Starting phenix.real_space_refine on Wed Mar 4 18:42:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zg7_11195/03_2026/6zg7_11195.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zg7_11195/03_2026/6zg7_11195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zg7_11195/03_2026/6zg7_11195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zg7_11195/03_2026/6zg7_11195.map" model { file = "/net/cci-nas-00/data/ceres_data/6zg7_11195/03_2026/6zg7_11195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zg7_11195/03_2026/6zg7_11195.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 S 41 5.16 5 C 5014 2.51 5 N 1260 2.21 5 O 1420 1.98 5 H 8004 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 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: 15739 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4300 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1958 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 764 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 46} Chain: "R" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1096 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1096 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1096 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1096 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1096 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.84, per 1000 atoms: 0.18 Number of scatterers: 15739 At special positions: 0 Unit cell: (70.216, 72.312, 188.64, 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) S 41 16.00 O 1420 8.00 N 1260 7.00 C 5014 6.00 H 8004 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 439.8 milliseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 3 sheets defined 77.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'G' and resid 2 through 48 removed outlier: 3.821A pdb=" N ARG G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.763A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 55 Processing helix chain 'G' and resid 79 through 98 removed outlier: 3.675A pdb=" N SER G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 121 removed outlier: 3.756A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N THR G 119 " --> pdb=" O ILE G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.500A pdb=" N SER G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 199 through 272 removed outlier: 4.336A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 120 removed outlier: 4.377A pdb=" N LEU H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 10 through 25 Processing helix chain 'I' and resid 27 through 36 removed outlier: 4.476A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 15 Processing helix chain 'R' and resid 17 through 39 removed outlier: 4.327A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 73 removed outlier: 3.702A pdb=" N SER R 48 " --> pdb=" O GLN R 44 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE R 73 " --> pdb=" O PHE R 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 14 Processing helix chain 'K' and resid 17 through 39 removed outlier: 4.158A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 43 removed outlier: 3.733A pdb=" N M3L K 43 " --> pdb=" O PRO K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 40 through 43' Processing helix chain 'K' and resid 44 through 73 removed outlier: 3.758A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 15 removed outlier: 3.849A pdb=" N PHE L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE L 9 " --> pdb=" O ALA L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 39 removed outlier: 3.562A pdb=" N VAL L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN L 39 " --> pdb=" O GLY L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 73 Processing helix chain 'M' and resid 2 through 15 removed outlier: 5.446A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE M 9 " --> pdb=" O ALA M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 39 removed outlier: 4.185A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 73 removed outlier: 4.143A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 15 Processing helix chain 'N' and resid 17 through 39 removed outlier: 4.538A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 74 removed outlier: 3.837A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL N 67 " --> pdb=" O PHE N 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'P' and resid 17 through 38 removed outlier: 3.969A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 41 No H-bonds generated for 'chain 'P' and resid 39 through 41' Processing helix chain 'P' and resid 42 through 73 removed outlier: 3.653A pdb=" N GLY P 61 " --> pdb=" O SER P 57 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1 through 5 Processing helix chain 'Q' and resid 6 through 15 Processing helix chain 'Q' and resid 17 through 39 removed outlier: 4.213A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY Q 26 " --> pdb=" O GLY Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 75 removed outlier: 4.355A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 15 Processing helix chain 'O' and resid 17 through 39 removed outlier: 4.161A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 74 removed outlier: 3.955A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 172 through 179 removed outlier: 5.432A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N HIS G 66 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ILE G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE G 68 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL G 108 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY G 70 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 11.158A pdb=" N VAL G 103 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N PHE G 128 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR G 127 " --> pdb=" O VAL I 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS I 43 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 26 through 31 removed outlier: 4.908A pdb=" N ASN H 29 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE H 20 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 45 through 47 642 hydrogen bonds defined for protein. 1908 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: 3.63 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7850 1.03 - 1.23: 174 1.23 - 1.42: 3177 1.42 - 1.61: 4581 1.61 - 1.81: 72 Bond restraints: 15854 Sorted by residual: bond pdb=" CA M3L M 43 " pdb=" HA M3L M 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" CA M3L N 43 " pdb=" HA M3L N 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" CA M3L R 43 " pdb=" HA M3L R 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" CA M3L P 43 " pdb=" HA M3L P 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" CA M3L L 43 " pdb=" HA M3L L 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 15849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 28257 1.74 - 3.47: 394 3.47 - 5.21: 35 5.21 - 6.94: 3 6.94 - 8.68: 2 Bond angle restraints: 28691 Sorted by residual: angle pdb=" N M3L K 43 " pdb=" CA M3L K 43 " pdb=" C M3L K 43 " ideal model delta sigma weight residual 111.00 119.68 -8.68 2.80e+00 1.28e-01 9.61e+00 angle pdb=" N VAL K 18 " pdb=" CA VAL K 18 " pdb=" C VAL K 18 " ideal model delta sigma weight residual 113.07 108.91 4.16 1.37e+00 5.33e-01 9.23e+00 angle pdb=" N GLN K 44 " pdb=" CA GLN K 44 " pdb=" C GLN K 44 " ideal model delta sigma weight residual 111.00 103.60 7.40 2.80e+00 1.28e-01 6.98e+00 angle pdb=" N VAL L 16 " pdb=" CA VAL L 16 " pdb=" C VAL L 16 " ideal model delta sigma weight residual 112.98 109.82 3.16 1.25e+00 6.40e-01 6.39e+00 angle pdb=" C SER M 57 " pdb=" N GLU M 58 " pdb=" CA GLU M 58 " ideal model delta sigma weight residual 121.18 116.50 4.68 1.98e+00 2.55e-01 5.58e+00 ... (remaining 28686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6541 17.97 - 35.94: 574 35.94 - 53.91: 205 53.91 - 71.87: 72 71.87 - 89.84: 16 Dihedral angle restraints: 7408 sinusoidal: 3966 harmonic: 3442 Sorted by residual: dihedral pdb=" CA MET O 60 " pdb=" C MET O 60 " pdb=" N GLY O 61 " pdb=" CA GLY O 61 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASP R 3 " pdb=" C ASP R 3 " pdb=" N THR R 4 " pdb=" CA THR R 4 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA M3L K 43 " pdb=" C M3L K 43 " pdb=" N GLN K 44 " pdb=" CA GLN K 44 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 7405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 712 0.029 - 0.057: 360 0.057 - 0.086: 124 0.086 - 0.115: 38 0.115 - 0.143: 21 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA PRO Q 40 " pdb=" N PRO Q 40 " pdb=" C PRO Q 40 " pdb=" CB PRO Q 40 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE G 178 " pdb=" N ILE G 178 " pdb=" C ILE G 178 " pdb=" CB ILE G 178 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA M3L K 43 " pdb=" N M3L K 43 " pdb=" C M3L K 43 " pdb=" CB M3L K 43 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1252 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN K 44 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C GLN K 44 " 0.062 2.00e-02 2.50e+03 pdb=" O GLN K 44 " -0.024 2.00e-02 2.50e+03 pdb=" N GLN K 45 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 20 " -0.014 2.00e-02 2.50e+03 1.05e-02 3.31e+00 pdb=" CG PHE H 20 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 20 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE H 20 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 20 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE H 20 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 20 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE H 20 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE H 20 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE H 20 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE H 20 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE H 20 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 47 " -0.014 2.00e-02 2.50e+03 7.82e-03 1.83e+00 pdb=" CG PHE N 47 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE N 47 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE N 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE N 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE N 47 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE N 47 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE N 47 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE N 47 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE N 47 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE N 47 " 0.000 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 943 2.19 - 2.79: 33278 2.79 - 3.40: 45997 3.40 - 4.00: 58873 4.00 - 4.60: 93269 Nonbonded interactions: 232360 Sorted by model distance: nonbonded pdb=" OD1 ASN H 85 " pdb="HE22 GLN H 91 " model vdw 1.591 2.450 nonbonded pdb=" O ASP Q 1 " pdb=" HG1 THR Q 4 " model vdw 1.624 2.450 nonbonded pdb=" O PRO G 136 " pdb=" HZ3 LYS G 218 " model vdw 1.649 2.450 nonbonded pdb=" O HIS G 66 " pdb=" HH TYR G 153 " model vdw 1.673 2.450 nonbonded pdb=" OD2 ASP H 37 " pdb=" HG SER Q 41 " model vdw 1.675 2.450 ... (remaining 232355 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: 0.00 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 1 through 74) selection = (chain 'N' and resid 1 through 74) selection = (chain 'O' and resid 1 through 74) selection = chain 'P' selection = (chain 'Q' and resid 1 through 74) selection = (chain 'R' and resid 1 through 74) } 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: 11.720 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: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.006 0.045 7850 Z= 0.274 Angle : 0.661 8.681 10600 Z= 0.364 Chirality : 0.040 0.143 1255 Planarity : 0.003 0.036 1324 Dihedral : 14.313 89.843 2727 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.27), residues: 1002 helix: 0.71 (0.19), residues: 762 sheet: -2.35 (0.56), residues: 84 loop : -1.90 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 128 TYR 0.014 0.002 TYR G 193 PHE 0.031 0.002 PHE H 20 TRP 0.002 0.001 TRP I 4 HIS 0.005 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 7850) covalent geometry : angle 0.66071 (10600) hydrogen bonds : bond 0.10272 ( 642) hydrogen bonds : angle 5.15729 ( 1908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: G 232 MET cc_start: 0.8474 (mmm) cc_final: 0.8257 (mmt) REVERT: H 136 GLU cc_start: 0.7734 (tt0) cc_final: 0.7524 (tt0) REVERT: I 14 TYR cc_start: 0.8997 (t80) cc_final: 0.8754 (t80) REVERT: I 29 GLU cc_start: 0.7588 (pp20) cc_final: 0.7321 (pp20) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1398 time to fit residues: 31.0966 Evaluate side-chains 124 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN H 85 ASN H 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106357 restraints weight = 30739.793| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.70 r_work: 0.3115 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7850 Z= 0.179 Angle : 0.530 4.394 10600 Z= 0.290 Chirality : 0.037 0.148 1255 Planarity : 0.004 0.047 1324 Dihedral : 5.992 52.430 1130 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.17 % Allowed : 7.53 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 1002 helix: 1.15 (0.19), residues: 759 sheet: -2.59 (0.52), residues: 86 loop : -1.74 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 38 TYR 0.012 0.001 TYR I 11 PHE 0.018 0.001 PHE H 20 TRP 0.001 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7850) covalent geometry : angle 0.53041 (10600) hydrogen bonds : bond 0.05101 ( 642) hydrogen bonds : angle 4.17129 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: G 232 MET cc_start: 0.8566 (mmm) cc_final: 0.8351 (mmt) REVERT: H 136 GLU cc_start: 0.8024 (tt0) cc_final: 0.7779 (tt0) REVERT: I 14 TYR cc_start: 0.9151 (t80) cc_final: 0.8887 (t80) outliers start: 9 outliers final: 8 residues processed: 137 average time/residue: 0.1346 time to fit residues: 27.9981 Evaluate side-chains 135 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 91 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103842 restraints weight = 31342.671| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.57 r_work: 0.3127 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7850 Z= 0.167 Angle : 0.504 4.629 10600 Z= 0.274 Chirality : 0.036 0.144 1255 Planarity : 0.003 0.040 1324 Dihedral : 5.832 52.822 1130 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.82 % Allowed : 9.09 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.27), residues: 1002 helix: 1.44 (0.19), residues: 760 sheet: -2.51 (0.52), residues: 85 loop : -1.51 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 38 TYR 0.013 0.001 TYR I 11 PHE 0.016 0.001 PHE H 20 TRP 0.001 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7850) covalent geometry : angle 0.50372 (10600) hydrogen bonds : bond 0.04822 ( 642) hydrogen bonds : angle 3.97602 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: G 232 MET cc_start: 0.8549 (mmm) cc_final: 0.8292 (mmt) REVERT: H 136 GLU cc_start: 0.7965 (tt0) cc_final: 0.7761 (tt0) REVERT: I 14 TYR cc_start: 0.9146 (t80) cc_final: 0.8876 (t80) outliers start: 14 outliers final: 12 residues processed: 134 average time/residue: 0.1399 time to fit residues: 28.3297 Evaluate side-chains 136 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 47 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.131683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109069 restraints weight = 30260.142| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.71 r_work: 0.3152 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7850 Z= 0.130 Angle : 0.468 4.923 10600 Z= 0.253 Chirality : 0.035 0.143 1255 Planarity : 0.003 0.033 1324 Dihedral : 5.650 53.042 1130 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.82 % Allowed : 10.26 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.28), residues: 1002 helix: 1.77 (0.19), residues: 760 sheet: -2.50 (0.52), residues: 87 loop : -1.16 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 38 TYR 0.015 0.001 TYR G 31 PHE 0.011 0.001 PHE H 20 TRP 0.002 0.001 TRP I 4 HIS 0.001 0.000 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7850) covalent geometry : angle 0.46840 (10600) hydrogen bonds : bond 0.04397 ( 642) hydrogen bonds : angle 3.76865 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 232 MET cc_start: 0.8684 (mmm) cc_final: 0.8373 (mmt) outliers start: 14 outliers final: 13 residues processed: 137 average time/residue: 0.1472 time to fit residues: 30.4105 Evaluate side-chains 137 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 242 MET Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104647 restraints weight = 31113.942| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.58 r_work: 0.3151 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7850 Z= 0.158 Angle : 0.486 5.004 10600 Z= 0.263 Chirality : 0.036 0.143 1255 Planarity : 0.003 0.037 1324 Dihedral : 5.656 52.734 1130 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.21 % Allowed : 11.56 % Favored : 86.23 % 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: 1.33 (0.28), residues: 1002 helix: 1.76 (0.19), residues: 760 sheet: -2.63 (0.50), residues: 90 loop : -1.15 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 38 TYR 0.013 0.001 TYR I 11 PHE 0.014 0.001 PHE H 20 TRP 0.002 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7850) covalent geometry : angle 0.48621 (10600) hydrogen bonds : bond 0.04516 ( 642) hydrogen bonds : angle 3.78500 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: G 194 ASP cc_start: 0.8491 (t70) cc_final: 0.8121 (t70) REVERT: G 232 MET cc_start: 0.8640 (mmm) cc_final: 0.8367 (mmt) outliers start: 17 outliers final: 15 residues processed: 136 average time/residue: 0.1392 time to fit residues: 28.9267 Evaluate side-chains 141 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 242 MET Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.125477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103952 restraints weight = 31147.739| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.58 r_work: 0.3145 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7850 Z= 0.155 Angle : 0.484 4.992 10600 Z= 0.263 Chirality : 0.036 0.142 1255 Planarity : 0.003 0.037 1324 Dihedral : 5.642 53.471 1130 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.47 % Allowed : 12.34 % Favored : 85.19 % 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 (0.28), residues: 1002 helix: 1.79 (0.19), residues: 760 sheet: -2.66 (0.50), residues: 90 loop : -1.07 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 38 TYR 0.013 0.001 TYR I 11 PHE 0.015 0.001 PHE H 20 TRP 0.003 0.001 TRP I 4 HIS 0.001 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7850) covalent geometry : angle 0.48410 (10600) hydrogen bonds : bond 0.04493 ( 642) hydrogen bonds : angle 3.74946 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: G 194 ASP cc_start: 0.8488 (t70) cc_final: 0.8125 (t70) REVERT: G 232 MET cc_start: 0.8667 (mmm) cc_final: 0.8386 (mmt) outliers start: 19 outliers final: 16 residues processed: 137 average time/residue: 0.1428 time to fit residues: 29.5730 Evaluate side-chains 144 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 24 ASP Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.129153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106661 restraints weight = 30482.664| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.69 r_work: 0.3148 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7850 Z= 0.185 Angle : 0.508 5.896 10600 Z= 0.276 Chirality : 0.036 0.142 1255 Planarity : 0.003 0.040 1324 Dihedral : 5.703 54.624 1130 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.73 % Allowed : 13.38 % Favored : 83.90 % 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: 1.29 (0.28), residues: 1002 helix: 1.70 (0.19), residues: 760 sheet: -2.52 (0.52), residues: 86 loop : -1.17 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 38 TYR 0.014 0.001 TYR I 11 PHE 0.019 0.001 PHE H 20 TRP 0.003 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 7850) covalent geometry : angle 0.50829 (10600) hydrogen bonds : bond 0.04683 ( 642) hydrogen bonds : angle 3.79406 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.311 Fit side-chains REVERT: G 232 MET cc_start: 0.8757 (mmm) cc_final: 0.8456 (mmt) outliers start: 21 outliers final: 20 residues processed: 134 average time/residue: 0.1371 time to fit residues: 28.0791 Evaluate side-chains 145 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 24 ASP Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain R residue 60 MET Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.124623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103176 restraints weight = 31308.834| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.57 r_work: 0.3134 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7850 Z= 0.180 Angle : 0.507 5.450 10600 Z= 0.276 Chirality : 0.036 0.143 1255 Planarity : 0.003 0.040 1324 Dihedral : 5.706 55.591 1130 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.73 % Allowed : 13.90 % Favored : 83.38 % 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: 1.28 (0.28), residues: 1002 helix: 1.70 (0.19), residues: 760 sheet: -2.58 (0.52), residues: 86 loop : -1.18 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 38 TYR 0.014 0.001 TYR I 11 PHE 0.018 0.001 PHE H 20 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 7850) covalent geometry : angle 0.50708 (10600) hydrogen bonds : bond 0.04682 ( 642) hydrogen bonds : angle 3.79541 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: G 232 MET cc_start: 0.8605 (mmm) cc_final: 0.8330 (mmt) outliers start: 21 outliers final: 21 residues processed: 139 average time/residue: 0.1353 time to fit residues: 28.6858 Evaluate side-chains 148 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 24 ASP Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain R residue 60 MET Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 55 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.127455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104865 restraints weight = 30988.892| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.70 r_work: 0.3174 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7850 Z= 0.154 Angle : 0.495 6.091 10600 Z= 0.267 Chirality : 0.036 0.155 1255 Planarity : 0.003 0.036 1324 Dihedral : 5.639 56.066 1130 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.60 % Allowed : 14.42 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.50 (0.28), residues: 1002 helix: 1.91 (0.19), residues: 750 sheet: -2.53 (0.52), residues: 86 loop : -1.18 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 38 TYR 0.012 0.001 TYR I 11 PHE 0.015 0.001 PHE H 20 TRP 0.003 0.001 TRP I 4 HIS 0.001 0.001 HIS G 117 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7850) covalent geometry : angle 0.49456 (10600) hydrogen bonds : bond 0.04503 ( 642) hydrogen bonds : angle 3.72494 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: G 232 MET cc_start: 0.8734 (mmm) cc_final: 0.8427 (mmt) outliers start: 20 outliers final: 18 residues processed: 136 average time/residue: 0.1444 time to fit residues: 29.9350 Evaluate side-chains 142 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 242 MET Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain R residue 60 MET Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.124285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102925 restraints weight = 31454.356| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.56 r_work: 0.3173 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7850 Z= 0.185 Angle : 0.520 6.287 10600 Z= 0.283 Chirality : 0.037 0.174 1255 Planarity : 0.003 0.042 1324 Dihedral : 5.693 56.791 1130 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.47 % Allowed : 15.06 % Favored : 82.47 % 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: 1.33 (0.28), residues: 1002 helix: 1.78 (0.19), residues: 751 sheet: -2.55 (0.52), residues: 86 loop : -1.23 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 38 TYR 0.014 0.001 TYR I 11 PHE 0.019 0.001 PHE H 20 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7850) covalent geometry : angle 0.52047 (10600) hydrogen bonds : bond 0.04699 ( 642) hydrogen bonds : angle 3.78306 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 232 MET cc_start: 0.8694 (mmm) cc_final: 0.8457 (mmt) outliers start: 19 outliers final: 19 residues processed: 133 average time/residue: 0.1410 time to fit residues: 28.3504 Evaluate side-chains 138 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain R residue 60 MET Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 47 PHE Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.124829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103504 restraints weight = 31261.940| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.57 r_work: 0.3142 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7850 Z= 0.166 Angle : 0.506 6.183 10600 Z= 0.274 Chirality : 0.036 0.159 1255 Planarity : 0.003 0.038 1324 Dihedral : 5.654 57.206 1130 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.21 % Allowed : 15.58 % Favored : 82.21 % 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: 1.43 (0.28), residues: 1002 helix: 1.85 (0.19), residues: 751 sheet: -2.53 (0.52), residues: 86 loop : -1.18 (0.49), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 38 TYR 0.013 0.001 TYR I 11 PHE 0.017 0.001 PHE H 20 TRP 0.004 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7850) covalent geometry : angle 0.50637 (10600) hydrogen bonds : bond 0.04587 ( 642) hydrogen bonds : angle 3.73541 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3577.18 seconds wall clock time: 61 minutes 26.68 seconds (3686.68 seconds total)