Starting phenix.real_space_refine on Wed Feb 12 09:33:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zik_11227/02_2025/6zik_11227.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zik_11227/02_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_11227/02_2025/6zik_11227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zik_11227/02_2025/6zik_11227.map" model { file = "/net/cci-nas-00/data/ceres_data/6zik_11227/02_2025/6zik_11227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zik_11227/02_2025/6zik_11227.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 7.09, per 1000 atoms: 0.92 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: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.66 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: 2.32 Time building geometry restraints manager: 2.16 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: 7.490 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.810 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.780 ------------------------------------------------------------------------------- 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= 0.322 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.001 TRP I 4 HIS 0.007 0.001 HIS G 66 PHE 0.021 0.002 PHE P 63 TYR 0.013 0.002 TYR G 193 ARG 0.010 0.001 ARG G 8 *********************** 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 : 0.866 Fit side-chains REVERT: G 8 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.5858 (tpt-90) REVERT: M 66 MET cc_start: 0.6191 (mmp) cc_final: 0.5792 (tmm) REVERT: Q 56 LEU cc_start: 0.8172 (tp) cc_final: 0.7935 (tp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1582 time to fit residues: 40.5638 Evaluate side-chains 144 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.141067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118151 restraints weight = 10956.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121013 restraints weight = 6529.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122779 restraints weight = 4673.620| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7850 Z= 0.235 Angle : 0.565 7.432 10600 Z= 0.297 Chirality : 0.040 0.147 1255 Planarity : 0.004 0.085 1324 Dihedral : 5.907 57.950 1130 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.73 % Allowed : 11.30 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.27), residues: 1002 helix: 1.63 (0.19), residues: 768 sheet: -0.94 (0.52), residues: 90 loop : -1.09 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.002 0.001 HIS H 66 PHE 0.020 0.002 PHE P 63 TYR 0.029 0.002 TYR G 171 ARG 0.006 0.001 ARG G 8 *********************** 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 195 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.893 Fit side-chains REVERT: G 8 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.6093 (tpt-90) REVERT: G 205 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7626 (mm-40) REVERT: H 91 GLN cc_start: 0.8599 (mp10) cc_final: 0.8377 (mp10) REVERT: H 132 GLN cc_start: 0.7118 (tm-30) cc_final: 0.6570 (tm-30) REVERT: L 60 MET cc_start: 0.6668 (mmt) cc_final: 0.6072 (mmt) REVERT: M 60 MET cc_start: 0.7109 (mtp) cc_final: 0.6905 (mtp) REVERT: M 66 MET cc_start: 0.6238 (mmp) cc_final: 0.5957 (tmm) REVERT: Q 54 PHE cc_start: 0.8463 (t80) cc_final: 0.8209 (t80) outliers start: 21 outliers final: 16 residues processed: 185 average time/residue: 0.1646 time to fit residues: 43.2281 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 : 0.847 ------------------------------------------------------------------------------- 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 71 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.140361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117137 restraints weight = 11062.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120108 restraints weight = 6529.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121934 restraints weight = 4640.624| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1514 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= 0.200 Angle : 0.530 6.889 10600 Z= 0.278 Chirality : 0.039 0.149 1255 Planarity : 0.004 0.068 1324 Dihedral : 5.717 57.872 1130 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.12 % Allowed : 15.45 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.27), residues: 1002 helix: 1.83 (0.19), residues: 769 sheet: -0.79 (0.52), residues: 88 loop : -1.09 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.013 0.002 HIS G 66 PHE 0.023 0.002 PHE P 54 TYR 0.025 0.001 TYR G 171 ARG 0.004 0.000 ARG G 8 *********************** 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 186 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.830 Fit side-chains REVERT: G 8 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.5979 (tpt-90) REVERT: G 205 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7617 (mm-40) REVERT: H 132 GLN cc_start: 0.7090 (tm-30) cc_final: 0.6668 (tm-30) REVERT: L 60 MET cc_start: 0.6622 (mmp) cc_final: 0.6105 (mmt) REVERT: M 66 MET cc_start: 0.6192 (mmp) cc_final: 0.5926 (tmm) REVERT: P 54 PHE cc_start: 0.8569 (t80) cc_final: 0.8247 (t80) REVERT: Q 60 MET cc_start: 0.7379 (mmm) cc_final: 0.6928 (mtp) REVERT: Q 65 LEU cc_start: 0.8704 (tp) cc_final: 0.8442 (tp) outliers start: 24 outliers final: 18 residues processed: 175 average time/residue: 0.1595 time to fit residues: 39.6322 Evaluate side-chains 170 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 70 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 33 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.138091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114983 restraints weight = 11059.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117844 restraints weight = 6534.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119633 restraints weight = 4658.369| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7850 Z= 0.251 Angle : 0.565 8.747 10600 Z= 0.292 Chirality : 0.041 0.185 1255 Planarity : 0.003 0.057 1324 Dihedral : 5.694 58.626 1130 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.27), residues: 1002 helix: 1.85 (0.19), residues: 769 sheet: -1.11 (0.50), residues: 88 loop : -1.06 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.002 0.001 HIS H 66 PHE 0.020 0.002 PHE P 54 TYR 0.026 0.002 TYR G 171 ARG 0.004 0.000 ARG H 34 *********************** 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 193 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.775 Fit side-chains REVERT: G 8 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.6143 (tpt-90) REVERT: G 205 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7630 (mm-40) REVERT: L 60 MET cc_start: 0.6783 (mmp) cc_final: 0.6476 (mmt) REVERT: M 66 MET cc_start: 0.6259 (mmp) cc_final: 0.5933 (tmm) REVERT: N 34 ILE cc_start: 0.9125 (mt) cc_final: 0.8903 (tt) REVERT: O 75 MET cc_start: 0.4685 (tmm) cc_final: 0.4321 (tmm) outliers start: 30 outliers final: 27 residues processed: 182 average time/residue: 0.1616 time to fit residues: 41.8387 Evaluate side-chains 178 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 32 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.0670 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.139508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116480 restraints weight = 11006.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119437 restraints weight = 6487.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121303 restraints weight = 4583.863| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7850 Z= 0.209 Angle : 0.548 8.013 10600 Z= 0.281 Chirality : 0.039 0.156 1255 Planarity : 0.003 0.050 1324 Dihedral : 5.605 58.386 1130 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.81 % Allowed : 18.96 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.27), residues: 1002 helix: 1.94 (0.19), residues: 767 sheet: -0.99 (0.51), residues: 91 loop : -1.10 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.005 0.001 HIS G 66 PHE 0.023 0.001 PHE M 8 TYR 0.015 0.001 TYR G 171 ARG 0.005 0.000 ARG I 23 *********************** 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 196 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.785 Fit side-chains REVERT: G 8 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.6150 (tpt-90) REVERT: G 205 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7600 (mm-40) REVERT: H 120 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6131 (pp) REVERT: L 60 MET cc_start: 0.6738 (mmp) cc_final: 0.6300 (mmt) REVERT: M 66 MET cc_start: 0.6136 (mmp) cc_final: 0.5863 (tmm) REVERT: Q 60 MET cc_start: 0.7295 (mmm) cc_final: 0.6808 (mtp) REVERT: Q 65 LEU cc_start: 0.8731 (tp) cc_final: 0.8505 (tp) REVERT: O 75 MET cc_start: 0.4684 (OUTLIER) cc_final: 0.4315 (tmm) outliers start: 37 outliers final: 26 residues processed: 182 average time/residue: 0.1727 time to fit residues: 44.3120 Evaluate side-chains 182 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 243 ILE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 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 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 75 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 0.4980 chunk 44 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.2674 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.142168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119359 restraints weight = 10857.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122334 restraints weight = 6374.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124176 restraints weight = 4505.552| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7850 Z= 0.163 Angle : 0.521 7.688 10600 Z= 0.268 Chirality : 0.039 0.198 1255 Planarity : 0.003 0.046 1324 Dihedral : 5.470 57.105 1130 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 5.06 % Allowed : 19.09 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.27), residues: 1002 helix: 2.10 (0.19), residues: 772 sheet: -0.86 (0.53), residues: 90 loop : -0.78 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 4 HIS 0.010 0.001 HIS G 66 PHE 0.018 0.001 PHE K 73 TYR 0.029 0.001 TYR G 171 ARG 0.005 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.838 Fit side-chains REVERT: G 8 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.6157 (tpt-90) REVERT: G 205 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7486 (mm-40) REVERT: H 91 GLN cc_start: 0.8485 (mp10) cc_final: 0.8155 (mt0) REVERT: Q 60 MET cc_start: 0.7116 (mmm) cc_final: 0.6856 (mtp) REVERT: Q 65 LEU cc_start: 0.8686 (tp) cc_final: 0.8429 (tp) REVERT: O 75 MET cc_start: 0.4534 (OUTLIER) cc_final: 0.4177 (tmm) outliers start: 39 outliers final: 26 residues processed: 188 average time/residue: 0.1585 time to fit residues: 42.6932 Evaluate side-chains 188 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 42 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 51 ILE Chi-restraints excluded: chain O residue 75 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 66 optimal weight: 0.0020 chunk 12 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.141111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117966 restraints weight = 11026.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120908 restraints weight = 6535.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122682 restraints weight = 4650.855| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2096 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= 0.190 Angle : 0.555 7.808 10600 Z= 0.277 Chirality : 0.039 0.204 1255 Planarity : 0.003 0.046 1324 Dihedral : 5.455 58.230 1130 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.68 % Allowed : 20.39 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.27), residues: 1002 helix: 2.14 (0.19), residues: 772 sheet: -0.89 (0.52), residues: 91 loop : -0.81 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 4 HIS 0.002 0.001 HIS G 66 PHE 0.016 0.001 PHE P 63 TYR 0.024 0.001 TYR G 171 ARG 0.004 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: G 8 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.6136 (tpt-90) REVERT: G 205 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7536 (mm-40) REVERT: H 91 GLN cc_start: 0.8508 (mp10) cc_final: 0.8194 (mt0) REVERT: H 120 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5969 (pp) REVERT: K 66 MET cc_start: 0.6237 (ppp) cc_final: 0.5895 (ppp) REVERT: N 34 ILE cc_start: 0.9120 (mt) cc_final: 0.8879 (tt) REVERT: Q 60 MET cc_start: 0.7321 (mmm) cc_final: 0.6932 (mtp) REVERT: O 75 MET cc_start: 0.4435 (OUTLIER) cc_final: 0.4016 (tmm) outliers start: 36 outliers final: 31 residues processed: 186 average time/residue: 0.1677 time to fit residues: 43.7696 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 : 0.828 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain 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 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 Chi-restraints excluded: chain O residue 75 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS G 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115497 restraints weight = 11187.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118309 restraints weight = 6606.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120129 restraints weight = 4702.846| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2103 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= 0.261 Angle : 0.612 8.309 10600 Z= 0.307 Chirality : 0.042 0.236 1255 Planarity : 0.003 0.048 1324 Dihedral : 5.579 58.789 1130 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.45 % Allowed : 20.65 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.27), residues: 1002 helix: 2.00 (0.18), residues: 772 sheet: -0.99 (0.52), residues: 90 loop : -0.87 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.006 0.001 HIS G 66 PHE 0.020 0.002 PHE K 73 TYR 0.027 0.002 TYR G 171 ARG 0.006 0.000 ARG I 23 *********************** 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 204 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.947 Fit side-chains REVERT: G 8 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.6072 (tpt-90) REVERT: G 205 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7618 (mm-40) REVERT: H 120 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5999 (pp) REVERT: H 132 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: Q 56 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7879 (mp) REVERT: O 75 MET cc_start: 0.4493 (tmm) cc_final: 0.4060 (tmm) outliers start: 42 outliers final: 33 residues processed: 191 average time/residue: 0.1643 time to fit residues: 44.7911 Evaluate side-chains 190 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 243 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain 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 32 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 60 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 0.2980 chunk 69 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS G 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116822 restraints weight = 11207.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119718 restraints weight = 6572.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121541 restraints weight = 4645.463| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7850 Z= 0.213 Angle : 0.598 8.795 10600 Z= 0.296 Chirality : 0.040 0.188 1255 Planarity : 0.003 0.048 1324 Dihedral : 5.580 58.120 1130 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.58 % Allowed : 21.17 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.27), residues: 1002 helix: 2.05 (0.18), residues: 772 sheet: -0.90 (0.52), residues: 91 loop : -0.92 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.005 0.001 HIS G 66 PHE 0.017 0.001 PHE P 63 TYR 0.019 0.001 TYR G 171 ARG 0.005 0.000 ARG I 23 *********************** 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 202 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: G 8 ARG cc_start: 0.7604 (mtm-85) cc_final: 0.6067 (tpt-90) REVERT: G 205 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7576 (mm-40) REVERT: H 120 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.5962 (pp) REVERT: Q 56 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7942 (mp) REVERT: Q 60 MET cc_start: 0.7192 (mmm) cc_final: 0.6920 (mtp) REVERT: O 75 MET cc_start: 0.4730 (tmm) cc_final: 0.4288 (tmm) outliers start: 43 outliers final: 36 residues processed: 189 average time/residue: 0.1652 time to fit residues: 44.8233 Evaluate side-chains 190 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 42 LEU 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 21 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.140340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117165 restraints weight = 11115.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120060 restraints weight = 6633.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121847 restraints weight = 4731.190| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7850 Z= 0.218 Angle : 0.613 9.580 10600 Z= 0.304 Chirality : 0.041 0.212 1255 Planarity : 0.003 0.048 1324 Dihedral : 5.583 58.048 1130 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.32 % Allowed : 21.04 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.27), residues: 1002 helix: 2.06 (0.18), residues: 772 sheet: -0.82 (0.52), residues: 91 loop : -1.00 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.003 0.001 HIS G 66 PHE 0.017 0.001 PHE P 63 TYR 0.019 0.001 TYR G 171 ARG 0.005 0.000 ARG I 23 ********************** 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 198 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.785 Fit side-chains REVERT: G 8 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.6069 (tpt-90) REVERT: G 205 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7559 (mm-40) REVERT: H 91 GLN cc_start: 0.8502 (mp10) cc_final: 0.7974 (mt0) REVERT: H 120 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5923 (pp) REVERT: Q 56 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7985 (mp) REVERT: Q 60 MET cc_start: 0.7215 (mmm) cc_final: 0.6990 (mtp) REVERT: O 75 MET cc_start: 0.4418 (tmm) cc_final: 0.4143 (tmm) outliers start: 41 outliers final: 38 residues processed: 185 average time/residue: 0.1833 time to fit residues: 48.8786 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 : 0.905 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 42 LEU 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 65 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.138010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115312 restraints weight = 11084.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118136 restraints weight = 6568.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119902 restraints weight = 4677.927| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2246 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= 0.262 Angle : 0.632 8.717 10600 Z= 0.312 Chirality : 0.041 0.194 1255 Planarity : 0.004 0.049 1324 Dihedral : 5.620 58.653 1130 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.58 % Allowed : 20.78 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.27), residues: 1002 helix: 1.95 (0.18), residues: 772 sheet: -0.97 (0.52), residues: 90 loop : -0.93 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.002 0.001 HIS H 51 PHE 0.019 0.002 PHE P 63 TYR 0.022 0.002 TYR G 171 ARG 0.004 0.000 ARG I 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2544.73 seconds wall clock time: 46 minutes 37.98 seconds (2797.98 seconds total)