cc_final: 0.8106 (mmmm) REVERT: B 223 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7881 (mm-30) REVERT: B 240 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: C 38 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8021 (tp) REVERT: C 109 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6447 (mm) REVERT: C 181 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7807 (ttp-110) REVERT: C 223 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7900 (tp30) REVERT: D 38 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7970 (tp) REVERT: D 56 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8444 (p) REVERT: E 58 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8102 (pp) REVERT: E 138 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8279 (ttm) REVERT: E 160 GLU cc_start: 0.7480 (tt0) cc_final: 0.7242 (mt-10) REVERT: E 164 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: E 181 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7920 (ttp-110) REVERT: E 219 LEU cc_start: 0.8253 (tp) cc_final: 0.8050 (tt) REVERT: E 240 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: F 5 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6546 (pt) REVERT: F 38 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8070 (tp) REVERT: F 138 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7693 (tpp) REVERT: F 149 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.6332 (m-30) REVERT: F 192 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7976 (mttp) REVERT: F 240 GLU cc_start: 0.8197 (tm-30) cc_final: 0.6956 (mp0) REVERT: G 138 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7851 (tpp) REVERT: G 178 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: G 234 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7534 (ttt) REVERT: G 240 GLU cc_start: 0.7340 (mp0) cc_final: 0.6989 (mp0) outliers start: 77 outliers final: 26 residues processed: 197 average time/residue: 1.3220 time to fit residues: 281.2920 Evaluate side-chains 180 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 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 58 ILE 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 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 D residue 38 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 241 LYS 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 164 GLU Chi-restraints excluded: chain E residue 181 ARG Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 5 LEU 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 181 ARG Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 192 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 76 optimal weight: 6.9990 chunk 91 optimal weight: 0.0030 chunk 131 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 106 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 104 optimal weight: 0.0060 chunk 40 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 178 GLN C 178 GLN D 178 GLN E 178 GLN F 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.111104 restraints weight = 12120.796| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.66 r_work: 0.2999 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.002 0.022 11550 Z= 0.115 Angle : 0.406 6.392 15568 Z= 0.219 Chirality : 0.037 0.122 1848 Planarity : 0.003 0.023 1953 Dihedral : 5.934 53.049 1546 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 4.71 % Allowed : 17.37 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.22), residues: 1358 helix: 3.02 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -0.30 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 139 HIS 0.002 0.001 HIS C 232 PHE 0.004 0.001 PHE C 44 TYR 0.005 0.001 TYR G 228 ARG 0.005 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.05332 ( 932) hydrogen bonds : angle 3.24450 ( 2733) covalent geometry : bond 0.00208 (11550) covalent geometry : angle 0.40564 (15568) *********************** 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 211 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 150 time to evaluate : 1.371 Fit side-chains REVERT: A 49 ILE cc_start: 0.8373 (tt) cc_final: 0.8130 (tt) REVERT: A 135 THR cc_start: 0.8131 (t) cc_final: 0.7921 (m) REVERT: A 138 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8077 (ttm) REVERT: A 223 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 240 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7018 (mp0) REVERT: B 110 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7918 (mmmm) REVERT: B 223 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7923 (mm-30) REVERT: B 240 GLU cc_start: 0.8140 (tm-30) cc_final: 0.6990 (mp0) REVERT: C 37 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8236 (mmtm) REVERT: C 38 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7946 (tp) REVERT: C 208 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: C 223 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7920 (tp30) REVERT: D 38 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7938 (tp) REVERT: D 56 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8366 (p) REVERT: E 54 ASP cc_start: 0.8128 (t0) cc_final: 0.7917 (t0) REVERT: E 58 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8141 (pp) REVERT: E 135 THR cc_start: 0.8095 (t) cc_final: 0.7850 (m) REVERT: E 240 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: F 6 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.5996 (mttt) REVERT: F 38 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8006 (tp) REVERT: F 138 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7630 (tpp) REVERT: F 240 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7028 (mp0) REVERT: G 16 ASP cc_start: 0.7692 (m-30) cc_final: 0.7321 (m-30) REVERT: G 28 ASP cc_start: 0.8184 (t70) cc_final: 0.7789 (t0) REVERT: G 138 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7779 (tpp) REVERT: G 234 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7520 (ttt) REVERT: G 240 GLU cc_start: 0.7271 (mp0) cc_final: 0.6953 (mp0) outliers start: 61 outliers final: 18 residues processed: 189 average time/residue: 1.2187 time to fit residues: 249.3486 Evaluate side-chains 160 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 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 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 C residue 208 GLU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 241 LYS 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 138 MET 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 138 MET 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 45 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 C 178 GLN E 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.104433 restraints weight = 12445.694| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.67 r_work: 0.2894 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11550 Z= 0.162 Angle : 0.460 6.578 15568 Z= 0.248 Chirality : 0.039 0.117 1848 Planarity : 0.003 0.023 1953 Dihedral : 5.290 50.800 1528 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.79 % Allowed : 17.37 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.22), residues: 1358 helix: 2.87 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 139 HIS 0.004 0.001 HIS C 232 PHE 0.008 0.001 PHE A 44 TYR 0.005 0.001 TYR F 202 ARG 0.003 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.06484 ( 932) hydrogen bonds : angle 3.39942 ( 2733) covalent geometry : bond 0.00372 (11550) covalent geometry : angle 0.46001 (15568) *********************** 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 209 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 147 time to evaluate : 1.255 Fit side-chains REVERT: A 49 ILE cc_start: 0.8456 (tt) cc_final: 0.8202 (tt) REVERT: A 58 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8232 (pp) REVERT: A 138 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8354 (tmm) REVERT: A 159 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7643 (mp0) REVERT: A 164 GLU cc_start: 0.7330 (tt0) cc_final: 0.6915 (tp30) REVERT: A 223 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7988 (mm-30) REVERT: A 240 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: B 223 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7966 (mm-30) REVERT: B 240 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: C 38 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7962 (tp) REVERT: C 159 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7423 (mp0) REVERT: C 223 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7898 (tp30) REVERT: D 56 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8362 (p) REVERT: E 160 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7229 (mt-10) REVERT: E 240 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: F 6 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.5988 (mttt) REVERT: F 38 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8016 (tp) REVERT: F 138 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7613 (tpp) REVERT: F 149 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6332 (m-30) REVERT: F 159 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7589 (mp0) REVERT: F 240 GLU cc_start: 0.8144 (tm-30) cc_final: 0.6915 (mp0) REVERT: G 16 ASP cc_start: 0.7678 (m-30) cc_final: 0.7278 (m-30) REVERT: G 28 ASP cc_start: 0.8149 (t70) cc_final: 0.7770 (t0) REVERT: G 138 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7835 (tpp) REVERT: G 178 GLN cc_start: 0.8166 (pt0) cc_final: 0.7745 (pt0) REVERT: G 181 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7958 (ttp-110) REVERT: G 234 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7470 (ttt) REVERT: G 240 GLU cc_start: 0.7316 (mp0) cc_final: 0.6952 (mp0) outliers start: 62 outliers final: 27 residues processed: 188 average time/residue: 1.3521 time to fit residues: 273.1630 Evaluate side-chains 180 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 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 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 135 THR Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 59 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 C 178 GLN G 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.125462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.105663 restraints weight = 12453.478| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.69 r_work: 0.2921 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11550 Z= 0.134 Angle : 0.433 6.472 15568 Z= 0.233 Chirality : 0.037 0.119 1848 Planarity : 0.003 0.022 1953 Dihedral : 4.938 48.219 1524 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.09 % Allowed : 17.92 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.22), residues: 1358 helix: 2.93 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -0.26 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 139 HIS 0.003 0.001 HIS G 198 PHE 0.004 0.001 PHE A 44 TYR 0.005 0.001 TYR B 202 ARG 0.004 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.05967 ( 932) hydrogen bonds : angle 3.34791 ( 2733) covalent geometry : bond 0.00278 (11550) covalent geometry : angle 0.43294 (15568) *********************** 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 189 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 136 time to evaluate : 1.258 Fit side-chains REVERT: A 49 ILE cc_start: 0.8458 (tt) cc_final: 0.8207 (tt) REVERT: A 58 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8213 (pp) REVERT: A 135 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7911 (m) REVERT: A 223 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7992 (mm-30) REVERT: A 240 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: B 223 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7929 (mm-30) REVERT: B 240 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: C 38 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8005 (tp) REVERT: C 159 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7335 (mp0) REVERT: C 208 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: C 223 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7938 (tp30) REVERT: D 56 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8353 (p) REVERT: E 58 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8164 (pp) REVERT: E 160 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7244 (mt-10) REVERT: E 240 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: F 38 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8018 (tp) REVERT: F 138 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7603 (tpp) REVERT: F 149 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6337 (m-30) REVERT: F 159 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7552 (mp0) REVERT: F 240 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7002 (mp0) REVERT: G 16 ASP cc_start: 0.7688 (m-30) cc_final: 0.7287 (m-30) REVERT: G 28 ASP cc_start: 0.8197 (t70) cc_final: 0.7807 (t0) REVERT: G 138 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7796 (tpp) REVERT: G 159 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7528 (mp0) REVERT: G 178 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: G 181 ARG cc_start: 0.8231 (ttp-110) cc_final: 0.7968 (ttp-110) REVERT: G 234 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7429 (ttt) REVERT: G 240 GLU cc_start: 0.7351 (mp0) cc_final: 0.6994 (mp0) outliers start: 53 outliers final: 23 residues processed: 168 average time/residue: 1.3689 time to fit residues: 248.3229 Evaluate side-chains 175 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 24 SER 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 236 LEU Chi-restraints excluded: chain B residue 240 GLU 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 D residue 56 THR Chi-restraints excluded: chain D residue 135 THR 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 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 109 LEU 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 123 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 C 178 GLN D 178 GLN F 141 GLN G 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.126615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.106736 restraints weight = 12351.597| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.71 r_work: 0.3058 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11550 Z= 0.129 Angle : 0.426 6.442 15568 Z= 0.229 Chirality : 0.037 0.118 1848 Planarity : 0.003 0.022 1953 Dihedral : 4.656 48.300 1520 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.63 % Allowed : 17.37 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.22), residues: 1358 helix: 2.96 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 139 HIS 0.003 0.001 HIS G 198 PHE 0.004 0.001 PHE E 33 TYR 0.005 0.001 TYR B 202 ARG 0.005 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.05801 ( 932) hydrogen bonds : angle 3.31399 ( 2733) covalent geometry : bond 0.00261 (11550) covalent geometry : angle 0.42621 (15568) *********************** 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 195 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 135 time to evaluate : 1.361 Fit side-chains REVERT: A 49 ILE cc_start: 0.8443 (tt) cc_final: 0.8199 (tt) REVERT: A 58 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8206 (pp) REVERT: A 135 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7891 (m) REVERT: A 159 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7622 (mp0) REVERT: A 223 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7937 (mm-30) REVERT: A 240 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: B 223 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7837 (mm-30) REVERT: B 240 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: C 38 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7948 (tp) REVERT: C 208 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: C 223 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7878 (tp30) REVERT: D 56 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8327 (p) REVERT: E 58 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8161 (pp) REVERT: E 160 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7201 (mt-10) REVERT: E 181 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7750 (ttp-110) REVERT: E 240 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: F 6 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5879 (mttt) REVERT: F 38 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8017 (tp) REVERT: F 138 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7619 (tpp) REVERT: F 240 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7005 (mp0) REVERT: G 16 ASP cc_start: 0.7681 (m-30) cc_final: 0.7285 (m-30) REVERT: G 28 ASP cc_start: 0.8201 (t70) cc_final: 0.7814 (t0) REVERT: G 138 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7785 (tpp) REVERT: G 159 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7497 (mp0) REVERT: G 181 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7964 (ttp-110) REVERT: G 212 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8278 (ttmt) REVERT: G 234 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7412 (ttt) REVERT: G 240 GLU cc_start: 0.7328 (mp0) cc_final: 0.6971 (mp0) outliers start: 60 outliers final: 29 residues processed: 174 average time/residue: 1.4641 time to fit residues: 275.3680 Evaluate side-chains 176 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 24 SER 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 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 D residue 56 THR Chi-restraints excluded: chain D residue 135 THR 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 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 178 GLN Chi-restraints excluded: chain G residue 212 LYS 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 105 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 64 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 D 178 GLN F 141 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120026 restraints weight = 12141.536| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.34 r_work: 0.3011 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11550 Z= 0.129 Angle : 0.425 6.452 15568 Z= 0.229 Chirality : 0.037 0.118 1848 Planarity : 0.003 0.025 1953 Dihedral : 4.638 48.837 1520 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.25 % Allowed : 17.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.22), residues: 1358 helix: 2.89 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 139 HIS 0.003 0.001 HIS G 198 PHE 0.004 0.001 PHE E 33 TYR 0.005 0.001 TYR B 202 ARG 0.004 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.05757 ( 932) hydrogen bonds : angle 3.30915 ( 2733) covalent geometry : bond 0.00261 (11550) covalent geometry : angle 0.42517 (15568) *********************** 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 186 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 131 time to evaluate : 1.433 Fit side-chains REVERT: A 49 ILE cc_start: 0.8506 (tt) cc_final: 0.8272 (tt) REVERT: A 58 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8288 (pp) REVERT: A 135 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7982 (m) REVERT: A 223 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 240 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: B 160 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6960 (mt-10) REVERT: B 223 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7889 (mm-30) REVERT: B 240 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: C 38 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8053 (tp) REVERT: C 208 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: C 223 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7916 (tp30) REVERT: D 40 GLU cc_start: 0.7803 (tt0) cc_final: 0.7357 (tt0) REVERT: D 56 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8470 (p) REVERT: D 181 ARG cc_start: 0.8221 (ttp-110) cc_final: 0.7987 (ttp-110) REVERT: E 58 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8249 (pp) REVERT: E 160 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7255 (mt-10) REVERT: E 181 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7764 (ttp-110) REVERT: E 240 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: F 6 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.5960 (mttt) REVERT: F 38 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8105 (tp) REVERT: F 138 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7699 (tpp) REVERT: F 149 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.6380 (m-30) REVERT: F 240 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7111 (mp0) REVERT: G 28 ASP cc_start: 0.8255 (t70) cc_final: 0.7846 (t0) REVERT: G 138 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7864 (tpp) REVERT: G 212 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8380 (ttmt) REVERT: G 234 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7497 (ttt) REVERT: G 240 GLU cc_start: 0.7292 (mp0) cc_final: 0.6995 (mp0) outliers start: 55 outliers final: 28 residues processed: 169 average time/residue: 1.2334 time to fit residues: 225.8777 Evaluate side-chains 173 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 24 SER 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 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 D residue 56 THR Chi-restraints excluded: chain D residue 135 THR 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 212 LYS 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 212 LYS 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 39 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 GLN F 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.135805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.118639 restraints weight = 12109.047| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.35 r_work: 0.2994 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3167 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= 0.139 Angle : 0.438 6.420 15568 Z= 0.236 Chirality : 0.038 0.119 1848 Planarity : 0.003 0.026 1953 Dihedral : 4.686 49.416 1520 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.86 % Allowed : 18.30 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.22), residues: 1358 helix: 2.84 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -0.30 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 139 HIS 0.003 0.001 HIS C 232 PHE 0.004 0.001 PHE F 153 TYR 0.004 0.001 TYR B 202 ARG 0.004 0.000 ARG F 181 Details of bonding type rmsd hydrogen bonds : bond 0.06006 ( 932) hydrogen bonds : angle 3.35415 ( 2733) covalent geometry : bond 0.00300 (11550) covalent geometry : angle 0.43754 (15568) ********************** 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 182 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 1.231 Fit side-chains REVERT: A 49 ILE cc_start: 0.8528 (tt) cc_final: 0.8292 (tt) REVERT: A 58 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8321 (pp) REVERT: A 135 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.8008 (m) REVERT: A 223 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8020 (mm-30) REVERT: A 240 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: B 160 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7015 (mt-10) REVERT: B 223 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 240 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: C 38 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8137 (tp) REVERT: C 223 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7951 (tp30) REVERT: D 40 GLU cc_start: 0.7853 (tt0) cc_final: 0.7386 (tt0) REVERT: D 56 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8483 (p) REVERT: E 58 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8296 (pp) REVERT: E 160 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7361 (mt-10) REVERT: E 181 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7798 (ttp-110) REVERT: E 240 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: F 6 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.5923 (mttt) REVERT: F 38 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8149 (tp) REVERT: F 138 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7737 (tpp) REVERT: F 149 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6363 (m-30) REVERT: F 240 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7152 (mp0) REVERT: G 28 ASP cc_start: 0.8266 (t70) cc_final: 0.7852 (t0) REVERT: G 138 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7901 (tpp) REVERT: G 212 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8413 (ttmt) REVERT: G 234 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7510 (ttt) REVERT: G 240 GLU cc_start: 0.7324 (mp0) cc_final: 0.6998 (mp0) outliers start: 50 outliers final: 29 residues processed: 166 average time/residue: 1.1952 time to fit residues: 214.9489 Evaluate side-chains 172 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 24 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 135 THR 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 D residue 56 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 234 MET 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 212 LYS 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 212 LYS 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 78 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.3375 r_free = 0.3375 target = 0.126914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.107600 restraints weight = 12293.156| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.64 r_work: 0.3130 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11550 Z= 0.140 Angle : 0.437 6.495 15568 Z= 0.236 Chirality : 0.038 0.122 1848 Planarity : 0.003 0.029 1953 Dihedral : 4.698 49.656 1520 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.55 % Allowed : 18.53 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.22), residues: 1358 helix: 2.84 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -0.31 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 139 HIS 0.003 0.001 HIS C 232 PHE 0.004 0.001 PHE D 153 TYR 0.004 0.001 TYR B 202 ARG 0.004 0.000 ARG F 181 Details of bonding type rmsd hydrogen bonds : bond 0.06008 ( 932) hydrogen bonds : angle 3.35922 ( 2733) covalent geometry : bond 0.00302 (11550) covalent geometry : angle 0.43652 (15568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7650.83 seconds wall clock time: 134 minutes 16.93 seconds (8056.93 seconds total)