Starting phenix.real_space_refine on Fri Aug 22 20:26:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zik_11227/08_2025/6zik_11227.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zik_11227/08_2025/6zik_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zik_11227/08_2025/6zik_11227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zik_11227/08_2025/6zik_11227.map" model { file = "/net/cci-nas-00/data/ceres_data/6zik_11227/08_2025/6zik_11227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zik_11227/08_2025/6zik_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-2.0-5787/lib/python3.9/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: 2.12, per 1000 atoms: 0.27 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: 0.81 Conformation dependent library (CDL) restraints added in 477.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.25 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: 1.41 Time building geometry restraints manager: 1.04 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: 8.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 aren 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 covalent geometry : bond 0.00503 ( 7850) covalent geometry : angle 0.72895 (10600) hydrogen bonds : bond 0.09536 ( 659) hydrogen bonds : angle 4.59899 ( 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 : 0.300 Fit side-chains REVERT: G 8 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.5859 (tpt-90) REVERT: M 66 MET cc_start: 0.6191 (mmp) cc_final: 0.5791 (tmm) REVERT: Q 56 LEU cc_start: 0.8172 (tp) cc_final: 0.7934 (tp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0761 time to fit residues: 19.7775 Evaluate side-chains 143 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116630 restraints weight = 11002.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119504 restraints weight = 6569.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121282 restraints weight = 4695.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122265 restraints weight = 3809.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122979 restraints weight = 3371.040| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1115 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= 0.179 Angle : 0.575 6.553 10600 Z= 0.303 Chirality : 0.041 0.149 1255 Planarity : 0.004 0.085 1324 Dihedral : 5.949 58.580 1130 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.73 % Allowed : 11.82 % Favored : 85.45 % 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 aren not related in a simple way. whole: 1.39 (0.27), residues: 1002 helix: 1.58 (0.19), residues: 768 sheet: -1.09 (0.51), residues: 90 loop : -1.10 (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 0.020 0.002 PHE P 63 TRP 0.003 0.001 TRP I 4 HIS 0.002 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7850) covalent geometry : angle 0.57547 (10600) hydrogen bonds : bond 0.04847 ( 659) hydrogen bonds : angle 3.86567 ( 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 192 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.411 Fit side-chains REVERT: G 8 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.6089 (tpt-90) REVERT: G 205 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7646 (mm-40) REVERT: H 91 GLN cc_start: 0.8632 (mp10) cc_final: 0.8383 (mp10) REVERT: H 132 GLN cc_start: 0.7087 (tm-30) cc_final: 0.6527 (tm-30) REVERT: L 60 MET cc_start: 0.6649 (mmt) cc_final: 0.6113 (mmt) REVERT: M 66 MET cc_start: 0.6236 (mmp) cc_final: 0.5926 (tmm) REVERT: Q 54 PHE cc_start: 0.8523 (t80) cc_final: 0.8275 (t80) outliers start: 21 outliers final: 16 residues processed: 182 average time/residue: 0.0821 time to fit residues: 21.3140 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 : 0.307 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.138348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115059 restraints weight = 11011.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117955 restraints weight = 6554.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119595 restraints weight = 4675.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120777 restraints weight = 3817.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121525 restraints weight = 3345.805| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7850 Z= 0.172 Angle : 0.561 7.031 10600 Z= 0.293 Chirality : 0.040 0.150 1255 Planarity : 0.004 0.070 1324 Dihedral : 5.826 58.425 1130 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.77 % Allowed : 16.10 % Favored : 80.13 % 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 aren not related in a simple way. whole: 1.51 (0.27), residues: 1002 helix: 1.68 (0.19), residues: 769 sheet: -1.05 (0.50), residues: 91 loop : -1.18 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 8 TYR 0.025 0.002 TYR G 171 PHE 0.023 0.002 PHE P 54 TRP 0.004 0.001 TRP I 4 HIS 0.013 0.002 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7850) covalent geometry : angle 0.56145 (10600) hydrogen bonds : bond 0.04704 ( 659) hydrogen bonds : angle 3.77141 ( 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 187 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.317 Fit side-chains REVERT: G 8 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.5986 (tpt-90) REVERT: G 205 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7606 (mm-40) REVERT: L 60 MET cc_start: 0.6798 (mmt) cc_final: 0.6395 (mmt) REVERT: M 66 MET cc_start: 0.6264 (mmp) cc_final: 0.6002 (tmm) REVERT: P 54 PHE cc_start: 0.8653 (t80) cc_final: 0.8368 (t80) outliers start: 29 outliers final: 22 residues processed: 175 average time/residue: 0.0778 time to fit residues: 19.5976 Evaluate side-chains 172 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 38 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 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 70 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 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: 0.6980 chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.140085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116780 restraints weight = 11073.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119706 restraints weight = 6586.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121582 restraints weight = 4690.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122669 restraints weight = 3768.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123376 restraints weight = 3305.614| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7850 Z= 0.144 Angle : 0.522 6.573 10600 Z= 0.272 Chirality : 0.039 0.169 1255 Planarity : 0.003 0.053 1324 Dihedral : 5.644 58.249 1130 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.90 % Allowed : 18.44 % Favored : 77.66 % 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 aren not related in a simple way. whole: 1.84 (0.27), residues: 1002 helix: 1.91 (0.19), residues: 769 sheet: -0.86 (0.52), residues: 88 loop : -1.07 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 34 TYR 0.025 0.001 TYR G 171 PHE 0.019 0.001 PHE P 54 TRP 0.005 0.001 TRP I 4 HIS 0.002 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7850) covalent geometry : angle 0.52230 (10600) hydrogen bonds : bond 0.04365 ( 659) hydrogen bonds : angle 3.60810 ( 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 202 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.287 Fit side-chains REVERT: G 8 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.6106 (tpt-90) REVERT: G 205 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7608 (mm-40) REVERT: H 132 GLN cc_start: 0.7132 (tm-30) cc_final: 0.6600 (tm-30) REVERT: L 60 MET cc_start: 0.6508 (mmp) cc_final: 0.6256 (mmt) REVERT: M 66 MET cc_start: 0.6194 (mmp) cc_final: 0.5939 (tmm) REVERT: Q 60 MET cc_start: 0.7387 (mmm) cc_final: 0.7006 (mtp) REVERT: Q 65 LEU cc_start: 0.8694 (tp) cc_final: 0.8473 (tp) REVERT: O 75 MET cc_start: 0.4546 (OUTLIER) cc_final: 0.4163 (tmm) outliers start: 30 outliers final: 20 residues processed: 189 average time/residue: 0.0770 time to fit residues: 20.8230 Evaluate side-chains 170 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 M residue 15 THR 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 33 ILE 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: 1.9990 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113590 restraints weight = 11226.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116498 restraints weight = 6603.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118252 restraints weight = 4665.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119369 restraints weight = 3757.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120003 restraints weight = 3281.680| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7850 Z= 0.200 Angle : 0.595 9.114 10600 Z= 0.304 Chirality : 0.041 0.154 1255 Planarity : 0.004 0.052 1324 Dihedral : 5.703 59.138 1130 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.19 % Allowed : 18.70 % Favored : 76.10 % 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 aren not related in a simple way. whole: 1.60 (0.27), residues: 1002 helix: 1.76 (0.19), residues: 769 sheet: -1.22 (0.50), residues: 88 loop : -1.09 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 23 TYR 0.019 0.002 TYR G 171 PHE 0.020 0.002 PHE P 73 TRP 0.004 0.001 TRP I 4 HIS 0.008 0.002 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 7850) covalent geometry : angle 0.59489 (10600) hydrogen bonds : bond 0.04738 ( 659) hydrogen bonds : angle 3.69805 ( 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 194 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.333 Fit side-chains REVERT: G 8 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.6097 (tpt-90) REVERT: G 205 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7594 (mm-40) REVERT: H 120 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6128 (pp) REVERT: M 66 MET cc_start: 0.6281 (mmp) cc_final: 0.5974 (tmm) REVERT: N 34 ILE cc_start: 0.9134 (mt) cc_final: 0.8904 (tt) REVERT: R 60 MET cc_start: 0.5617 (ptp) cc_final: 0.5362 (ptp) REVERT: O 75 MET cc_start: 0.4643 (tmm) cc_final: 0.4300 (tmm) outliers start: 40 outliers final: 28 residues processed: 182 average time/residue: 0.0798 time to fit residues: 20.6284 Evaluate side-chains 174 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 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 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 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 70 LEU Chi-restraints excluded: chain M residue 15 THR 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 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: 0.5980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115325 restraints weight = 11148.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118283 restraints weight = 6563.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120112 restraints weight = 4621.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121089 restraints weight = 3704.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121867 restraints weight = 3262.227| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1870 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= 0.163 Angle : 0.563 7.563 10600 Z= 0.289 Chirality : 0.040 0.166 1255 Planarity : 0.003 0.047 1324 Dihedral : 5.646 58.723 1130 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.94 % Allowed : 19.87 % 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 aren not related in a simple way. whole: 1.70 (0.27), residues: 1002 helix: 1.85 (0.19), residues: 769 sheet: -1.29 (0.50), residues: 90 loop : -1.07 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 23 TYR 0.012 0.001 TYR G 171 PHE 0.025 0.001 PHE M 8 TRP 0.004 0.001 TRP I 4 HIS 0.002 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 7850) covalent geometry : angle 0.56331 (10600) hydrogen bonds : bond 0.04496 ( 659) hydrogen bonds : angle 3.66003 ( 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 196 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.304 Fit side-chains REVERT: G 8 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.6122 (tpt-90) REVERT: G 205 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7566 (mm-40) REVERT: G 225 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8459 (mm-40) REVERT: H 120 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5977 (pp) REVERT: M 66 MET cc_start: 0.6185 (mmp) cc_final: 0.5948 (tmm) REVERT: Q 60 MET cc_start: 0.7314 (mmm) cc_final: 0.6747 (mtp) REVERT: R 60 MET cc_start: 0.5501 (ptp) cc_final: 0.5234 (ptp) REVERT: O 75 MET cc_start: 0.4598 (tmm) cc_final: 0.4245 (tmm) outliers start: 38 outliers final: 32 residues processed: 185 average time/residue: 0.0786 time to fit residues: 20.8709 Evaluate side-chains 185 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 M residue 15 THR 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 32 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 51 ILE 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: 0.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114976 restraints weight = 11123.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117813 restraints weight = 6507.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119465 restraints weight = 4614.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120651 restraints weight = 3743.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121396 restraints weight = 3276.013| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7850 Z= 0.173 Angle : 0.583 8.142 10600 Z= 0.298 Chirality : 0.041 0.239 1255 Planarity : 0.003 0.048 1324 Dihedral : 5.661 59.094 1130 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.58 % Allowed : 21.04 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.27), residues: 1002 helix: 1.86 (0.19), residues: 767 sheet: -1.14 (0.50), residues: 90 loop : -1.07 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 23 TYR 0.029 0.002 TYR G 171 PHE 0.020 0.002 PHE M 8 TRP 0.004 0.001 TRP I 4 HIS 0.006 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 7850) covalent geometry : angle 0.58323 (10600) hydrogen bonds : bond 0.04522 ( 659) hydrogen bonds : angle 3.68277 ( 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 206 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.282 Fit side-chains REVERT: G 8 ARG cc_start: 0.7603 (mtm-85) cc_final: 0.6142 (tpt-90) REVERT: G 195 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6968 (t70) REVERT: G 205 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7603 (mm-40) REVERT: H 120 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.6013 (pp) REVERT: M 66 MET cc_start: 0.6160 (mmp) cc_final: 0.5932 (tmm) REVERT: Q 56 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7904 (mp) REVERT: R 60 MET cc_start: 0.5679 (ptp) cc_final: 0.5265 (ptp) REVERT: O 54 PHE cc_start: 0.8272 (t80) cc_final: 0.7968 (t80) REVERT: O 75 MET cc_start: 0.4608 (tmm) cc_final: 0.4252 (tmm) outliers start: 43 outliers final: 33 residues processed: 194 average time/residue: 0.0780 time to fit residues: 21.7171 Evaluate side-chains 191 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 M residue 15 THR 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 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 33 ILE Chi-restraints excluded: chain O residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 90 optimal weight: 0.0570 chunk 64 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116825 restraints weight = 11130.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119794 restraints weight = 6559.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121636 restraints weight = 4635.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122689 restraints weight = 3717.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123397 restraints weight = 3269.459| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7850 Z= 0.142 Angle : 0.558 8.594 10600 Z= 0.284 Chirality : 0.040 0.210 1255 Planarity : 0.003 0.047 1324 Dihedral : 5.551 58.114 1130 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.16 % Allowed : 23.12 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.27), residues: 1002 helix: 1.95 (0.19), residues: 772 sheet: -0.92 (0.52), residues: 91 loop : -0.75 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 covalent geometry : bond 0.00314 ( 7850) covalent geometry : angle 0.55808 (10600) hydrogen bonds : bond 0.04263 ( 659) hydrogen bonds : angle 3.64194 ( 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 193 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.304 Fit side-chains REVERT: G 8 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.6063 (tpt-90) REVERT: G 195 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6864 (t70) REVERT: G 205 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7556 (mm-40) REVERT: Q 56 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7968 (mp) REVERT: Q 60 MET cc_start: 0.7211 (mmm) cc_final: 0.6968 (mtp) REVERT: Q 65 LEU cc_start: 0.8690 (tp) cc_final: 0.8445 (tp) REVERT: R 60 MET cc_start: 0.5267 (ptp) cc_final: 0.5028 (ptp) REVERT: O 54 PHE cc_start: 0.8209 (t80) cc_final: 0.7945 (t80) REVERT: O 75 MET cc_start: 0.4556 (tmm) cc_final: 0.4140 (tmm) outliers start: 32 outliers final: 28 residues processed: 183 average time/residue: 0.0778 time to fit residues: 20.4685 Evaluate side-chains 184 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 63 PHE 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 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 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 27 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.117037 restraints weight = 10990.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119970 restraints weight = 6585.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121795 restraints weight = 4693.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122932 restraints weight = 3800.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123690 restraints weight = 3315.228| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7850 Z= 0.142 Angle : 0.570 8.548 10600 Z= 0.288 Chirality : 0.040 0.193 1255 Planarity : 0.003 0.047 1324 Dihedral : 5.519 58.195 1130 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.19 % Allowed : 22.60 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.27), residues: 1002 helix: 2.02 (0.19), residues: 772 sheet: -0.93 (0.52), residues: 91 loop : -0.75 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 23 TYR 0.018 0.001 TYR G 171 PHE 0.017 0.001 PHE P 63 TRP 0.003 0.001 TRP I 4 HIS 0.004 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7850) covalent geometry : angle 0.57003 (10600) hydrogen bonds : bond 0.04250 ( 659) hydrogen bonds : angle 3.62777 ( 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 197 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.332 Fit side-chains REVERT: G 8 ARG cc_start: 0.7526 (mtm-85) cc_final: 0.6063 (tpt-90) REVERT: G 195 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6871 (t70) REVERT: G 205 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7550 (mm-40) REVERT: H 120 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5937 (pp) REVERT: H 132 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: K 58 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6783 (tp30) REVERT: M 60 MET cc_start: 0.6719 (mtp) cc_final: 0.6486 (mtp) REVERT: Q 56 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7979 (mp) REVERT: Q 60 MET cc_start: 0.7192 (mmm) cc_final: 0.6944 (mtp) REVERT: R 60 MET cc_start: 0.5296 (ptp) cc_final: 0.5056 (ptp) REVERT: O 75 MET cc_start: 0.4613 (tmm) cc_final: 0.4195 (tmm) outliers start: 40 outliers final: 35 residues processed: 185 average time/residue: 0.0802 time to fit residues: 21.2769 Evaluate side-chains 195 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 168 VAL 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 H residue 132 GLN Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 58 GLU 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 N residue 32 LEU Chi-restraints excluded: chain N residue 63 PHE 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 Q residue 71 ILE 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 33 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 60 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.0670 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116589 restraints weight = 11022.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119523 restraints weight = 6577.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121341 restraints weight = 4683.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122268 restraints weight = 3777.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123087 restraints weight = 3349.046| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7850 Z= 0.148 Angle : 0.582 9.038 10600 Z= 0.292 Chirality : 0.040 0.197 1255 Planarity : 0.003 0.047 1324 Dihedral : 5.519 58.486 1130 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.45 % Allowed : 22.60 % Favored : 71.95 % 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 aren not related in a simple way. whole: 2.04 (0.27), residues: 1002 helix: 2.02 (0.19), residues: 772 sheet: -0.91 (0.52), residues: 91 loop : -0.76 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 23 TYR 0.021 0.001 TYR G 171 PHE 0.018 0.001 PHE P 63 TRP 0.004 0.001 TRP I 4 HIS 0.001 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7850) covalent geometry : angle 0.58180 (10600) hydrogen bonds : bond 0.04281 ( 659) hydrogen bonds : angle 3.62302 ( 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 199 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.335 Fit side-chains REVERT: G 8 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.6053 (tpt-90) REVERT: G 195 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6857 (t70) REVERT: G 205 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7571 (mm-40) REVERT: H 91 GLN cc_start: 0.8525 (mp10) cc_final: 0.8012 (mt0) REVERT: H 120 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5865 (pp) REVERT: K 58 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7029 (tp30) REVERT: M 60 MET cc_start: 0.6736 (mtp) cc_final: 0.6489 (mtp) REVERT: Q 56 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7977 (mp) REVERT: Q 60 MET cc_start: 0.7150 (mmm) cc_final: 0.6855 (mtp) REVERT: O 75 MET cc_start: 0.4609 (tmm) cc_final: 0.4335 (tmm) outliers start: 42 outliers final: 36 residues processed: 187 average time/residue: 0.0783 time to fit residues: 21.1735 Evaluate side-chains 195 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 168 VAL 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 18 VAL Chi-restraints excluded: chain K residue 58 GLU 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 N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 63 PHE 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 Q residue 71 ILE 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 33 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 60 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115405 restraints weight = 11116.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118268 restraints weight = 6629.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120049 restraints weight = 4744.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121039 restraints weight = 3845.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121815 restraints weight = 3396.609| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7850 Z= 0.175 Angle : 0.623 9.794 10600 Z= 0.311 Chirality : 0.041 0.194 1255 Planarity : 0.003 0.048 1324 Dihedral : 5.566 58.715 1130 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.32 % Allowed : 22.73 % Favored : 71.95 % 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 aren not related in a simple way. whole: 1.93 (0.27), residues: 1002 helix: 1.94 (0.19), residues: 772 sheet: -1.11 (0.51), residues: 90 loop : -0.68 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 23 TYR 0.021 0.002 TYR G 171 PHE 0.019 0.002 PHE P 63 TRP 0.004 0.001 TRP I 4 HIS 0.006 0.001 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 7850) covalent geometry : angle 0.62310 (10600) hydrogen bonds : bond 0.04472 ( 659) hydrogen bonds : angle 3.66512 ( 1962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1577.52 seconds wall clock time: 28 minutes 12.23 seconds (1692.23 seconds total)