Starting phenix.real_space_refine on Fri Nov 15 22:09:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctw_45921/11_2024/9ctw_45921.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctw_45921/11_2024/9ctw_45921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctw_45921/11_2024/9ctw_45921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctw_45921/11_2024/9ctw_45921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctw_45921/11_2024/9ctw_45921.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ctw_45921/11_2024/9ctw_45921.cif" } resolution = 3.01 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= 0.012 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 44 5.16 5 C 6226 2.51 5 N 1636 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9754 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1688 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain: "D" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1651 Classifications: {'peptide': 220} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Chain: "E" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1688 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain: "F" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1651 Classifications: {'peptide': 220} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1538 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1538 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Time building chain proxies: 7.28, per 1000 atoms: 0.75 Number of scatterers: 9754 At special positions: 0 Unit cell: (139.92, 92.432, 133.136, 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 44 16.00 O 1848 8.00 N 1636 7.00 C 6226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 202 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 202 " distance=2.04 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: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 19.4% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.126A pdb=" N VAL C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.580A pdb=" N HIS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.883A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'E' and resid 83 through 87 removed outlier: 4.060A pdb=" N VAL E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 187 through 193 removed outlier: 3.843A pdb=" N HIS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.900A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.525A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 165 No H-bonds generated for 'chain 'F' and resid 163 through 165' Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.525A pdb=" N TRP A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 71 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 74 through 107 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.745A pdb=" N PHE A 112 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 3.588A pdb=" N TRP B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 71 removed outlier: 3.969A pdb=" N TRP B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 74 through 107 Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.725A pdb=" N PHE B 112 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.250A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.250A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.690A pdb=" N ASN C 141 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 137 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.762A pdb=" N LYS C 153 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.553A pdb=" N GLU D 10 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=AA9, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 131 removed outlier: 6.076A pdb=" N TYR D 182 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.133A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS E 111 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL E 13 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N MET E 37 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR E 53 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.133A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS E 111 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL E 13 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR E 101 " --> pdb=" O GLN E 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.673A pdb=" N ASN E 141 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL E 137 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR E 177 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.779A pdb=" N LYS E 153 " --> pdb=" O THR E 197 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.495A pdb=" N GLU F 10 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA F 92 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 49 through 51 Processing sheet with id=AC2, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AC3, first strand: chain 'F' and resid 127 through 131 removed outlier: 6.024A pdb=" N TYR F 182 " --> pdb=" O GLY F 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AC5, first strand: chain 'A' and resid 127 through 133 removed outlier: 4.452A pdb=" N ILE A 118 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU A 167 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 200 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 180 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG A 198 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 182 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR A 196 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 184 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 194 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG A 186 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY A 192 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 149 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 127 through 133 removed outlier: 4.448A pdb=" N ILE B 118 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU B 167 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 200 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 180 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG B 198 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY B 182 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR B 196 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER B 184 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 194 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 186 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY B 192 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 149 " --> pdb=" O LEU B 156 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 2.97 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: 3077 1.34 - 1.46: 2453 1.46 - 1.58: 4410 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 10002 Sorted by residual: bond pdb=" CA TRP A 58 " pdb=" C TRP A 58 " ideal model delta sigma weight residual 1.521 1.533 -0.012 1.11e-02 8.12e+03 1.10e+00 bond pdb=" C ASP E 98 " pdb=" N PRO E 99 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 1.00e+00 bond pdb=" C LEU A 54 " pdb=" O LEU A 54 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.16e-02 7.43e+03 8.94e-01 bond pdb=" C ASP C 98 " pdb=" N PRO C 99 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.11e-01 bond pdb=" C ASN C 80 " pdb=" N PRO C 81 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.22e-01 ... (remaining 9997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 13234 1.28 - 2.57: 316 2.57 - 3.85: 58 3.85 - 5.13: 8 5.13 - 6.42: 4 Bond angle restraints: 13620 Sorted by residual: angle pdb=" CA PRO C 81 " pdb=" C PRO C 81 " pdb=" O PRO C 81 " ideal model delta sigma weight residual 123.07 119.37 3.70 1.38e+00 5.25e-01 7.20e+00 angle pdb=" C ARG E 54 " pdb=" N ALA E 55 " pdb=" CA ALA E 55 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.76e+00 angle pdb=" C ARG C 54 " pdb=" N ALA C 55 " pdb=" CA ALA C 55 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.75e+00 angle pdb=" C TYR B 204 " pdb=" N LYS B 205 " pdb=" CA LYS B 205 " ideal model delta sigma weight residual 121.54 125.22 -3.68 1.91e+00 2.74e-01 3.72e+00 angle pdb=" CA VAL D 190 " pdb=" C VAL D 190 " pdb=" N PRO D 191 " ideal model delta sigma weight residual 117.33 119.27 -1.94 1.01e+00 9.80e-01 3.68e+00 ... (remaining 13615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.53: 5415 12.53 - 25.07: 358 25.07 - 37.60: 96 37.60 - 50.13: 24 50.13 - 62.67: 9 Dihedral angle restraints: 5902 sinusoidal: 2266 harmonic: 3636 Sorted by residual: dihedral pdb=" CA MET D 34 " pdb=" C MET D 34 " pdb=" N ASN D 35 " pdb=" CA ASN D 35 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA MET F 34 " pdb=" C MET F 34 " pdb=" N ASN F 35 " pdb=" CA ASN F 35 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASN F 35 " pdb=" C ASN F 35 " pdb=" N TRP F 36 " pdb=" CA TRP F 36 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 952 0.031 - 0.063: 373 0.063 - 0.094: 119 0.094 - 0.126: 73 0.126 - 0.157: 13 Chirality restraints: 1530 Sorted by residual: chirality pdb=" CA ILE C 52 " pdb=" N ILE C 52 " pdb=" C ILE C 52 " pdb=" CB ILE C 52 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA ILE E 52 " pdb=" N ILE E 52 " pdb=" C ILE E 52 " pdb=" CB ILE E 52 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1527 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 155 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO F 156 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 156 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 156 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 155 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO D 156 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 122 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 123 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " 0.018 5.00e-02 4.00e+02 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2900 2.83 - 3.34: 7928 3.34 - 3.86: 15348 3.86 - 4.38: 17820 4.38 - 4.90: 32393 Nonbonded interactions: 76389 Sorted by model distance: nonbonded pdb=" OG1 THR C 186 " pdb=" OD1 ASP C 188 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR E 186 " pdb=" OD1 ASP E 188 " model vdw 2.330 3.040 nonbonded pdb=" NH1 ARG D 40 " pdb=" O GLU D 89 " model vdw 2.332 3.120 nonbonded pdb=" NH1 ARG F 40 " pdb=" O GLU F 89 " model vdw 2.335 3.120 nonbonded pdb=" O THR F 194 " pdb=" OG SER F 197 " model vdw 2.355 3.040 ... (remaining 76384 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.630 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.003 0.029 10002 Z= 0.190 Angle : 0.511 6.416 13620 Z= 0.277 Chirality : 0.043 0.157 1530 Planarity : 0.004 0.046 1718 Dihedral : 9.735 62.666 3550 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.86 % Favored : 95.98 % Rotamer: Outliers : 0.74 % Allowed : 3.80 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: -0.16 (0.24), residues: 1244 helix: 1.13 (0.36), residues: 196 sheet: 0.35 (0.24), residues: 496 loop : -0.95 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 33 HIS 0.002 0.001 HIS A 154 PHE 0.018 0.002 PHE F 109 TYR 0.010 0.001 TYR E 53 ARG 0.002 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 1.094 Fit side-chains REVERT: C 107 LYS cc_start: 0.8653 (tttt) cc_final: 0.8090 (tptt) REVERT: C 174 ASP cc_start: 0.7479 (p0) cc_final: 0.6820 (t0) REVERT: E 107 LYS cc_start: 0.8633 (tttt) cc_final: 0.8126 (tptt) REVERT: E 174 ASP cc_start: 0.7429 (p0) cc_final: 0.6929 (t0) REVERT: F 103 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8676 (pm20) REVERT: A 107 ARG cc_start: 0.7152 (mtp180) cc_final: 0.6800 (mtp85) REVERT: A 135 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 166 LYS cc_start: 0.8777 (mttt) cc_final: 0.8218 (mmtm) REVERT: B 135 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8216 (mt-10) REVERT: B 166 LYS cc_start: 0.8506 (mttt) cc_final: 0.7980 (mmtm) outliers start: 8 outliers final: 3 residues processed: 164 average time/residue: 0.2574 time to fit residues: 56.8283 Evaluate side-chains 108 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 157 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10002 Z= 0.265 Angle : 0.582 9.463 13620 Z= 0.307 Chirality : 0.045 0.157 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.200 54.824 1370 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.26 % Rotamer: Outliers : 1.39 % Allowed : 8.80 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.19 (0.24), residues: 1244 helix: 1.70 (0.36), residues: 196 sheet: 0.58 (0.24), residues: 530 loop : -0.96 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 33 HIS 0.005 0.001 HIS C 202 PHE 0.022 0.002 PHE F 109 TYR 0.012 0.002 TYR E 53 ARG 0.003 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.185 Fit side-chains REVERT: C 107 LYS cc_start: 0.8507 (tttt) cc_final: 0.7921 (tptt) REVERT: C 174 ASP cc_start: 0.7457 (p0) cc_final: 0.6867 (t0) REVERT: E 107 LYS cc_start: 0.8473 (tttt) cc_final: 0.7941 (tptt) REVERT: E 174 ASP cc_start: 0.7457 (p0) cc_final: 0.6926 (t0) REVERT: F 142 MET cc_start: 0.5809 (mmm) cc_final: 0.5498 (mmm) REVERT: A 107 ARG cc_start: 0.7161 (mtp180) cc_final: 0.6817 (mtp85) REVERT: A 135 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8278 (mt-10) REVERT: A 166 LYS cc_start: 0.8808 (mttt) cc_final: 0.8305 (mmtm) REVERT: B 135 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8183 (mt-10) REVERT: B 166 LYS cc_start: 0.8582 (mttt) cc_final: 0.8032 (mmtt) outliers start: 15 outliers final: 10 residues processed: 114 average time/residue: 0.1951 time to fit residues: 33.0769 Evaluate side-chains 103 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 93 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 111 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10002 Z= 0.177 Angle : 0.512 8.912 13620 Z= 0.269 Chirality : 0.043 0.146 1530 Planarity : 0.004 0.044 1718 Dihedral : 4.968 52.640 1370 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 1.20 % Allowed : 11.02 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.32 (0.25), residues: 1244 helix: 1.95 (0.36), residues: 196 sheet: 0.60 (0.24), residues: 544 loop : -0.90 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 33 HIS 0.003 0.001 HIS C 202 PHE 0.016 0.001 PHE D 109 TYR 0.011 0.001 TYR C 53 ARG 0.002 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.012 Fit side-chains REVERT: C 107 LYS cc_start: 0.8528 (tttt) cc_final: 0.7941 (tptt) REVERT: C 174 ASP cc_start: 0.7333 (p0) cc_final: 0.6773 (t0) REVERT: E 107 LYS cc_start: 0.8468 (tttt) cc_final: 0.7920 (tptt) REVERT: E 174 ASP cc_start: 0.7432 (p0) cc_final: 0.6924 (t0) REVERT: F 142 MET cc_start: 0.5894 (mmm) cc_final: 0.5565 (mmm) REVERT: A 107 ARG cc_start: 0.7056 (mtp180) cc_final: 0.6685 (mtp85) REVERT: A 135 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8235 (mt-10) REVERT: A 166 LYS cc_start: 0.8798 (mttt) cc_final: 0.8324 (mmtm) REVERT: B 135 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8139 (mt-10) REVERT: B 166 LYS cc_start: 0.8625 (mttt) cc_final: 0.8094 (mmtt) outliers start: 13 outliers final: 10 residues processed: 107 average time/residue: 0.1970 time to fit residues: 31.3577 Evaluate side-chains 107 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN D 39 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN F 39 GLN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 10002 Z= 0.427 Angle : 0.672 8.624 13620 Z= 0.350 Chirality : 0.049 0.175 1530 Planarity : 0.005 0.044 1718 Dihedral : 5.660 58.360 1370 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.23 % Favored : 94.61 % Rotamer: Outliers : 2.59 % Allowed : 10.83 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: -0.02 (0.24), residues: 1244 helix: 1.57 (0.35), residues: 196 sheet: 0.45 (0.23), residues: 542 loop : -1.16 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 33 HIS 0.005 0.002 HIS A 154 PHE 0.027 0.002 PHE D 109 TYR 0.012 0.002 TYR D 52 ARG 0.004 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.134 Fit side-chains REVERT: C 107 LYS cc_start: 0.8582 (tttt) cc_final: 0.8009 (tptt) REVERT: C 174 ASP cc_start: 0.7338 (p0) cc_final: 0.6827 (t0) REVERT: E 107 LYS cc_start: 0.8574 (tttt) cc_final: 0.8027 (tptt) REVERT: E 174 ASP cc_start: 0.7465 (p0) cc_final: 0.7008 (t0) REVERT: F 142 MET cc_start: 0.6037 (mmm) cc_final: 0.5651 (mmt) REVERT: A 107 ARG cc_start: 0.7217 (mtp180) cc_final: 0.6851 (mtp85) REVERT: A 135 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8267 (mt-10) REVERT: A 166 LYS cc_start: 0.8808 (mttt) cc_final: 0.8315 (mmtm) REVERT: B 135 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8170 (mt-10) REVERT: B 137 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7841 (mt-10) REVERT: B 166 LYS cc_start: 0.8624 (mttt) cc_final: 0.8109 (mmtm) outliers start: 28 outliers final: 20 residues processed: 124 average time/residue: 0.2376 time to fit residues: 41.2554 Evaluate side-chains 119 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 102 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10002 Z= 0.209 Angle : 0.533 8.654 13620 Z= 0.281 Chirality : 0.044 0.153 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.262 55.934 1370 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.78 % Favored : 96.06 % Rotamer: Outliers : 2.41 % Allowed : 12.31 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.25 (0.25), residues: 1244 helix: 1.90 (0.35), residues: 196 sheet: 0.63 (0.24), residues: 540 loop : -1.04 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 33 HIS 0.003 0.001 HIS B 155 PHE 0.018 0.001 PHE F 109 TYR 0.009 0.001 TYR C 53 ARG 0.002 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.064 Fit side-chains REVERT: C 107 LYS cc_start: 0.8535 (tttt) cc_final: 0.7940 (tptt) REVERT: C 174 ASP cc_start: 0.7365 (p0) cc_final: 0.6792 (t0) REVERT: E 107 LYS cc_start: 0.8537 (tttt) cc_final: 0.7973 (tptt) REVERT: E 174 ASP cc_start: 0.7463 (p0) cc_final: 0.6992 (t0) REVERT: F 142 MET cc_start: 0.6050 (mmm) cc_final: 0.5701 (mmt) REVERT: A 90 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6842 (mp) REVERT: A 107 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6712 (mtp85) REVERT: A 135 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 166 LYS cc_start: 0.8805 (mttt) cc_final: 0.8320 (mmtm) REVERT: B 90 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6711 (mp) REVERT: B 135 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 137 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 166 LYS cc_start: 0.8630 (mttt) cc_final: 0.8159 (mmtm) outliers start: 26 outliers final: 19 residues processed: 117 average time/residue: 0.2076 time to fit residues: 35.5958 Evaluate side-chains 120 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10002 Z= 0.250 Angle : 0.563 8.712 13620 Z= 0.293 Chirality : 0.044 0.156 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.302 55.800 1370 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.98 % Favored : 94.86 % Rotamer: Outliers : 2.69 % Allowed : 12.04 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.25 (0.25), residues: 1244 helix: 1.90 (0.35), residues: 196 sheet: 0.63 (0.24), residues: 540 loop : -1.03 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 PHE 0.021 0.002 PHE D 109 TYR 0.011 0.001 TYR C 53 ARG 0.002 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 1.093 Fit side-chains REVERT: C 107 LYS cc_start: 0.8556 (tttt) cc_final: 0.7960 (tptt) REVERT: C 174 ASP cc_start: 0.7361 (p0) cc_final: 0.6792 (t0) REVERT: D 90 ASP cc_start: 0.8115 (m-30) cc_final: 0.7883 (m-30) REVERT: E 107 LYS cc_start: 0.8563 (tttt) cc_final: 0.7995 (tptt) REVERT: E 174 ASP cc_start: 0.7428 (p0) cc_final: 0.6939 (t0) REVERT: F 142 MET cc_start: 0.6103 (mmm) cc_final: 0.5743 (mmt) REVERT: A 90 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6811 (mp) REVERT: A 107 ARG cc_start: 0.7095 (mtp180) cc_final: 0.6709 (mtp85) REVERT: A 135 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8248 (mt-10) REVERT: A 166 LYS cc_start: 0.8779 (mttt) cc_final: 0.8303 (mmtm) REVERT: B 90 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6644 (mp) REVERT: B 135 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 137 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7930 (mt-10) REVERT: B 166 LYS cc_start: 0.8619 (mttt) cc_final: 0.8140 (mmtm) outliers start: 29 outliers final: 26 residues processed: 115 average time/residue: 0.1988 time to fit residues: 33.6255 Evaluate side-chains 123 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10002 Z= 0.237 Angle : 0.556 8.793 13620 Z= 0.288 Chirality : 0.044 0.156 1530 Planarity : 0.004 0.046 1718 Dihedral : 5.271 56.808 1370 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 2.78 % Allowed : 12.50 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.29 (0.25), residues: 1244 helix: 1.95 (0.35), residues: 196 sheet: 0.59 (0.24), residues: 544 loop : -0.93 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 PHE 0.020 0.002 PHE F 109 TYR 0.010 0.001 TYR C 53 ARG 0.002 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.082 Fit side-chains REVERT: C 107 LYS cc_start: 0.8553 (tttt) cc_final: 0.7951 (tptt) REVERT: C 174 ASP cc_start: 0.7405 (p0) cc_final: 0.6837 (t0) REVERT: D 90 ASP cc_start: 0.8125 (m-30) cc_final: 0.7874 (m-30) REVERT: D 112 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: E 107 LYS cc_start: 0.8572 (tttt) cc_final: 0.8010 (tptt) REVERT: E 174 ASP cc_start: 0.7429 (p0) cc_final: 0.6940 (t0) REVERT: F 142 MET cc_start: 0.6046 (mmm) cc_final: 0.5673 (mmt) REVERT: A 90 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6809 (mp) REVERT: A 107 ARG cc_start: 0.7087 (mtp180) cc_final: 0.6693 (mtp85) REVERT: A 135 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8240 (mt-10) REVERT: A 166 LYS cc_start: 0.8779 (mttt) cc_final: 0.8308 (mmtm) REVERT: B 90 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6623 (mp) REVERT: B 135 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8144 (mt-10) REVERT: B 137 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7974 (mt-10) REVERT: B 166 LYS cc_start: 0.8611 (mttt) cc_final: 0.8140 (mmtm) outliers start: 30 outliers final: 27 residues processed: 111 average time/residue: 0.1984 time to fit residues: 32.2946 Evaluate side-chains 122 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10002 Z= 0.318 Angle : 0.610 8.932 13620 Z= 0.316 Chirality : 0.046 0.162 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.506 58.682 1370 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.82 % Favored : 95.02 % Rotamer: Outliers : 2.96 % Allowed : 12.31 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.19 (0.25), residues: 1244 helix: 1.82 (0.35), residues: 196 sheet: 0.56 (0.24), residues: 540 loop : -1.01 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 33 HIS 0.005 0.001 HIS A 155 PHE 0.023 0.002 PHE F 109 TYR 0.011 0.002 TYR C 53 ARG 0.003 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 1.150 Fit side-chains REVERT: C 107 LYS cc_start: 0.8582 (tttt) cc_final: 0.7978 (tptt) REVERT: C 174 ASP cc_start: 0.7353 (p0) cc_final: 0.6797 (t0) REVERT: D 90 ASP cc_start: 0.8121 (m-30) cc_final: 0.7843 (m-30) REVERT: D 112 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8067 (pt0) REVERT: E 107 LYS cc_start: 0.8570 (tttt) cc_final: 0.8021 (tptt) REVERT: E 174 ASP cc_start: 0.7433 (p0) cc_final: 0.6955 (t0) REVERT: F 142 MET cc_start: 0.6064 (mmm) cc_final: 0.5668 (mmt) REVERT: A 90 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6773 (mp) REVERT: A 107 ARG cc_start: 0.7123 (mtp180) cc_final: 0.6713 (mtp85) REVERT: A 135 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8241 (mt-10) REVERT: A 166 LYS cc_start: 0.8782 (mttt) cc_final: 0.8300 (mmtm) REVERT: B 90 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6606 (mp) REVERT: B 102 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8023 (tp) REVERT: B 135 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8158 (mt-10) REVERT: B 137 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8028 (mt-10) REVERT: B 166 LYS cc_start: 0.8614 (mttt) cc_final: 0.8118 (mmtm) outliers start: 32 outliers final: 26 residues processed: 115 average time/residue: 0.2027 time to fit residues: 34.0211 Evaluate side-chains 123 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10002 Z= 0.220 Angle : 0.549 8.692 13620 Z= 0.285 Chirality : 0.044 0.153 1530 Planarity : 0.004 0.046 1718 Dihedral : 5.316 59.836 1370 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.10 % Favored : 95.74 % Rotamer: Outliers : 2.87 % Allowed : 12.41 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.32 (0.25), residues: 1244 helix: 1.96 (0.35), residues: 196 sheet: 0.64 (0.24), residues: 540 loop : -0.95 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 PHE 0.020 0.002 PHE F 109 TYR 0.009 0.001 TYR C 53 ARG 0.002 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.229 Fit side-chains REVERT: C 107 LYS cc_start: 0.8555 (tttt) cc_final: 0.7957 (tptt) REVERT: C 174 ASP cc_start: 0.7406 (p0) cc_final: 0.6833 (t0) REVERT: D 90 ASP cc_start: 0.8119 (m-30) cc_final: 0.7851 (m-30) REVERT: D 112 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: E 107 LYS cc_start: 0.8559 (tttt) cc_final: 0.7991 (tptt) REVERT: E 174 ASP cc_start: 0.7445 (p0) cc_final: 0.6973 (t0) REVERT: F 81 MET cc_start: 0.8981 (tmm) cc_final: 0.8654 (ttp) REVERT: F 142 MET cc_start: 0.6134 (mmm) cc_final: 0.5732 (mmt) REVERT: A 90 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6722 (mp) REVERT: A 107 ARG cc_start: 0.7054 (mtp180) cc_final: 0.6644 (mtp85) REVERT: A 135 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8224 (mt-10) REVERT: A 166 LYS cc_start: 0.8814 (mttt) cc_final: 0.8344 (mmtm) REVERT: B 90 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6607 (mp) REVERT: B 102 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7973 (tp) REVERT: B 135 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8139 (mt-10) REVERT: B 137 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 166 LYS cc_start: 0.8609 (mttt) cc_final: 0.8134 (mmtm) outliers start: 31 outliers final: 27 residues processed: 112 average time/residue: 0.2016 time to fit residues: 33.4065 Evaluate side-chains 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN B 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10002 Z= 0.220 Angle : 0.544 8.580 13620 Z= 0.283 Chirality : 0.044 0.152 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.260 60.443 1370 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.78 % Allowed : 12.41 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.34 (0.25), residues: 1244 helix: 2.00 (0.35), residues: 196 sheet: 0.60 (0.24), residues: 544 loop : -0.89 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 PHE 0.019 0.002 PHE F 109 TYR 0.010 0.001 TYR C 53 ARG 0.002 0.000 ARG A 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 1.546 Fit side-chains REVERT: C 107 LYS cc_start: 0.8557 (tttt) cc_final: 0.7957 (tptt) REVERT: C 174 ASP cc_start: 0.7404 (p0) cc_final: 0.6828 (t0) REVERT: D 90 ASP cc_start: 0.8128 (m-30) cc_final: 0.7831 (m-30) REVERT: D 112 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: E 107 LYS cc_start: 0.8572 (tttt) cc_final: 0.8005 (tptt) REVERT: E 174 ASP cc_start: 0.7407 (p0) cc_final: 0.6935 (t0) REVERT: F 81 MET cc_start: 0.9001 (tmm) cc_final: 0.8782 (ttp) REVERT: F 142 MET cc_start: 0.6194 (mmm) cc_final: 0.5789 (mmt) REVERT: A 90 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6757 (mp) REVERT: A 102 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8082 (tp) REVERT: A 107 ARG cc_start: 0.7052 (mtp180) cc_final: 0.6632 (mtp85) REVERT: A 135 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8222 (mt-10) REVERT: A 166 LYS cc_start: 0.8802 (mttt) cc_final: 0.8329 (mmtm) REVERT: B 90 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6620 (mp) REVERT: B 102 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7963 (tp) REVERT: B 135 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 137 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8011 (mt-10) REVERT: B 166 LYS cc_start: 0.8612 (mttt) cc_final: 0.8136 (mmtm) outliers start: 30 outliers final: 25 residues processed: 112 average time/residue: 0.2053 time to fit residues: 33.7833 Evaluate side-chains 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.163660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126747 restraints weight = 10695.799| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.81 r_work: 0.3179 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10002 Z= 0.236 Angle : 0.555 8.232 13620 Z= 0.288 Chirality : 0.044 0.155 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.301 61.711 1370 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.96 % Allowed : 12.41 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.33 (0.25), residues: 1244 helix: 1.98 (0.35), residues: 196 sheet: 0.59 (0.24), residues: 544 loop : -0.90 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 PHE 0.020 0.002 PHE F 109 TYR 0.010 0.001 TYR C 53 ARG 0.002 0.000 ARG A 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2375.12 seconds wall clock time: 44 minutes 2.47 seconds (2642.47 seconds total)