Starting phenix.real_space_refine on Tue Mar 3 21:34:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upn_26673/03_2026/7upn_26673.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upn_26673/03_2026/7upn_26673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7upn_26673/03_2026/7upn_26673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upn_26673/03_2026/7upn_26673.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7upn_26673/03_2026/7upn_26673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upn_26673/03_2026/7upn_26673.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.027 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 58 5.16 5 C 5698 2.51 5 N 1526 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1248 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 6, 'TRANS': 156} Chain: "C" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1771 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 684 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "H" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1248 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 6, 'TRANS': 156} Chain: "F" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1771 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 684 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "I" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2218 SG CYS C 135 91.948 47.665 47.487 1.00 94.84 S ATOM 2230 SG CYS C 137 95.347 47.388 45.860 1.00 97.86 S ATOM 2412 SG CYS C 157 94.166 50.756 46.865 1.00 93.10 S ATOM 2433 SG CYS C 160 95.075 48.157 49.582 1.00 84.53 S ATOM 6653 SG CYS F 135 55.449 44.735 47.627 1.00 94.28 S ATOM 6665 SG CYS F 137 52.062 45.021 45.976 1.00100.38 S ATOM 6847 SG CYS F 157 53.228 41.650 46.990 1.00 93.43 S ATOM 6868 SG CYS F 160 52.307 44.252 49.701 1.00 84.59 S Time building chain proxies: 2.15, per 1000 atoms: 0.24 Number of scatterers: 8872 At special positions: 0 Unit cell: (148.5, 94.6, 106.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 58 16.00 O 1588 8.00 N 1526 7.00 C 5698 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: 0.61 Conformation dependent library (CDL) restraints added in 353.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 137 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 135 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 157 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 160 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 137 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 135 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 157 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 160 " Number of angles added : 12 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 26.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 29 through 42 removed outlier: 3.918A pdb=" N ALA A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'C' and resid 41 through 52 Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 123 through 135 removed outlier: 3.593A pdb=" N TRP C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 132 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 169 removed outlier: 3.516A pdb=" N GLN C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 48 Processing helix chain 'E' and resid 66 through 83 removed outlier: 3.698A pdb=" N MET E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE E 77 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR E 78 " --> pdb=" O CYS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 111 removed outlier: 4.231A pdb=" N LEU E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE E 109 " --> pdb=" O MET E 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 36 removed outlier: 4.233A pdb=" N LEU H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE H 34 " --> pdb=" O ILE H 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.919A pdb=" N ALA B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'F' and resid 41 through 52 Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 123 through 135 removed outlier: 3.592A pdb=" N TRP F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE F 132 " --> pdb=" O PHE F 128 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 169 removed outlier: 3.516A pdb=" N GLN F 162 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 Processing helix chain 'F' and resid 218 through 223 Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 39 through 48 Processing helix chain 'G' and resid 66 through 83 removed outlier: 3.698A pdb=" N MET G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE G 77 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR G 78 " --> pdb=" O CYS G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 111 removed outlier: 4.231A pdb=" N LEU G 101 " --> pdb=" O PRO G 97 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU G 102 " --> pdb=" O GLU G 98 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE G 109 " --> pdb=" O MET G 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 36 removed outlier: 4.233A pdb=" N LEU I 27 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY I 33 " --> pdb=" O ARG I 29 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 removed outlier: 3.699A pdb=" N ARG A 55 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN A 111 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N MET A 100 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL A 128 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER A 21 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL A 12 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 18 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR A 5 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN A 163 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE A 7 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N CYS A 161 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP A 9 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 61 through 64 removed outlier: 4.263A pdb=" N GLU C 69 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 28 through 32 removed outlier: 8.382A pdb=" N VAL E 60 " --> pdb=" O TYR E 18 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LYS E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 12 through 18 removed outlier: 3.867A pdb=" N ALA H 73 " --> pdb=" O PHE H 4 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 46 Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 57 removed outlier: 3.698A pdb=" N ARG B 55 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLN B 111 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N MET B 100 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL B 128 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER B 21 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL B 12 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 18 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR B 5 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN B 163 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE B 7 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N CYS B 161 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP B 9 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 61 through 64 removed outlier: 4.265A pdb=" N GLU F 69 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 28 through 32 removed outlier: 8.382A pdb=" N VAL G 60 " --> pdb=" O TYR G 18 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LYS G 20 " --> pdb=" O VAL G 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 12 through 18 removed outlier: 3.867A pdb=" N ALA I 73 " --> pdb=" O PHE I 4 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 45 through 46 248 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2515 1.33 - 1.45: 1621 1.45 - 1.57: 4878 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9104 Sorted by residual: bond pdb=" CA GLU F 64 " pdb=" C GLU F 64 " ideal model delta sigma weight residual 1.533 1.507 0.026 9.60e-03 1.09e+04 7.50e+00 bond pdb=" CA ASN F 65 " pdb=" C ASN F 65 " ideal model delta sigma weight residual 1.522 1.497 0.025 1.18e-02 7.18e+03 4.49e+00 bond pdb=" CA ASN C 65 " pdb=" C ASN C 65 " ideal model delta sigma weight residual 1.521 1.500 0.022 1.17e-02 7.31e+03 3.48e+00 bond pdb=" C TYR C 68 " pdb=" O TYR C 68 " ideal model delta sigma weight residual 1.235 1.216 0.020 1.21e-02 6.83e+03 2.61e+00 bond pdb=" C LEU C 23 " pdb=" N PRO C 24 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.56e+00 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 11978 1.46 - 2.91: 253 2.91 - 4.37: 35 4.37 - 5.82: 12 5.82 - 7.28: 6 Bond angle restraints: 12284 Sorted by residual: angle pdb=" C HIS I 10 " pdb=" CA HIS I 10 " pdb=" CB HIS I 10 " ideal model delta sigma weight residual 110.42 116.96 -6.54 1.99e+00 2.53e-01 1.08e+01 angle pdb=" C HIS H 10 " pdb=" CA HIS H 10 " pdb=" CB HIS H 10 " ideal model delta sigma weight residual 110.42 116.92 -6.50 1.99e+00 2.53e-01 1.07e+01 angle pdb=" CA PRO F 24 " pdb=" N PRO F 24 " pdb=" CD PRO F 24 " ideal model delta sigma weight residual 112.00 107.59 4.41 1.40e+00 5.10e-01 9.93e+00 angle pdb=" CA PRO C 24 " pdb=" N PRO C 24 " pdb=" CD PRO C 24 " ideal model delta sigma weight residual 112.00 107.66 4.34 1.40e+00 5.10e-01 9.62e+00 angle pdb=" N PRO C 24 " pdb=" CA PRO C 24 " pdb=" C PRO C 24 " ideal model delta sigma weight residual 112.47 118.61 -6.14 2.06e+00 2.36e-01 8.89e+00 ... (remaining 12279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4765 17.61 - 35.22: 485 35.22 - 52.83: 78 52.83 - 70.44: 18 70.44 - 88.05: 12 Dihedral angle restraints: 5358 sinusoidal: 2214 harmonic: 3144 Sorted by residual: dihedral pdb=" CA LEU C 23 " pdb=" C LEU C 23 " pdb=" N PRO C 24 " pdb=" CA PRO C 24 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU F 23 " pdb=" C LEU F 23 " pdb=" N PRO F 24 " pdb=" CA PRO F 24 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CB GLU E 59 " pdb=" CG GLU E 59 " pdb=" CD GLU E 59 " pdb=" OE1 GLU E 59 " ideal model delta sinusoidal sigma weight residual 0.00 -88.05 88.05 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 5355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 987 0.044 - 0.088: 231 0.088 - 0.132: 56 0.132 - 0.176: 6 0.176 - 0.220: 2 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA PRO C 24 " pdb=" N PRO C 24 " pdb=" C PRO C 24 " pdb=" CB PRO C 24 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PRO F 24 " pdb=" N PRO F 24 " pdb=" C PRO F 24 " pdb=" CB PRO F 24 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLN C 66 " pdb=" N GLN C 66 " pdb=" C GLN C 66 " pdb=" CB GLN C 66 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 1279 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 23 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO C 24 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 24 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 24 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 23 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO F 24 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO F 24 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO F 24 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 91 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO H 92 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO H 92 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 92 " 0.017 5.00e-02 4.00e+02 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2443 2.81 - 3.33: 7770 3.33 - 3.85: 13561 3.85 - 4.38: 14798 4.38 - 4.90: 26239 Nonbonded interactions: 64811 Sorted by model distance: nonbonded pdb=" O LYS G 80 " pdb=" OG1 THR G 84 " model vdw 2.284 3.040 nonbonded pdb=" O LYS E 80 " pdb=" OG1 THR E 84 " model vdw 2.285 3.040 nonbonded pdb=" O ASP F 87 " pdb=" N ARG F 95 " model vdw 2.329 3.120 nonbonded pdb=" O ASP C 87 " pdb=" N ARG C 95 " model vdw 2.329 3.120 nonbonded pdb=" OE2 GLU C 123 " pdb=" NE1 TRP C 127 " model vdw 2.347 3.120 ... (remaining 64806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.002 0.059 9112 Z= 0.121 Angle : 0.533 7.278 12296 Z= 0.282 Chirality : 0.041 0.220 1282 Planarity : 0.005 0.104 1562 Dihedral : 14.658 88.054 3330 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.37 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.25), residues: 1072 helix: 0.49 (0.32), residues: 270 sheet: 0.85 (0.66), residues: 72 loop : -1.66 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 33 TYR 0.006 0.001 TYR C 213 PHE 0.012 0.001 PHE B 113 TRP 0.009 0.001 TRP C 28 HIS 0.005 0.001 HIS H 10 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9104) covalent geometry : angle 0.52851 (12284) hydrogen bonds : bond 0.17926 ( 248) hydrogen bonds : angle 6.58781 ( 690) metal coordination : bond 0.00263 ( 8) metal coordination : angle 2.16455 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.7820 (ppp) cc_final: 0.7067 (ppp) REVERT: C 225 MET cc_start: 0.7755 (ttm) cc_final: 0.7341 (ttm) REVERT: E 70 LEU cc_start: 0.8979 (tp) cc_final: 0.8751 (tt) REVERT: E 76 TYR cc_start: 0.7799 (t80) cc_final: 0.7498 (t80) REVERT: E 99 ILE cc_start: 0.8069 (tp) cc_final: 0.7748 (tt) REVERT: H 52 ASP cc_start: 0.9406 (p0) cc_final: 0.9179 (p0) REVERT: H 55 LYS cc_start: 0.8768 (tmmt) cc_final: 0.8357 (ptmm) REVERT: B 61 MET cc_start: 0.7656 (ppp) cc_final: 0.7052 (ppp) REVERT: F 225 MET cc_start: 0.7752 (ttm) cc_final: 0.7343 (ttm) REVERT: I 55 LYS cc_start: 0.8866 (tmmt) cc_final: 0.8574 (ptmm) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.0804 time to fit residues: 17.5717 Evaluate side-chains 116 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN C 220 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN F 220 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.085710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.063531 restraints weight = 37672.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.065293 restraints weight = 19279.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.066528 restraints weight = 13228.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.067120 restraints weight = 10600.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.067567 restraints weight = 9391.708| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9112 Z= 0.113 Angle : 0.548 7.080 12296 Z= 0.282 Chirality : 0.043 0.216 1282 Planarity : 0.005 0.105 1562 Dihedral : 3.868 23.547 1176 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.09 % Favored : 92.35 % Rotamer: Outliers : 0.95 % Allowed : 9.43 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.25), residues: 1072 helix: 0.42 (0.31), residues: 296 sheet: 0.28 (0.56), residues: 96 loop : -1.82 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 63 TYR 0.016 0.001 TYR G 76 PHE 0.010 0.001 PHE A 113 TRP 0.010 0.001 TRP C 130 HIS 0.005 0.001 HIS H 10 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9104) covalent geometry : angle 0.53295 (12284) hydrogen bonds : bond 0.03432 ( 248) hydrogen bonds : angle 5.13844 ( 690) metal coordination : bond 0.00341 ( 8) metal coordination : angle 4.15060 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8017 (ppp) cc_final: 0.7352 (ppp) REVERT: H 26 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: H 52 ASP cc_start: 0.9545 (p0) cc_final: 0.9306 (p0) REVERT: H 55 LYS cc_start: 0.8918 (tmmt) cc_final: 0.8457 (ptmm) REVERT: B 61 MET cc_start: 0.7929 (ppp) cc_final: 0.7254 (ppp) outliers start: 9 outliers final: 2 residues processed: 123 average time/residue: 0.0752 time to fit residues: 13.9887 Evaluate side-chains 113 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain B residue 143 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 18 optimal weight: 0.0030 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 0.0570 chunk 81 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.4112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN H 49 GLN F 220 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.084720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.064226 restraints weight = 36912.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.065934 restraints weight = 18411.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.067113 restraints weight = 12562.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.067767 restraints weight = 10097.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.068051 restraints weight = 8920.528| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9112 Z= 0.129 Angle : 0.549 11.930 12296 Z= 0.280 Chirality : 0.042 0.215 1282 Planarity : 0.005 0.108 1562 Dihedral : 3.975 23.911 1176 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.93 % Favored : 91.51 % Rotamer: Outliers : 1.27 % Allowed : 10.49 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.25), residues: 1072 helix: 0.45 (0.31), residues: 306 sheet: 0.18 (0.48), residues: 124 loop : -1.94 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 63 TYR 0.008 0.001 TYR F 70 PHE 0.010 0.001 PHE A 113 TRP 0.015 0.001 TRP C 71 HIS 0.004 0.001 HIS H 10 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9104) covalent geometry : angle 0.53040 (12284) hydrogen bonds : bond 0.03470 ( 248) hydrogen bonds : angle 4.97740 ( 690) metal coordination : bond 0.00464 ( 8) metal coordination : angle 4.60863 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8151 (ppp) cc_final: 0.7398 (ppp) REVERT: H 6 MET cc_start: 0.6064 (mmm) cc_final: 0.5824 (mtt) REVERT: H 52 ASP cc_start: 0.9550 (p0) cc_final: 0.9303 (p0) REVERT: H 55 LYS cc_start: 0.8909 (tmmt) cc_final: 0.8382 (ptmm) REVERT: B 61 MET cc_start: 0.8135 (ppp) cc_final: 0.7392 (ppp) REVERT: F 225 MET cc_start: 0.7731 (ttm) cc_final: 0.7328 (ttm) REVERT: I 26 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8400 (pm20) outliers start: 12 outliers final: 4 residues processed: 130 average time/residue: 0.0816 time to fit residues: 15.8019 Evaluate side-chains 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain I residue 26 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 HIS I 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.082599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.061953 restraints weight = 37197.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.063790 restraints weight = 18798.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.064957 restraints weight = 12859.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.065590 restraints weight = 10352.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.065737 restraints weight = 9163.155| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9112 Z= 0.168 Angle : 0.613 13.212 12296 Z= 0.308 Chirality : 0.045 0.208 1282 Planarity : 0.005 0.113 1562 Dihedral : 4.280 23.917 1176 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.14 % Favored : 90.30 % Rotamer: Outliers : 1.80 % Allowed : 10.81 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.25), residues: 1072 helix: 0.33 (0.31), residues: 310 sheet: -0.13 (0.47), residues: 134 loop : -2.06 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 63 TYR 0.014 0.001 TYR I 45 PHE 0.011 0.001 PHE B 8 TRP 0.015 0.001 TRP F 78 HIS 0.004 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9104) covalent geometry : angle 0.58921 (12284) hydrogen bonds : bond 0.03836 ( 248) hydrogen bonds : angle 5.12073 ( 690) metal coordination : bond 0.00602 ( 8) metal coordination : angle 5.40239 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8294 (ppp) cc_final: 0.7350 (ppp) REVERT: E 75 MET cc_start: 0.8029 (mtp) cc_final: 0.7513 (mtm) REVERT: H 52 ASP cc_start: 0.9521 (p0) cc_final: 0.9282 (p0) REVERT: H 55 LYS cc_start: 0.8750 (tmmt) cc_final: 0.8206 (ptmm) REVERT: B 61 MET cc_start: 0.8318 (ppp) cc_final: 0.7417 (ppp) REVERT: F 60 MET cc_start: 0.7715 (ptp) cc_final: 0.7408 (ptt) REVERT: I 26 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8374 (pm20) outliers start: 17 outliers final: 8 residues processed: 117 average time/residue: 0.0764 time to fit residues: 13.5094 Evaluate side-chains 107 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain I residue 26 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 6 optimal weight: 0.0980 chunk 20 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.082415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.061644 restraints weight = 37284.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.063502 restraints weight = 19054.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.064679 restraints weight = 13180.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.065258 restraints weight = 10680.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.065748 restraints weight = 9534.193| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9112 Z= 0.152 Angle : 0.606 11.704 12296 Z= 0.303 Chirality : 0.044 0.193 1282 Planarity : 0.005 0.117 1562 Dihedral : 4.359 26.873 1176 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.96 % Favored : 90.49 % Rotamer: Outliers : 2.12 % Allowed : 12.50 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.25), residues: 1072 helix: 0.31 (0.32), residues: 300 sheet: -0.10 (0.47), residues: 128 loop : -2.06 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 9 TYR 0.008 0.001 TYR G 79 PHE 0.011 0.001 PHE B 113 TRP 0.015 0.001 TRP F 78 HIS 0.004 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9104) covalent geometry : angle 0.58774 (12284) hydrogen bonds : bond 0.03559 ( 248) hydrogen bonds : angle 5.06834 ( 690) metal coordination : bond 0.00559 ( 8) metal coordination : angle 4.81503 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8292 (ppp) cc_final: 0.7362 (ppp) REVERT: H 26 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8260 (pm20) REVERT: H 55 LYS cc_start: 0.8761 (tmmt) cc_final: 0.8206 (ptmm) REVERT: B 61 MET cc_start: 0.8322 (ppp) cc_final: 0.7475 (ppp) REVERT: F 60 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7512 (ptt) REVERT: F 71 TRP cc_start: 0.5851 (p-90) cc_final: 0.5465 (p-90) REVERT: I 26 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8337 (pm20) REVERT: I 52 ASP cc_start: 0.9306 (p0) cc_final: 0.8904 (p0) outliers start: 20 outliers final: 15 residues processed: 111 average time/residue: 0.0791 time to fit residues: 13.2608 Evaluate side-chains 112 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain I residue 26 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.083611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.063049 restraints weight = 36922.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.064938 restraints weight = 18851.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.066112 restraints weight = 12995.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.066738 restraints weight = 10494.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.066956 restraints weight = 9339.067| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9112 Z= 0.108 Angle : 0.580 12.305 12296 Z= 0.287 Chirality : 0.043 0.198 1282 Planarity : 0.005 0.117 1562 Dihedral : 4.152 26.631 1176 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.21 % Favored : 91.23 % Rotamer: Outliers : 1.69 % Allowed : 13.77 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.25), residues: 1072 helix: 0.37 (0.32), residues: 310 sheet: -0.14 (0.48), residues: 124 loop : -2.13 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 176 TYR 0.009 0.001 TYR G 79 PHE 0.010 0.001 PHE B 113 TRP 0.009 0.001 TRP C 78 HIS 0.003 0.001 HIS H 10 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9104) covalent geometry : angle 0.56702 (12284) hydrogen bonds : bond 0.02949 ( 248) hydrogen bonds : angle 4.87907 ( 690) metal coordination : bond 0.00426 ( 8) metal coordination : angle 4.00525 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8220 (ppp) cc_final: 0.7427 (ppp) REVERT: E 105 MET cc_start: 0.9143 (mmm) cc_final: 0.8837 (mmm) REVERT: H 26 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: H 55 LYS cc_start: 0.8763 (tmmt) cc_final: 0.8320 (ptmm) REVERT: B 61 MET cc_start: 0.8240 (ppp) cc_final: 0.7388 (ppp) REVERT: I 15 PHE cc_start: 0.5828 (p90) cc_final: 0.5522 (p90) REVERT: I 26 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: I 52 ASP cc_start: 0.9265 (p0) cc_final: 0.8829 (p0) outliers start: 16 outliers final: 7 residues processed: 113 average time/residue: 0.0805 time to fit residues: 13.6897 Evaluate side-chains 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain I residue 26 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.080043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.058400 restraints weight = 36923.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.060257 restraints weight = 19179.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.061435 restraints weight = 13293.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.062083 restraints weight = 10788.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.062296 restraints weight = 9577.853| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9112 Z= 0.161 Angle : 0.631 12.007 12296 Z= 0.314 Chirality : 0.045 0.205 1282 Planarity : 0.006 0.121 1562 Dihedral : 4.364 27.136 1176 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.14 % Favored : 90.30 % Rotamer: Outliers : 1.80 % Allowed : 14.19 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.24), residues: 1072 helix: 0.30 (0.32), residues: 300 sheet: -0.18 (0.47), residues: 128 loop : -2.11 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 9 TYR 0.013 0.001 TYR F 70 PHE 0.011 0.001 PHE A 8 TRP 0.016 0.001 TRP C 78 HIS 0.006 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9104) covalent geometry : angle 0.61122 (12284) hydrogen bonds : bond 0.03690 ( 248) hydrogen bonds : angle 5.00617 ( 690) metal coordination : bond 0.00547 ( 8) metal coordination : angle 5.11331 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8331 (ppp) cc_final: 0.7728 (ppp) REVERT: C 96 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7665 (p0) REVERT: E 105 MET cc_start: 0.9119 (mmm) cc_final: 0.8892 (mmm) REVERT: H 26 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: B 61 MET cc_start: 0.8361 (ppp) cc_final: 0.7799 (ppp) REVERT: F 71 TRP cc_start: 0.5977 (p-90) cc_final: 0.5503 (p-90) REVERT: G 63 ARG cc_start: 0.8407 (mmm160) cc_final: 0.8139 (mmm160) REVERT: G 105 MET cc_start: 0.9107 (mmm) cc_final: 0.8862 (mmm) REVERT: I 26 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: I 52 ASP cc_start: 0.9305 (p0) cc_final: 0.8904 (p0) REVERT: I 74 THR cc_start: 0.8955 (m) cc_final: 0.8689 (t) outliers start: 17 outliers final: 12 residues processed: 105 average time/residue: 0.0788 time to fit residues: 12.4422 Evaluate side-chains 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 115 CYS Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain I residue 26 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.082363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.062049 restraints weight = 36783.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.063328 restraints weight = 20568.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.063788 restraints weight = 14079.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.063855 restraints weight = 12328.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063976 restraints weight = 11582.211| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9112 Z= 0.104 Angle : 0.589 11.835 12296 Z= 0.290 Chirality : 0.044 0.256 1282 Planarity : 0.005 0.119 1562 Dihedral : 4.174 28.284 1176 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.46 % Favored : 91.98 % Rotamer: Outliers : 1.38 % Allowed : 14.51 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.24), residues: 1072 helix: 0.36 (0.32), residues: 298 sheet: -0.52 (0.53), residues: 96 loop : -2.01 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 63 TYR 0.009 0.001 TYR G 79 PHE 0.011 0.001 PHE B 46 TRP 0.012 0.001 TRP C 78 HIS 0.003 0.001 HIS H 10 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9104) covalent geometry : angle 0.57785 (12284) hydrogen bonds : bond 0.02724 ( 248) hydrogen bonds : angle 4.82540 ( 690) metal coordination : bond 0.00423 ( 8) metal coordination : angle 3.67642 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.428 Fit side-chains REVERT: A 61 MET cc_start: 0.8180 (ppp) cc_final: 0.7416 (ppp) REVERT: C 96 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7621 (p0) REVERT: H 26 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: B 61 MET cc_start: 0.8202 (ppp) cc_final: 0.7404 (ppp) REVERT: F 60 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.8010 (ppp) REVERT: F 96 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7611 (p0) REVERT: G 63 ARG cc_start: 0.8439 (mmm160) cc_final: 0.8164 (mmm160) REVERT: I 15 PHE cc_start: 0.5836 (p90) cc_final: 0.5476 (p90) REVERT: I 26 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8225 (pm20) REVERT: I 74 THR cc_start: 0.8921 (m) cc_final: 0.8607 (t) outliers start: 13 outliers final: 8 residues processed: 109 average time/residue: 0.0807 time to fit residues: 13.3210 Evaluate side-chains 108 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain I residue 26 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 HIS F 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.080640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.059406 restraints weight = 36679.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.061145 restraints weight = 18759.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.062215 restraints weight = 12982.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.063005 restraints weight = 10581.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.063410 restraints weight = 9332.420| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9112 Z= 0.169 Angle : 0.647 10.814 12296 Z= 0.322 Chirality : 0.046 0.294 1282 Planarity : 0.006 0.122 1562 Dihedral : 4.417 27.352 1176 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.86 % Favored : 90.58 % Rotamer: Outliers : 1.38 % Allowed : 14.83 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.24), residues: 1072 helix: 0.34 (0.32), residues: 288 sheet: -0.14 (0.48), residues: 116 loop : -2.00 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 63 TYR 0.011 0.001 TYR G 79 PHE 0.012 0.001 PHE E 29 TRP 0.018 0.001 TRP C 78 HIS 0.007 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9104) covalent geometry : angle 0.62680 (12284) hydrogen bonds : bond 0.03737 ( 248) hydrogen bonds : angle 4.97463 ( 690) metal coordination : bond 0.00591 ( 8) metal coordination : angle 5.21500 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.366 Fit side-chains REVERT: A 61 MET cc_start: 0.8355 (ppp) cc_final: 0.7739 (ppp) REVERT: C 96 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7689 (p0) REVERT: E 75 MET cc_start: 0.8134 (mtp) cc_final: 0.7842 (mtm) REVERT: H 26 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: B 61 MET cc_start: 0.8386 (ppp) cc_final: 0.7815 (ppp) REVERT: F 60 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8024 (ppp) REVERT: F 96 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7648 (p0) REVERT: G 63 ARG cc_start: 0.8357 (mmm160) cc_final: 0.8131 (mmm160) REVERT: G 75 MET cc_start: 0.8162 (mtp) cc_final: 0.7906 (mtm) REVERT: G 105 MET cc_start: 0.9071 (mmm) cc_final: 0.8723 (mmm) REVERT: I 26 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8215 (pm20) REVERT: I 52 ASP cc_start: 0.9271 (p0) cc_final: 0.8830 (p0) REVERT: I 74 THR cc_start: 0.8973 (m) cc_final: 0.8761 (t) outliers start: 13 outliers final: 8 residues processed: 105 average time/residue: 0.0759 time to fit residues: 12.1057 Evaluate side-chains 106 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain I residue 26 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 61 optimal weight: 0.0770 chunk 32 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.082172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.062217 restraints weight = 36559.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.063347 restraints weight = 21618.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.063789 restraints weight = 14471.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.064064 restraints weight = 12230.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.064349 restraints weight = 11607.525| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9112 Z= 0.115 Angle : 0.627 11.158 12296 Z= 0.309 Chirality : 0.044 0.282 1282 Planarity : 0.005 0.121 1562 Dihedral : 4.341 29.169 1176 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.84 % Favored : 91.70 % Rotamer: Outliers : 1.48 % Allowed : 15.25 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.24), residues: 1072 helix: 0.41 (0.33), residues: 286 sheet: -0.15 (0.47), residues: 116 loop : -2.02 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 63 TYR 0.009 0.001 TYR G 79 PHE 0.012 0.001 PHE B 46 TRP 0.013 0.001 TRP F 71 HIS 0.004 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9104) covalent geometry : angle 0.61540 (12284) hydrogen bonds : bond 0.02942 ( 248) hydrogen bonds : angle 4.82650 ( 690) metal coordination : bond 0.00430 ( 8) metal coordination : angle 3.93572 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.366 Fit side-chains REVERT: A 61 MET cc_start: 0.8222 (ppp) cc_final: 0.7459 (ppp) REVERT: C 96 ASN cc_start: 0.7837 (OUTLIER) cc_final: 0.7592 (p0) REVERT: E 105 MET cc_start: 0.9185 (mmm) cc_final: 0.8852 (mmm) REVERT: H 26 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: H 74 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8449 (t) REVERT: B 61 MET cc_start: 0.8250 (ppp) cc_final: 0.7762 (ppp) REVERT: F 96 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7616 (p0) REVERT: G 63 ARG cc_start: 0.8407 (mmm160) cc_final: 0.8165 (mmm160) REVERT: G 105 MET cc_start: 0.9080 (mmm) cc_final: 0.8739 (mmm) REVERT: I 15 PHE cc_start: 0.5933 (p90) cc_final: 0.5560 (p90) REVERT: I 26 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8232 (pm20) REVERT: I 52 ASP cc_start: 0.9321 (p0) cc_final: 0.8889 (p0) REVERT: I 74 THR cc_start: 0.8946 (m) cc_final: 0.8746 (t) outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 0.0751 time to fit residues: 12.1437 Evaluate side-chains 107 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain I residue 26 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.080350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059174 restraints weight = 36472.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.060875 restraints weight = 18889.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.062043 restraints weight = 13160.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.062618 restraints weight = 10687.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.063125 restraints weight = 9552.771| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9112 Z= 0.151 Angle : 0.652 10.575 12296 Z= 0.321 Chirality : 0.045 0.276 1282 Planarity : 0.006 0.123 1562 Dihedral : 4.415 27.969 1176 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.24 % Favored : 90.30 % Rotamer: Outliers : 1.48 % Allowed : 15.15 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.24), residues: 1072 helix: 0.33 (0.32), residues: 286 sheet: -0.20 (0.47), residues: 116 loop : -2.01 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 9 TYR 0.010 0.001 TYR G 79 PHE 0.011 0.001 PHE B 113 TRP 0.033 0.001 TRP F 78 HIS 0.006 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9104) covalent geometry : angle 0.63424 (12284) hydrogen bonds : bond 0.03475 ( 248) hydrogen bonds : angle 4.90142 ( 690) metal coordination : bond 0.00523 ( 8) metal coordination : angle 4.83633 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.30 seconds wall clock time: 29 minutes 39.09 seconds (1779.09 seconds total)