Starting phenix.real_space_refine on Fri Sep 11 04:38:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zik_11227/09_2026/6zik_11227.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zik_11227/09_2026/6zik_11227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zik_11227/09_2026/6zik_11227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zik_11227/09_2026/6zik_11227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zik_11227/09_2026/6zik_11227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zik_11227/09_2026/6zik_11227.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6zik_11227/09_2026/6zik_11227.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zik_11227/09_2026/6zik_11227.cif" } resolution = 3.66 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: 4 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 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 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: 7735 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2115 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 979 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 369 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} 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: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} 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: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} 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: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} 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: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} 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: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} 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: "R" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} 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: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} 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: 1.67, per 1000 atoms: 0.22 Number of scatterers: 7735 At special positions: 0 Unit cell: (70.216, 68.12, 188.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1420 8.00 N 1260 7.00 C 5014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 450.2 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: 38 helices and 3 sheets defined 77.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'G' and resid 2 through 55 removed outlier: 3.667A pdb=" N ARG G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 4.212A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 99 removed outlier: 3.800A pdb=" N SER G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 116 removed outlier: 3.918A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 121 removed outlier: 3.688A pdb=" N SER G 121 " --> pdb=" O HIS G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.607A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 3.520A 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: 3.808A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 118 Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 2 through 8 removed outlier: 3.565A pdb=" N GLN I 6 " --> pdb=" O ALA I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 24 Processing helix chain 'I' and resid 27 through 36 removed outlier: 3.633A pdb=" N ALA I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 15 Processing helix chain 'K' and resid 17 through 39 removed outlier: 3.759A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 43 Processing helix chain 'K' and resid 44 through 73 removed outlier: 4.237A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 16 removed outlier: 3.892A pdb=" N VAL L 16 " --> pdb=" O GLY L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 39 removed outlier: 4.079A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 73 removed outlier: 3.624A pdb=" N MET L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 15 removed outlier: 3.973A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 39 removed outlier: 3.896A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 73 removed outlier: 4.251A 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: 4.036A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 74 removed outlier: 3.734A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'P' and resid 17 through 39 removed outlier: 3.981A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 73 removed outlier: 3.785A pdb=" N GLY P 61 " --> pdb=" O SER P 57 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 15 removed outlier: 3.575A pdb=" N PHE Q 8 " --> pdb=" O THR Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 39 removed outlier: 4.150A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 74 removed outlier: 3.604A pdb=" N LEU Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 15 removed outlier: 3.519A pdb=" N PHE R 8 " --> pdb=" O THR R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 39 removed outlier: 4.382A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 73 removed outlier: 4.111A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 15 Processing helix chain 'O' and resid 17 through 39 removed outlier: 4.072A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 62 removed outlier: 3.605A pdb=" N LEU O 52 " --> pdb=" O SER O 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 73 Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.089A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N HIS G 66 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE G 68 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL G 108 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY G 70 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU G 125 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE G 105 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N THR G 127 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY G 107 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LYS G 129 " --> pdb=" O GLY G 107 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR G 127 " --> pdb=" O VAL I 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 25 through 31 removed outlier: 6.257A pdb=" N PHE H 20 " --> pdb=" O PHE H 27 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN H 29 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE H 18 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.314A 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 removed outlier: 3.667A pdb=" N GLN H 35 " --> pdb=" O HIS H 66 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1962 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2449 1.34 - 1.46: 1363 1.46 - 1.58: 3966 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 7850 Sorted by residual: bond pdb=" CB MET K 60 " pdb=" CG MET K 60 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" CG1 ILE H 135 " pdb=" CD1 ILE H 135 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.03e+00 bond pdb=" CG MET K 60 " pdb=" SD MET K 60 " ideal model delta sigma weight residual 1.803 1.769 0.034 2.50e-02 1.60e+03 1.86e+00 bond pdb=" CA GLY H 80 " pdb=" C GLY H 80 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.20e-02 6.94e+03 1.67e+00 bond pdb=" CB VAL K 16 " pdb=" CG1 VAL K 16 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 ... (remaining 7845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10366 2.10 - 4.20: 196 4.20 - 6.30: 28 6.30 - 8.40: 9 8.40 - 10.50: 1 Bond angle restraints: 10600 Sorted by residual: angle pdb=" CB MET K 60 " pdb=" CG MET K 60 " pdb=" SD MET K 60 " ideal model delta sigma weight residual 112.70 123.20 -10.50 3.00e+00 1.11e-01 1.23e+01 angle pdb=" CG MET K 60 " pdb=" SD MET K 60 " pdb=" CE MET K 60 " ideal model delta sigma weight residual 100.90 93.97 6.93 2.20e+00 2.07e-01 9.91e+00 angle pdb=" CA LYS H 114 " pdb=" CB LYS H 114 " pdb=" CG LYS H 114 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.91e+00 angle pdb=" N GLN K 44 " pdb=" CA GLN K 44 " pdb=" C GLN K 44 " ideal model delta sigma weight residual 111.00 102.79 8.21 2.80e+00 1.28e-01 8.60e+00 angle pdb=" C SER H 117 " pdb=" N GLU H 118 " pdb=" CA GLU H 118 " ideal model delta sigma weight residual 122.65 118.04 4.61 1.60e+00 3.91e-01 8.31e+00 ... (remaining 10595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4156 17.95 - 35.90: 373 35.90 - 53.85: 58 53.85 - 71.80: 9 71.80 - 89.75: 7 Dihedral angle restraints: 4603 sinusoidal: 1660 harmonic: 2943 Sorted by residual: dihedral pdb=" CA GLY G 79 " pdb=" C GLY G 79 " pdb=" N ALA G 80 " pdb=" CA ALA G 80 " ideal model delta harmonic sigma weight residual -180.00 -159.22 -20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA LEU Q 56 " pdb=" C LEU Q 56 " pdb=" N SER Q 57 " pdb=" CA SER Q 57 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PHE Q 73 " pdb=" C PHE Q 73 " pdb=" N ALA Q 74 " pdb=" CA ALA Q 74 " ideal model delta harmonic sigma weight residual -180.00 -162.16 -17.84 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 4600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 712 0.030 - 0.061: 354 0.061 - 0.091: 127 0.091 - 0.121: 54 0.121 - 0.152: 8 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA M3L R 43 " pdb=" N M3L R 43 " pdb=" C M3L R 43 " pdb=" CB M3L R 43 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.76e-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 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA M3L P 43 " pdb=" N M3L P 43 " pdb=" C M3L P 43 " pdb=" CB M3L P 43 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 1252 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 59 " -0.077 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO G 60 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN K 44 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLN K 44 " -0.067 2.00e-02 2.50e+03 pdb=" O GLN K 44 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN K 45 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 52 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO H 53 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 53 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 53 " -0.027 5.00e-02 4.00e+02 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 131 2.69 - 3.24: 8231 3.24 - 3.79: 12851 3.79 - 4.35: 16154 4.35 - 4.90: 27431 Nonbonded interactions: 64798 Sorted by model distance: nonbonded pdb=" OG1 THR M 4 " pdb=" OD1 ASP N 3 " model vdw 2.134 3.040 nonbonded pdb=" OG SER P 21 " pdb=" O SER P 57 " model vdw 2.159 3.040 nonbonded pdb=" OG SER M 21 " pdb=" O SER M 57 " model vdw 2.170 3.040 nonbonded pdb=" OD1 ASN G 15 " pdb=" NZ LYS G 18 " model vdw 2.179 3.120 nonbonded pdb=" OG1 THR K 4 " pdb=" OD1 ASP L 3 " model vdw 2.207 3.040 ... (remaining 64793 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.840 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.400 Find NCS groups from input model: 0.090 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.005 0.056 7850 Z= 0.225 Angle : 0.729 10.502 10600 Z= 0.386 Chirality : 0.044 0.152 1255 Planarity : 0.005 0.117 1324 Dihedral : 14.227 89.754 2727 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 1.08 (0.27), residues: 1002 helix: 1.35 (0.19), residues: 763 sheet: -1.09 (0.50), residues: 90 loop : -1.13 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 8 TYR 0.013 0.002 TYR G 193 PHE 0.021 0.002 PHE P 63 TRP 0.002 0.001 TRP I 4 HIS 0.007 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 ( 7850) covalent geometry : angle 0.72895 / 0.39 (10600) hydrogen bonds : bond 0.09536 / 6.62 ( 659) hydrogen bonds : angle 4.59899 / 3.33 ( 1962) *********************** 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 179 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.286 Fit side-chains REVERT: G 8 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.5858 (tpt-90) REVERT: M 66 MET cc_start: 0.6192 (mmp) cc_final: 0.5792 (tmm) REVERT: Q 56 LEU cc_start: 0.8173 (tp) cc_final: 0.7935 (tp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0697 time to fit residues: 18.3705 Evaluate side-chains 144 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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: 0.5980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117353 restraints weight = 10996.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120125 restraints weight = 6579.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121902 restraints weight = 4735.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123028 restraints weight = 3841.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123604 restraints weight = 3361.894| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7850 Z= 0.181 Angle : 0.577 7.066 10600 Z= 0.303 Chirality : 0.041 0.147 1255 Planarity : 0.004 0.085 1324 Dihedral : 5.942 58.247 1130 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.73 % Allowed : 11.95 % Favored : 85.32 % 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: 1.40 (0.27), residues: 1002 helix: 1.58 (0.19), residues: 768 sheet: -1.09 (0.51), residues: 90 loop : -1.08 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 8 TYR 0.029 0.002 TYR G 171 PHE 0.021 0.002 PHE P 63 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS G 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 7850) covalent geometry : angle 0.57718 / 0.30 (10600) hydrogen bonds : bond 0.04852 / 3.26 ( 659) hydrogen bonds : angle 3.87105 / 2.83 ( 1962) *********************** 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 191 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.196 Fit side-chains REVERT: G 8 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.6060 (tpt-90) REVERT: G 205 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7644 (mm-40) REVERT: H 91 GLN cc_start: 0.8618 (mp10) cc_final: 0.8334 (mp10) REVERT: H 132 GLN cc_start: 0.7100 (tm-30) cc_final: 0.6548 (tm-30) REVERT: L 60 MET cc_start: 0.6717 (mmt) cc_final: 0.6223 (mmt) REVERT: M 66 MET cc_start: 0.6244 (mmp) cc_final: 0.5946 (tmm) REVERT: Q 54 PHE cc_start: 0.8529 (t80) cc_final: 0.8299 (t80) outliers start: 21 outliers final: 16 residues processed: 181 average time/residue: 0.0661 time to fit residues: 17.0882 Evaluate side-chains 168 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 75 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.0010 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.4364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117665 restraints weight = 10906.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120592 restraints weight = 6479.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122442 restraints weight = 4617.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123584 restraints weight = 3725.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124176 restraints weight = 3259.792| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1520 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= 0.140 Angle : 0.529 6.880 10600 Z= 0.277 Chirality : 0.039 0.173 1255 Planarity : 0.004 0.068 1324 Dihedral : 5.713 57.734 1130 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.51 % Allowed : 15.58 % Favored : 80.91 % 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: 1.75 (0.27), residues: 1002 helix: 1.83 (0.19), residues: 769 sheet: -0.79 (0.52), residues: 88 loop : -1.10 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 8 TYR 0.025 0.001 TYR G 171 PHE 0.022 0.001 PHE P 54 TRP 0.005 0.001 TRP I 4 HIS 0.013 0.002 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 7850) covalent geometry : angle 0.52918 / 0.28 (10600) hydrogen bonds : bond 0.04448 / 2.99 ( 659) hydrogen bonds : angle 3.68095 / 2.68 ( 1962) *********************** 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 194 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.296 Fit side-chains REVERT: G 8 ARG cc_start: 0.7630 (mtm-85) cc_final: 0.5958 (tpt-90) REVERT: G 205 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7578 (mm-40) REVERT: H 132 GLN cc_start: 0.7055 (tm-30) cc_final: 0.6650 (tm-30) REVERT: M 66 MET cc_start: 0.6182 (mmp) cc_final: 0.5963 (tmm) REVERT: P 54 PHE cc_start: 0.8564 (t80) cc_final: 0.8228 (t80) REVERT: Q 60 MET cc_start: 0.7349 (mmm) cc_final: 0.6916 (mtp) REVERT: Q 65 LEU cc_start: 0.8688 (tp) cc_final: 0.8429 (tp) outliers start: 27 outliers final: 19 residues processed: 182 average time/residue: 0.0682 time to fit residues: 18.0102 Evaluate side-chains 171 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 33 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115966 restraints weight = 11127.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118879 restraints weight = 6632.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120759 restraints weight = 4728.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121980 restraints weight = 3800.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122549 restraints weight = 3304.960| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7850 Z= 0.165 Angle : 0.562 8.671 10600 Z= 0.289 Chirality : 0.040 0.178 1255 Planarity : 0.003 0.055 1324 Dihedral : 5.692 58.208 1130 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.16 % Allowed : 18.05 % Favored : 77.79 % 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: 1.74 (0.27), residues: 1002 helix: 1.85 (0.19), residues: 769 sheet: -1.09 (0.51), residues: 88 loop : -1.06 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 34 TYR 0.026 0.002 TYR G 171 PHE 0.019 0.002 PHE P 54 TRP 0.005 0.001 TRP I 4 HIS 0.002 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 7850) covalent geometry : angle 0.56152 / 0.29 (10600) hydrogen bonds : bond 0.04521 / 3.06 ( 659) hydrogen bonds : angle 3.66288 / 2.66 ( 1962) *********************** 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 191 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.215 Fit side-chains REVERT: G 8 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.6117 (tpt-90) REVERT: G 205 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7584 (mm-40) REVERT: M 66 MET cc_start: 0.6173 (mmp) cc_final: 0.5940 (tmm) REVERT: N 34 ILE cc_start: 0.9084 (mt) cc_final: 0.8873 (tt) REVERT: O 75 MET cc_start: 0.4759 (OUTLIER) cc_final: 0.4381 (tmm) outliers start: 32 outliers final: 26 residues processed: 178 average time/residue: 0.0676 time to fit residues: 17.5712 Evaluate side-chains 174 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 75 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.140567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117645 restraints weight = 11061.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120637 restraints weight = 6447.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122523 restraints weight = 4545.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123650 restraints weight = 3635.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124213 restraints weight = 3166.454| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7850 Z= 0.139 Angle : 0.536 7.942 10600 Z= 0.274 Chirality : 0.039 0.155 1255 Planarity : 0.003 0.048 1324 Dihedral : 5.589 58.207 1130 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.42 % Allowed : 19.74 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.27), residues: 1002 helix: 1.98 (0.19), residues: 769 sheet: -0.91 (0.52), residues: 91 loop : -1.01 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 23 TYR 0.016 0.001 TYR G 171 PHE 0.018 0.001 PHE P 73 TRP 0.005 0.001 TRP I 4 HIS 0.011 0.002 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 7850) covalent geometry : angle 0.53571 / 0.27 (10600) hydrogen bonds : bond 0.04318 / 2.93 ( 659) hydrogen bonds : angle 3.58867 / 2.62 ( 1962) *********************** 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 198 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.325 Fit side-chains REVERT: G 8 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.6125 (tpt-90) REVERT: G 205 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7534 (mm-40) REVERT: N 34 ILE cc_start: 0.9078 (mt) cc_final: 0.8851 (tt) REVERT: Q 60 MET cc_start: 0.7365 (mmm) cc_final: 0.6963 (mtp) REVERT: Q 65 LEU cc_start: 0.8691 (tp) cc_final: 0.8458 (tp) REVERT: R 60 MET cc_start: 0.5391 (ptp) cc_final: 0.5180 (ptp) REVERT: O 75 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.4270 (tmm) outliers start: 34 outliers final: 21 residues processed: 183 average time/residue: 0.0683 time to fit residues: 18.0276 Evaluate side-chains 173 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 75 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.136621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113182 restraints weight = 11253.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116069 restraints weight = 6747.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117629 restraints weight = 4794.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.118877 restraints weight = 3924.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119479 restraints weight = 3427.925| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7850 Z= 0.204 Angle : 0.610 8.772 10600 Z= 0.313 Chirality : 0.042 0.244 1255 Planarity : 0.004 0.048 1324 Dihedral : 5.741 59.388 1130 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.19 % Allowed : 19.61 % Favored : 75.19 % 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: 1.62 (0.27), residues: 1002 helix: 1.71 (0.18), residues: 774 sheet: -1.18 (0.51), residues: 90 loop : -0.79 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 23 TYR 0.027 0.002 TYR G 171 PHE 0.022 0.002 PHE M 8 TRP 0.004 0.001 TRP I 4 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 7850) covalent geometry : angle 0.60980 / 0.31 (10600) hydrogen bonds : bond 0.04730 / 3.20 ( 659) hydrogen bonds : angle 3.72389 / 2.71 ( 1962) *********************** 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 203 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.324 Fit side-chains REVERT: G 8 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.6247 (tpt-90) REVERT: G 205 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7572 (mm-40) REVERT: H 120 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6028 (pp) REVERT: R 60 MET cc_start: 0.5644 (ptp) cc_final: 0.5391 (ptp) REVERT: O 75 MET cc_start: 0.4638 (tmm) cc_final: 0.4294 (tmm) outliers start: 40 outliers final: 34 residues processed: 190 average time/residue: 0.0698 time to fit residues: 19.0844 Evaluate side-chains 189 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 60 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.138334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115018 restraints weight = 11137.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117874 restraints weight = 6643.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119673 restraints weight = 4745.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120762 restraints weight = 3834.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121368 restraints weight = 3368.015| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1989 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= 0.173 Angle : 0.588 8.270 10600 Z= 0.300 Chirality : 0.041 0.231 1255 Planarity : 0.004 0.052 1324 Dihedral : 5.682 58.922 1130 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.19 % Allowed : 20.65 % Favored : 74.16 % 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: 1.74 (0.27), residues: 1002 helix: 1.83 (0.18), residues: 772 sheet: -1.18 (0.51), residues: 90 loop : -0.86 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 23 TYR 0.015 0.001 TYR G 171 PHE 0.018 0.002 PHE P 63 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 0.00392 / 0.17 ( 7850) covalent geometry : angle 0.58826 / 0.30 (10600) hydrogen bonds : bond 0.04506 / 3.06 ( 659) hydrogen bonds : angle 3.67714 / 2.67 ( 1962) *********************** 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 201 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.287 Fit side-chains REVERT: G 8 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.6144 (tpt-90) REVERT: G 184 ILE cc_start: 0.8726 (mm) cc_final: 0.8420 (tt) REVERT: G 195 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.7013 (t70) REVERT: H 120 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.5999 (pp) REVERT: Q 56 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7941 (mp) REVERT: Q 60 MET cc_start: 0.7270 (mmm) cc_final: 0.6921 (mtp) REVERT: R 60 MET cc_start: 0.5569 (ptp) cc_final: 0.5296 (ptp) REVERT: O 75 MET cc_start: 0.4545 (tmm) cc_final: 0.4199 (tmm) outliers start: 40 outliers final: 36 residues processed: 187 average time/residue: 0.0679 time to fit residues: 18.5927 Evaluate side-chains 194 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 66 MET Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 60 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 90 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.139038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115895 restraints weight = 11160.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118774 restraints weight = 6592.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120589 restraints weight = 4682.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121736 restraints weight = 3770.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122422 restraints weight = 3288.512| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7850 Z= 0.157 Angle : 0.594 8.509 10600 Z= 0.298 Chirality : 0.041 0.224 1255 Planarity : 0.003 0.047 1324 Dihedral : 5.666 58.507 1130 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.97 % Allowed : 20.52 % Favored : 73.51 % 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: 1.86 (0.27), residues: 1002 helix: 1.92 (0.18), residues: 772 sheet: -1.12 (0.51), residues: 90 loop : -0.86 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 23 TYR 0.015 0.001 TYR G 171 PHE 0.020 0.001 PHE K 73 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 7850) covalent geometry : angle 0.59423 / 0.30 (10600) hydrogen bonds : bond 0.04397 / 2.99 ( 659) hydrogen bonds : angle 3.68055 / 2.67 ( 1962) *********************** 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 207 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.193 Fit side-chains REVERT: G 8 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.6073 (tpt-90) REVERT: G 184 ILE cc_start: 0.8776 (mm) cc_final: 0.8458 (tt) REVERT: G 195 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.7010 (t70) REVERT: H 96 GLU cc_start: 0.7511 (tt0) cc_final: 0.7284 (tp30) REVERT: H 120 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5931 (pp) REVERT: K 58 GLU cc_start: 0.6976 (tp30) cc_final: 0.6769 (tp30) REVERT: Q 56 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7954 (mp) REVERT: Q 60 MET cc_start: 0.7315 (mmm) cc_final: 0.6956 (mtp) REVERT: R 60 MET cc_start: 0.5354 (ptp) cc_final: 0.5018 (ptp) REVERT: O 75 MET cc_start: 0.4543 (tmm) cc_final: 0.4136 (tmm) outliers start: 46 outliers final: 36 residues processed: 194 average time/residue: 0.0701 time to fit residues: 19.6519 Evaluate side-chains 193 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 60 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 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 = 0.3699 r_free = 0.3699 target = 0.138979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116038 restraints weight = 11113.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118846 restraints weight = 6574.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120562 restraints weight = 4701.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121681 restraints weight = 3823.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122194 restraints weight = 3350.564| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7850 Z= 0.159 Angle : 0.602 8.630 10600 Z= 0.300 Chirality : 0.041 0.184 1255 Planarity : 0.003 0.048 1324 Dihedral : 5.673 58.669 1130 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.45 % Allowed : 21.04 % Favored : 73.51 % 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: 1.87 (0.27), residues: 1002 helix: 1.92 (0.19), residues: 772 sheet: -1.13 (0.52), residues: 90 loop : -0.87 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 23 TYR 0.016 0.001 TYR G 171 PHE 0.018 0.001 PHE P 63 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 0.00360 / 0.16 ( 7850) covalent geometry : angle 0.60202 / 0.30 (10600) hydrogen bonds : bond 0.04385 / 2.98 ( 659) hydrogen bonds : angle 3.67402 / 2.66 ( 1962) *********************** 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 203 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.292 Fit side-chains REVERT: G 8 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.6079 (tpt-90) REVERT: G 18 LYS cc_start: 0.8356 (mtmt) cc_final: 0.8056 (pttm) REVERT: G 195 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6868 (t70) REVERT: G 205 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7561 (mm-40) REVERT: H 120 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.5982 (pp) REVERT: Q 56 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7947 (mp) REVERT: Q 60 MET cc_start: 0.7379 (mmm) cc_final: 0.6963 (mtp) REVERT: R 60 MET cc_start: 0.5338 (ptp) cc_final: 0.5085 (ptp) REVERT: O 75 MET cc_start: 0.4771 (tmm) cc_final: 0.4342 (tmm) outliers start: 42 outliers final: 37 residues processed: 189 average time/residue: 0.0674 time to fit residues: 18.2910 Evaluate side-chains 196 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 63 PHE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.140274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116609 restraints weight = 11030.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119679 restraints weight = 6474.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121560 restraints weight = 4550.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.122666 restraints weight = 3647.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123405 restraints weight = 3189.259| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7850 Z= 0.147 Angle : 0.590 8.846 10600 Z= 0.296 Chirality : 0.040 0.196 1255 Planarity : 0.003 0.047 1324 Dihedral : 5.626 58.184 1130 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.32 % Allowed : 21.17 % Favored : 73.51 % 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: 1.95 (0.27), residues: 1002 helix: 1.98 (0.19), residues: 772 sheet: -0.97 (0.52), residues: 91 loop : -0.93 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 23 TYR 0.016 0.001 TYR G 171 PHE 0.017 0.001 PHE P 63 TRP 0.004 0.001 TRP I 4 HIS 0.001 0.000 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 7850) covalent geometry : angle 0.59044 / 0.30 (10600) hydrogen bonds : bond 0.04239 / 2.89 ( 659) hydrogen bonds : angle 3.62991 / 2.62 ( 1962) ********************** 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 202 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.267 Fit side-chains REVERT: G 8 ARG cc_start: 0.7525 (mtm-85) cc_final: 0.6039 (tpt-90) REVERT: G 18 LYS cc_start: 0.8321 (mtmt) cc_final: 0.8040 (pttm) REVERT: G 205 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7540 (mm-40) REVERT: H 91 GLN cc_start: 0.8510 (mp10) cc_final: 0.7974 (mt0) REVERT: H 120 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5834 (pp) REVERT: H 132 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6765 (tm-30) REVERT: Q 56 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7974 (mp) REVERT: Q 60 MET cc_start: 0.7218 (mmm) cc_final: 0.6912 (mtp) REVERT: Q 75 MET cc_start: 0.5170 (tpt) cc_final: 0.4944 (tpt) REVERT: O 75 MET cc_start: 0.4589 (tmm) cc_final: 0.4364 (tmm) outliers start: 41 outliers final: 35 residues processed: 190 average time/residue: 0.0682 time to fit residues: 18.5771 Evaluate side-chains 190 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 63 PHE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.138676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115413 restraints weight = 11155.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118270 restraints weight = 6715.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119995 restraints weight = 4818.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121098 restraints weight = 3907.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121705 restraints weight = 3431.265| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7850 Z= 0.170 Angle : 0.624 9.596 10600 Z= 0.309 Chirality : 0.041 0.197 1255 Planarity : 0.003 0.048 1324 Dihedral : 5.674 58.766 1130 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.32 % Allowed : 22.21 % Favored : 72.47 % 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: 1.86 (0.27), residues: 1002 helix: 1.90 (0.18), residues: 774 sheet: -1.09 (0.52), residues: 90 loop : -0.84 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 23 TYR 0.016 0.002 TYR G 171 PHE 0.019 0.001 PHE P 63 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 7850) covalent geometry : angle 0.62381 / 0.31 (10600) hydrogen bonds : bond 0.04439 / 3.02 ( 659) hydrogen bonds : angle 3.68908 / 2.67 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1364.49 seconds wall clock time: 24 minutes 20.81 seconds (1460.81 seconds total)