Starting phenix.real_space_refine on Sat Sep 12 11:38:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zg7_11195/09_2026/6zg7_11195.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zg7_11195/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6zg7_11195/09_2026/6zg7_11195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zg7_11195/09_2026/6zg7_11195.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zg7_11195/09_2026/6zg7_11195.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zg7_11195/09_2026/6zg7_11195.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zg7_11195/09_2026/6zg7_11195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zg7_11195/09_2026/6zg7_11195.map" } 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-2.2.1-6174/lib/python3.11/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: 2.69, per 1000 atoms: 0.17 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: 1.47 Conformation dependent library (CDL) restraints added in 495.7 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: 0.35 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: 4.01 Time building geometry restraints manager: 2.03 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: 6523 17.97 - 35.94: 569 35.94 - 53.91: 202 53.91 - 71.87: 69 71.87 - 89.84: 13 Dihedral angle restraints: 7376 sinusoidal: 3934 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 7373 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: 12.730 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: 0.130 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.880 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:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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/Z covalent geometry : bond 0.00606 / 0.27 ( 7850) covalent geometry : angle 0.66071 / 0.36 (10600) hydrogen bonds : bond 0.10272 / 6.88 ( 642) hydrogen bonds : angle 5.15729 / 3.74 ( 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 : 0.433 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: 0.1460 time to fit residues: 32.9458 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 : 0.446 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3525 r_free = 0.3525 target = 0.124296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102971 restraints weight = 31422.453| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.57 r_work: 0.3139 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0976 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= 0.170 Angle : 0.527 4.550 10600 Z= 0.288 Chirality : 0.037 0.149 1255 Planarity : 0.003 0.045 1324 Dihedral : 5.955 52.134 1130 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.55 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: 0.49 (0.27), residues: 1002 helix: 1.14 (0.19), residues: 761 sheet: -2.58 (0.53), residues: 86 loop : -1.68 (0.45), residues: 155 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 0.017 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/Z covalent geometry : bond 0.00363 / 0.17 ( 7850) covalent geometry : angle 0.52683 / 0.29 (10600) hydrogen bonds : bond 0.05116 / 3.47 ( 642) hydrogen bonds : angle 4.17548 / 2.90 ( 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 : 0.418 Fit side-chains revert: symmetry clash REVERT: H 136 GLU cc_start: 0.7999 (tt0) cc_final: 0.7769 (tt0) REVERT: I 14 TYR cc_start: 0.9128 (t80) cc_final: 0.8853 (t80) outliers start: 9 outliers final: 9 residues processed: 137 average time/residue: 0.1483 time to fit residues: 31.4443 Evaluate side-chains 136 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 ASN 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: 2.9990 chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106354 restraints weight = 30752.206| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.69 r_work: 0.3109 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7850 Z= 0.187 Angle : 0.523 4.609 10600 Z= 0.285 Chirality : 0.036 0.143 1255 Planarity : 0.003 0.044 1324 Dihedral : 5.844 52.962 1130 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.95 % Allowed : 9.35 % Favored : 88.70 % 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: 0.78 (0.27), residues: 1002 helix: 1.34 (0.19), residues: 760 sheet: -2.54 (0.52), residues: 85 loop : -1.52 (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 0.002 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 ( 7850) covalent geometry : angle 0.52285 / 0.29 (10600) hydrogen bonds : bond 0.04971 / 3.36 ( 642) hydrogen bonds : angle 4.03189 / 2.78 ( 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 140 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: H 68 GLU cc_start: 0.7289 (tp30) cc_final: 0.6987 (tp30) REVERT: H 136 GLU cc_start: 0.7980 (tt0) cc_final: 0.7765 (tt0) REVERT: I 14 TYR cc_start: 0.9164 (t80) cc_final: 0.8907 (t80) outliers start: 15 outliers final: 13 residues processed: 132 average time/residue: 0.1485 time to fit residues: 30.1019 Evaluate side-chains 135 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9990 chunk 89 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108810 restraints weight = 30306.680| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.70 r_work: 0.3197 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7850 Z= 0.133 Angle : 0.477 4.730 10600 Z= 0.257 Chirality : 0.035 0.143 1255 Planarity : 0.003 0.033 1324 Dihedral : 5.605 53.512 1130 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.69 % Allowed : 10.52 % Favored : 87.79 % 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: 1.27 (0.28), residues: 1002 helix: 1.70 (0.19), residues: 760 sheet: -2.61 (0.51), residues: 89 loop : -1.12 (0.48), residues: 153 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 0.012 0.001 PHE H 20 TRP 0.002 0.001 TRP I 4 HIS 0.001 0.000 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 7850) covalent geometry : angle 0.47721 / 0.26 (10600) hydrogen bonds : bond 0.04466 / 3.02 ( 642) hydrogen bonds : angle 3.79752 / 2.60 ( 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 143 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 68 GLU cc_start: 0.7194 (tp30) cc_final: 0.6945 (tp30) outliers start: 13 outliers final: 12 residues processed: 136 average time/residue: 0.1538 time to fit residues: 32.0676 Evaluate side-chains 138 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102872 restraints weight = 31472.651| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.58 r_work: 0.3147 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1509 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= 0.176 Angle : 0.501 4.599 10600 Z= 0.273 Chirality : 0.036 0.142 1255 Planarity : 0.003 0.040 1324 Dihedral : 5.637 53.585 1130 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.95 % Allowed : 11.43 % Favored : 86.62 % 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: 1.18 (0.28), residues: 1002 helix: 1.64 (0.19), residues: 760 sheet: -2.67 (0.50), residues: 90 loop : -1.17 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 38 TYR 0.014 0.001 TYR G 31 PHE 0.016 0.001 PHE H 20 TRP 0.002 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 7850) covalent geometry : angle 0.50112 / 0.27 (10600) hydrogen bonds : bond 0.04690 / 3.17 ( 642) hydrogen bonds : angle 3.84442 / 2.64 ( 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 144 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: H 68 GLU cc_start: 0.7274 (tp30) cc_final: 0.6991 (tp30) outliers start: 15 outliers final: 14 residues processed: 136 average time/residue: 0.1493 time to fit residues: 31.3734 Evaluate side-chains 140 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS 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: 0.8980 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106945 restraints weight = 30524.135| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.68 r_work: 0.3149 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7850 Z= 0.176 Angle : 0.502 4.832 10600 Z= 0.274 Chirality : 0.036 0.142 1255 Planarity : 0.003 0.040 1324 Dihedral : 5.630 53.637 1130 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.34 % Allowed : 12.47 % 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: 1.22 (0.28), residues: 1002 helix: 1.63 (0.19), residues: 760 sheet: -2.45 (0.54), residues: 80 loop : -1.21 (0.47), residues: 162 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 0.018 0.001 PHE H 20 TRP 0.002 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 7850) covalent geometry : angle 0.50185 / 0.27 (10600) hydrogen bonds : bond 0.04688 / 3.17 ( 642) hydrogen bonds : angle 3.83637 / 2.64 ( 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 148 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: H 68 GLU cc_start: 0.7250 (tp30) cc_final: 0.7044 (tp30) outliers start: 18 outliers final: 17 residues processed: 138 average time/residue: 0.1466 time to fit residues: 31.1943 Evaluate side-chains 145 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS 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 L residue 71 ILE Chi-restraints excluded: chain M residue 51 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106227 restraints weight = 30532.114| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.69 r_work: 0.3115 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7850 Z= 0.190 Angle : 0.516 5.073 10600 Z= 0.282 Chirality : 0.037 0.142 1255 Planarity : 0.004 0.043 1324 Dihedral : 5.654 53.501 1130 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.16 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: 1.19 (0.27), residues: 1002 helix: 1.61 (0.19), residues: 760 sheet: -2.49 (0.54), residues: 80 loop : -1.20 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 38 TYR 0.014 0.002 TYR I 11 PHE 0.020 0.001 PHE H 20 TRP 0.002 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 ( 7850) covalent geometry : angle 0.51560 / 0.28 (10600) hydrogen bonds : bond 0.04785 / 3.23 ( 642) hydrogen bonds : angle 3.85264 / 2.65 ( 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 150 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: G 194 ASP cc_start: 0.8510 (t70) cc_final: 0.8288 (t0) outliers start: 21 outliers final: 19 residues processed: 138 average time/residue: 0.1575 time to fit residues: 33.0374 Evaluate side-chains 148 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 51 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103040 restraints weight = 31333.590| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.56 r_work: 0.3123 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7850 Z= 0.174 Angle : 0.509 5.633 10600 Z= 0.276 Chirality : 0.037 0.157 1255 Planarity : 0.003 0.040 1324 Dihedral : 5.610 53.484 1130 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.47 % Allowed : 14.81 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.68 (0.19), residues: 760 sheet: -2.49 (0.54), residues: 80 loop : -1.16 (0.47), residues: 162 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 0.002 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 7850) covalent geometry : angle 0.50870 / 0.28 (10600) hydrogen bonds : bond 0.04687 / 3.17 ( 642) hydrogen bonds : angle 3.81319 / 2.62 ( 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 150 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 194 ASP cc_start: 0.8476 (t70) cc_final: 0.8263 (t0) REVERT: H 68 GLU cc_start: 0.7253 (tp30) cc_final: 0.7052 (tp30) outliers start: 19 outliers final: 19 residues processed: 140 average time/residue: 0.1564 time to fit residues: 33.4933 Evaluate side-chains 148 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS 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 R residue 60 MET Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 51 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: 0.9980 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108816 restraints weight = 30291.860| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.70 r_work: 0.3133 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7850 Z= 0.132 Angle : 0.480 5.766 10600 Z= 0.258 Chirality : 0.036 0.148 1255 Planarity : 0.003 0.034 1324 Dihedral : 5.460 53.443 1130 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.47 % Allowed : 14.94 % Favored : 82.60 % 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: 1.61 (0.28), residues: 1002 helix: 1.98 (0.19), residues: 751 sheet: -2.64 (0.52), residues: 85 loop : -1.06 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 38 TYR 0.011 0.001 TYR G 31 PHE 0.014 0.001 PHE Q 69 TRP 0.004 0.001 TRP I 4 HIS 0.001 0.000 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 7850) covalent geometry : angle 0.47952 / 0.26 (10600) hydrogen bonds : bond 0.04329 / 2.93 ( 642) hydrogen bonds : angle 3.68276 / 2.51 ( 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 150 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 194 ASP cc_start: 0.8449 (t70) cc_final: 0.8178 (t70) outliers start: 19 outliers final: 18 residues processed: 140 average time/residue: 0.1508 time to fit residues: 32.5567 Evaluate side-chains 143 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS 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 51 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 37 optimal weight: 0.0970 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 32 ASN ** 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 = 0.3538 r_free = 0.3538 target = 0.125441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104109 restraints weight = 31249.331| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.57 r_work: 0.3138 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7850 Z= 0.157 Angle : 0.497 6.169 10600 Z= 0.269 Chirality : 0.036 0.142 1255 Planarity : 0.003 0.039 1324 Dihedral : 5.465 53.240 1130 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.47 % Allowed : 14.94 % Favored : 82.60 % 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: 1.58 (0.28), residues: 1002 helix: 1.93 (0.19), residues: 751 sheet: -2.41 (0.54), residues: 80 loop : -1.10 (0.48), residues: 171 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 0.004 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 7850) covalent geometry : angle 0.49727 / 0.27 (10600) hydrogen bonds : bond 0.04477 / 3.03 ( 642) hydrogen bonds : angle 3.70791 / 2.54 ( 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 144 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 194 ASP cc_start: 0.8418 (t70) cc_final: 0.8051 (t70) outliers start: 19 outliers final: 18 residues processed: 134 average time/residue: 0.1470 time to fit residues: 29.9780 Evaluate side-chains 140 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 78 CYS 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 51 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104643 restraints weight = 31121.503| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.57 r_work: 0.3137 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7850 Z= 0.151 Angle : 0.495 6.178 10600 Z= 0.267 Chirality : 0.036 0.142 1255 Planarity : 0.003 0.038 1324 Dihedral : 5.435 53.083 1130 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.34 % Allowed : 15.19 % 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: 1.63 (0.28), residues: 1002 helix: 1.97 (0.19), residues: 751 sheet: -2.40 (0.54), residues: 80 loop : -1.09 (0.48), residues: 171 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 0.015 0.001 PHE H 20 TRP 0.004 0.001 TRP I 4 HIS 0.002 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 7850) covalent geometry : angle 0.49453 / 0.27 (10600) hydrogen bonds : bond 0.04435 / 3.00 ( 642) hydrogen bonds : angle 3.67977 / 2.52 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3977.22 seconds wall clock time: 68 minutes 28.43 seconds (4108.43 seconds total)