Starting phenix.real_space_refine on Sat Jun 14 14:57:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxs_19578/06_2025/8rxs_19578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxs_19578/06_2025/8rxs_19578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rxs_19578/06_2025/8rxs_19578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxs_19578/06_2025/8rxs_19578.map" model { file = "/net/cci-nas-00/data/ceres_data/8rxs_19578/06_2025/8rxs_19578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxs_19578/06_2025/8rxs_19578.cif" } resolution = 2.8 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 5070 2.51 5 N 1404 2.21 5 O 1518 1.98 5 H 8245 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16267 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2711 Classifications: {'peptide': 180} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 168} Chain: "B" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2711 Classifications: {'peptide': 180} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 168} Chain: "C" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2711 Classifications: {'peptide': 180} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "D" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2711 Classifications: {'peptide': 180} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "E" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2712 Classifications: {'peptide': 180} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "F" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2711 Classifications: {'peptide': 180} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 168} Time building chain proxies: 8.67, per 1000 atoms: 0.53 Number of scatterers: 16267 At special positions: 0 Unit cell: (105.78, 113.52, 69.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 O 1518 8.00 N 1404 7.00 C 5070 6.00 H 8245 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 18 sheets defined 35.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.115A pdb=" N ARG A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.568A pdb=" N SER A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 148 " --> pdb=" O GLU A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 148' Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.514A pdb=" N VAL A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 44 through 56 removed outlier: 4.286A pdb=" N ARG B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 99 through 102 removed outlier: 3.540A pdb=" N ALA B 102 " --> pdb=" O THR B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 142 through 148 removed outlier: 3.985A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 168 removed outlier: 3.568A pdb=" N VAL B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 44 through 55 removed outlier: 4.116A pdb=" N ARG C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 97 through 102 removed outlier: 3.511A pdb=" N LEU C 101 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 102 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 159 through 170 Processing helix chain 'D' and resid 43 through 56 removed outlier: 4.518A pdb=" N ASP D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.520A pdb=" N ASN D 100 " --> pdb=" O PRO D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 142 through 148 removed outlier: 3.850A pdb=" N LEU D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.675A pdb=" N VAL D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 44 through 56 removed outlier: 4.250A pdb=" N ARG E 48 " --> pdb=" O GLU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 159 through 170 Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 81 through 93 Processing helix chain 'F' and resid 122 through 131 Processing helix chain 'F' and resid 142 through 150 removed outlier: 3.960A pdb=" N LEU F 148 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 168 removed outlier: 3.584A pdb=" N VAL F 163 " --> pdb=" O ASN F 159 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 3.612A pdb=" N VAL A 15 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 64 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 69 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.464A pdb=" N GLU A 105 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ALA A 139 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 removed outlier: 3.657A pdb=" N GLU A 109 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 12 removed outlier: 3.573A pdb=" N VAL B 15 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 64 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 69 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 106 removed outlier: 6.562A pdb=" N GLU B 105 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N ALA B 139 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA B 157 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 138 " --> pdb=" O ALA B 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.842A pdb=" N GLU B 109 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 12 removed outlier: 3.730A pdb=" N VAL C 15 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU C 22 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR C 33 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.327A pdb=" N LEU C 136 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA C 157 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE C 138 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 109 through 110 removed outlier: 3.647A pdb=" N GLU C 109 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 12 removed outlier: 5.473A pdb=" N SER D 31 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL D 67 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR D 33 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU D 69 " --> pdb=" O THR D 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 104 through 106 removed outlier: 6.044A pdb=" N LEU D 136 " --> pdb=" O PHE D 155 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA D 157 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE D 138 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 109 through 110 removed outlier: 4.017A pdb=" N GLU D 109 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 12 removed outlier: 5.900A pdb=" N SER E 31 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL E 67 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR E 33 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU E 69 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL E 35 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 105 through 106 removed outlier: 6.541A pdb=" N GLU E 105 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ALA E 139 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU E 136 " --> pdb=" O PHE E 155 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA E 157 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE E 138 " --> pdb=" O ALA E 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 109 through 110 removed outlier: 3.615A pdb=" N GLU E 109 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 5 removed outlier: 3.596A pdb=" N VAL F 15 " --> pdb=" O ILE F 12 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 5 removed outlier: 3.527A pdb=" N GLY F 70 " --> pdb=" O SER F 20 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER F 31 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL F 67 " --> pdb=" O SER F 31 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR F 33 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU F 69 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL F 35 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 104 through 106 removed outlier: 6.470A pdb=" N GLU F 105 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ALA F 139 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ALA F 157 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE F 138 " --> pdb=" O ALA F 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 316 hydrogen bonds defined for protein. 912 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: 5.14 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8227 1.03 - 1.23: 21 1.23 - 1.42: 3177 1.42 - 1.62: 4938 1.62 - 1.81: 42 Bond restraints: 16405 Sorted by residual: bond pdb=" CB GLU B 94 " pdb=" CG GLU B 94 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CB GLU A 94 " pdb=" CG GLU A 94 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.54e+00 bond pdb=" CA ASP F 132 " pdb=" CB ASP F 132 " ideal model delta sigma weight residual 1.533 1.551 -0.018 1.60e-02 3.91e+03 1.21e+00 bond pdb=" C PRO B 177 " pdb=" N PRO B 178 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.69e-01 bond pdb=" C LYS E 179 " pdb=" N PRO E 180 " ideal model delta sigma weight residual 1.341 1.356 -0.015 1.60e-02 3.91e+03 8.63e-01 ... (remaining 16400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 29146 1.51 - 3.01: 614 3.01 - 4.52: 88 4.52 - 6.02: 7 6.02 - 7.53: 3 Bond angle restraints: 29858 Sorted by residual: angle pdb=" N ILE D 123 " pdb=" CA ILE D 123 " pdb=" CB ILE D 123 " ideal model delta sigma weight residual 110.50 112.86 -2.36 6.30e-01 2.52e+00 1.40e+01 angle pdb=" N GLY C 70 " pdb=" CA GLY C 70 " pdb=" C GLY C 70 " ideal model delta sigma weight residual 112.34 119.87 -7.53 2.04e+00 2.40e-01 1.36e+01 angle pdb=" C ILE D 123 " pdb=" CA ILE D 123 " pdb=" CB ILE D 123 " ideal model delta sigma weight residual 114.35 110.50 3.85 1.06e+00 8.90e-01 1.32e+01 angle pdb=" N THR B 149 " pdb=" CA THR B 149 " pdb=" C THR B 149 " ideal model delta sigma weight residual 114.62 110.69 3.93 1.14e+00 7.69e-01 1.19e+01 angle pdb=" N ILE F 14 " pdb=" CA ILE F 14 " pdb=" C ILE F 14 " ideal model delta sigma weight residual 112.96 109.66 3.30 1.00e+00 1.00e+00 1.09e+01 ... (remaining 29853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6780 17.54 - 35.08: 679 35.08 - 52.61: 196 52.61 - 70.15: 59 70.15 - 87.69: 15 Dihedral angle restraints: 7729 sinusoidal: 4308 harmonic: 3421 Sorted by residual: dihedral pdb=" CA GLY C 70 " pdb=" C GLY C 70 " pdb=" N PRO C 71 " pdb=" CA PRO C 71 " ideal model delta harmonic sigma weight residual 180.00 122.92 57.08 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA PRO C 71 " pdb=" C PRO C 71 " pdb=" N ALA C 72 " pdb=" CA ALA C 72 " ideal model delta harmonic sigma weight residual -180.00 -155.95 -24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA LYS F 131 " pdb=" C LYS F 131 " pdb=" N ASP F 132 " pdb=" CA ASP F 132 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 7726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 898 0.033 - 0.067: 315 0.067 - 0.100: 85 0.100 - 0.133: 47 0.133 - 0.166: 5 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA PRO B 178 " pdb=" N PRO B 178 " pdb=" C PRO B 178 " pdb=" CB PRO B 178 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE F 96 " pdb=" N ILE F 96 " pdb=" C ILE F 96 " pdb=" CB ILE F 96 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE F 12 " pdb=" N ILE F 12 " pdb=" C ILE F 12 " pdb=" CB ILE F 12 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 1347 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 94 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" CD GLU A 94 " 0.048 2.00e-02 2.50e+03 pdb=" OE1 GLU A 94 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU A 94 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 176 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO A 177 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 132 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C ASP F 132 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP F 132 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN F 133 " 0.011 2.00e-02 2.50e+03 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 360 2.10 - 2.73: 28747 2.73 - 3.35: 47418 3.35 - 3.98: 60553 3.98 - 4.60: 95438 Nonbonded interactions: 232516 Sorted by model distance: nonbonded pdb=" OE1 GLU A 115 " pdb=" H GLU A 115 " model vdw 1.480 2.450 nonbonded pdb=" OE1 GLU C 145 " pdb=" H GLU C 145 " model vdw 1.502 2.450 nonbonded pdb=" OE1 GLU F 115 " pdb=" H GLU F 115 " model vdw 1.558 2.450 nonbonded pdb=" OE1 GLN F 17 " pdb=" H GLN F 17 " model vdw 1.603 2.450 nonbonded pdb="HH22 ARG C 9 " pdb=" OD2 ASP C 132 " model vdw 1.610 2.450 ... (remaining 232511 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' selection = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 1 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 105 through 180)) 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: 13.060 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: 0.280 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.900 Find NCS groups from input model: 0.420 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:10.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 0.043 8160 Z= 0.125 Angle : 0.609 7.528 11100 Z= 0.320 Chirality : 0.041 0.166 1350 Planarity : 0.004 0.056 1446 Dihedral : 16.042 87.691 2982 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.65 % Favored : 93.07 % Rotamer: Outliers : 0.45 % Allowed : 20.98 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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 (0.26), residues: 1068 helix: 0.56 (0.30), residues: 348 sheet: -1.88 (0.33), residues: 246 loop : -2.01 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 151 PHE 0.007 0.001 PHE B 58 TYR 0.003 0.001 TYR F 166 ARG 0.004 0.000 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.19584 ( 314) hydrogen bonds : angle 7.89912 ( 912) covalent geometry : bond 0.00280 ( 8160) covalent geometry : angle 0.60900 (11100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 242 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8137 (t) cc_final: 0.7892 (p) REVERT: A 64 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7625 (tttp) REVERT: B 77 THR cc_start: 0.8150 (t) cc_final: 0.7503 (t) REVERT: B 95 GLN cc_start: 0.8155 (tp40) cc_final: 0.7890 (mt0) REVERT: B 148 LEU cc_start: 0.8783 (tt) cc_final: 0.8582 (mm) REVERT: B 174 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8147 (mm-40) REVERT: C 5 PHE cc_start: 0.7875 (m-10) cc_final: 0.7591 (m-80) REVERT: C 64 LYS cc_start: 0.8689 (tttt) cc_final: 0.8362 (ttmm) REVERT: D 47 ASP cc_start: 0.8419 (m-30) cc_final: 0.8214 (m-30) REVERT: E 17 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8291 (mm-40) REVERT: E 77 THR cc_start: 0.8920 (p) cc_final: 0.8650 (p) REVERT: F 22 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7446 (mt-10) REVERT: F 105 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6955 (mt-10) REVERT: F 145 GLU cc_start: 0.7972 (mp0) cc_final: 0.7715 (mp0) outliers start: 4 outliers final: 1 residues processed: 246 average time/residue: 2.4888 time to fit residues: 651.3385 Evaluate side-chains 152 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.0970 chunk 45 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS B 57 GLN D 135 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.079988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.065520 restraints weight = 52676.901| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.43 r_work: 0.2859 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8160 Z= 0.127 Angle : 0.633 6.669 11100 Z= 0.319 Chirality : 0.042 0.163 1350 Planarity : 0.005 0.046 1446 Dihedral : 5.545 102.099 1119 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.02 % Favored : 92.70 % Rotamer: Outliers : 1.81 % Allowed : 27.10 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -1.39 (0.27), residues: 1068 helix: 0.72 (0.30), residues: 360 sheet: -1.46 (0.34), residues: 246 loop : -1.92 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 130 PHE 0.010 0.001 PHE C 5 TYR 0.008 0.001 TYR E 166 ARG 0.004 0.000 ARG C 9 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 314) hydrogen bonds : angle 5.74867 ( 912) covalent geometry : bond 0.00295 ( 8160) covalent geometry : angle 0.63320 (11100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8468 (tttp) REVERT: C 29 LEU cc_start: 0.8427 (mt) cc_final: 0.8170 (mm) REVERT: C 64 LYS cc_start: 0.8466 (tttt) cc_final: 0.8042 (ttmm) REVERT: D 47 ASP cc_start: 0.8807 (m-30) cc_final: 0.8588 (m-30) REVERT: E 17 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8270 (mm-40) REVERT: E 59 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8179 (mp0) REVERT: E 145 GLU cc_start: 0.9023 (tp30) cc_final: 0.8747 (tp30) REVERT: F 22 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8347 (mt-10) REVERT: F 145 GLU cc_start: 0.8287 (mp0) cc_final: 0.7821 (mp0) outliers start: 16 outliers final: 6 residues processed: 173 average time/residue: 2.3562 time to fit residues: 435.5553 Evaluate side-chains 150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.0170 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 GLN D 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.078774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.064123 restraints weight = 52480.285| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.43 r_work: 0.2841 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8160 Z= 0.114 Angle : 0.581 6.747 11100 Z= 0.291 Chirality : 0.041 0.160 1350 Planarity : 0.004 0.039 1446 Dihedral : 4.447 49.651 1116 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.02 % Favored : 92.70 % Rotamer: Outliers : 2.15 % Allowed : 26.53 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: 1068 helix: 0.90 (0.30), residues: 366 sheet: -1.17 (0.35), residues: 246 loop : -1.78 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 130 PHE 0.011 0.001 PHE C 5 TYR 0.006 0.001 TYR A 166 ARG 0.002 0.000 ARG C 9 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 314) hydrogen bonds : angle 5.26572 ( 912) covalent geometry : bond 0.00270 ( 8160) covalent geometry : angle 0.58075 (11100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8315 (tttp) REVERT: C 5 PHE cc_start: 0.8487 (m-80) cc_final: 0.8279 (m-80) REVERT: C 29 LEU cc_start: 0.8305 (mt) cc_final: 0.8063 (mm) REVERT: C 64 LYS cc_start: 0.8436 (tttt) cc_final: 0.8016 (ttmm) REVERT: D 47 ASP cc_start: 0.8744 (m-30) cc_final: 0.8542 (m-30) REVERT: E 17 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8205 (mm-40) REVERT: E 59 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8152 (mp0) REVERT: E 145 GLU cc_start: 0.9016 (tp30) cc_final: 0.8786 (tp30) REVERT: F 22 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8290 (mt-10) REVERT: F 94 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8416 (tm-30) REVERT: F 145 GLU cc_start: 0.8252 (mp0) cc_final: 0.7803 (mp0) outliers start: 19 outliers final: 8 residues processed: 169 average time/residue: 2.2726 time to fit residues: 410.5140 Evaluate side-chains 155 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 132 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.076368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.061594 restraints weight = 53175.231| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.47 r_work: 0.2792 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8160 Z= 0.153 Angle : 0.584 6.016 11100 Z= 0.293 Chirality : 0.041 0.165 1350 Planarity : 0.004 0.041 1446 Dihedral : 4.397 47.614 1116 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.21 % Favored : 92.51 % Rotamer: Outliers : 2.27 % Allowed : 26.19 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -0.89 (0.28), residues: 1068 helix: 0.92 (0.29), residues: 372 sheet: -1.29 (0.34), residues: 276 loop : -1.37 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 151 PHE 0.011 0.001 PHE C 5 TYR 0.004 0.001 TYR E 166 ARG 0.003 0.000 ARG E 9 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 314) hydrogen bonds : angle 5.01409 ( 912) covalent geometry : bond 0.00360 ( 8160) covalent geometry : angle 0.58388 (11100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8396 (tttp) REVERT: A 162 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8441 (mt-10) REVERT: B 95 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: C 29 LEU cc_start: 0.8302 (mt) cc_final: 0.8068 (mm) REVERT: C 64 LYS cc_start: 0.8473 (tttt) cc_final: 0.8056 (ttmm) REVERT: D 145 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8641 (mp0) REVERT: E 17 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8207 (mm-40) REVERT: E 59 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8224 (mp0) REVERT: E 145 GLU cc_start: 0.9024 (tp30) cc_final: 0.8768 (tp30) REVERT: F 22 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8372 (mt-10) REVERT: F 145 GLU cc_start: 0.8259 (mp0) cc_final: 0.7665 (mp0) outliers start: 20 outliers final: 9 residues processed: 170 average time/residue: 2.3217 time to fit residues: 421.4551 Evaluate side-chains 153 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 132 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN D 17 GLN D 103 ASN F 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.075780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.060735 restraints weight = 53389.817| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.53 r_work: 0.2779 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8160 Z= 0.130 Angle : 0.574 6.709 11100 Z= 0.286 Chirality : 0.041 0.163 1350 Planarity : 0.004 0.041 1446 Dihedral : 4.278 40.296 1116 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.12 % Favored : 92.70 % Rotamer: Outliers : 1.93 % Allowed : 25.62 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -0.77 (0.28), residues: 1068 helix: 0.95 (0.29), residues: 372 sheet: -1.19 (0.34), residues: 276 loop : -1.26 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 151 PHE 0.004 0.001 PHE F 155 TYR 0.004 0.001 TYR E 166 ARG 0.002 0.000 ARG E 9 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 314) hydrogen bonds : angle 4.85917 ( 912) covalent geometry : bond 0.00309 ( 8160) covalent geometry : angle 0.57351 (11100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8441 (tttp) REVERT: A 162 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8455 (mt-10) REVERT: B 95 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7961 (mt0) REVERT: C 29 LEU cc_start: 0.8244 (mt) cc_final: 0.8011 (mm) REVERT: C 64 LYS cc_start: 0.8484 (tttt) cc_final: 0.8055 (ttmm) REVERT: D 145 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8647 (mm-30) REVERT: E 17 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8224 (mm-40) REVERT: E 40 THR cc_start: 0.9175 (p) cc_final: 0.8893 (t) REVERT: E 59 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8262 (mp0) REVERT: E 145 GLU cc_start: 0.9029 (tp30) cc_final: 0.8739 (tp30) REVERT: E 151 HIS cc_start: 0.8058 (t-90) cc_final: 0.7683 (t-90) REVERT: F 22 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8388 (mt-10) REVERT: F 145 GLU cc_start: 0.8246 (mp0) cc_final: 0.7620 (mp0) outliers start: 17 outliers final: 9 residues processed: 166 average time/residue: 2.2878 time to fit residues: 405.9374 Evaluate side-chains 154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 132 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.059929 restraints weight = 52962.354| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.44 r_work: 0.2771 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8160 Z= 0.149 Angle : 0.583 8.595 11100 Z= 0.288 Chirality : 0.041 0.162 1350 Planarity : 0.004 0.058 1446 Dihedral : 4.248 32.343 1116 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.60 % Rotamer: Outliers : 2.27 % Allowed : 25.51 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 1.52 % 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: -0.72 (0.28), residues: 1068 helix: 0.95 (0.29), residues: 372 sheet: -1.14 (0.34), residues: 276 loop : -1.21 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 24 PHE 0.004 0.001 PHE F 32 TYR 0.003 0.001 TYR B 166 ARG 0.002 0.000 ARG E 9 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 314) hydrogen bonds : angle 4.74258 ( 912) covalent geometry : bond 0.00350 ( 8160) covalent geometry : angle 0.58264 (11100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8890 (t) cc_final: 0.8677 (p) REVERT: A 17 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8478 (mp10) REVERT: A 64 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8442 (tttp) REVERT: A 145 GLU cc_start: 0.8199 (mp0) cc_final: 0.7934 (pm20) REVERT: A 162 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8443 (mt-10) REVERT: B 20 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7916 (t) REVERT: B 95 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: C 29 LEU cc_start: 0.8241 (mt) cc_final: 0.8008 (mm) REVERT: C 64 LYS cc_start: 0.8464 (tttt) cc_final: 0.8028 (ttmm) REVERT: D 145 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8668 (mm-30) REVERT: E 17 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8132 (mm-40) REVERT: E 40 THR cc_start: 0.9164 (p) cc_final: 0.8892 (t) REVERT: E 59 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8355 (mp0) REVERT: E 145 GLU cc_start: 0.9025 (tp30) cc_final: 0.8663 (tp30) REVERT: E 151 HIS cc_start: 0.8145 (t-90) cc_final: 0.7736 (t-90) REVERT: F 22 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8357 (mt-10) REVERT: F 145 GLU cc_start: 0.8224 (mp0) cc_final: 0.7591 (mp0) outliers start: 20 outliers final: 11 residues processed: 169 average time/residue: 2.3446 time to fit residues: 423.9992 Evaluate side-chains 159 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 132 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN F 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.057892 restraints weight = 53965.895| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.48 r_work: 0.2721 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8160 Z= 0.207 Angle : 0.600 8.174 11100 Z= 0.301 Chirality : 0.041 0.166 1350 Planarity : 0.005 0.052 1446 Dihedral : 4.371 27.977 1116 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.77 % Favored : 92.04 % Rotamer: Outliers : 1.81 % Allowed : 25.62 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.69 (0.27), residues: 1068 helix: 0.95 (0.29), residues: 366 sheet: -1.09 (0.34), residues: 276 loop : -1.17 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 151 PHE 0.007 0.001 PHE C 32 TYR 0.005 0.001 TYR A 166 ARG 0.003 0.000 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 314) hydrogen bonds : angle 4.73599 ( 912) covalent geometry : bond 0.00477 ( 8160) covalent geometry : angle 0.60014 (11100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8882 (t) cc_final: 0.8476 (p) REVERT: A 17 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8597 (mm-40) REVERT: A 64 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8459 (tttp) REVERT: A 145 GLU cc_start: 0.8161 (mp0) cc_final: 0.7946 (pm20) REVERT: B 20 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7982 (t) REVERT: B 95 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7706 (mt0) REVERT: C 64 LYS cc_start: 0.8496 (tttt) cc_final: 0.8058 (ttmm) REVERT: D 145 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8662 (mm-30) REVERT: E 17 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8162 (mm-40) REVERT: E 40 THR cc_start: 0.9187 (p) cc_final: 0.8928 (t) REVERT: E 59 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8363 (mp0) REVERT: E 64 LYS cc_start: 0.8428 (ttmm) cc_final: 0.7907 (tttp) REVERT: E 145 GLU cc_start: 0.9007 (tp30) cc_final: 0.8765 (tp30) REVERT: E 151 HIS cc_start: 0.8259 (t-90) cc_final: 0.7851 (t-90) REVERT: E 179 LYS cc_start: 0.6806 (pttp) cc_final: 0.6118 (mmtt) REVERT: F 22 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8410 (mt-10) REVERT: F 145 GLU cc_start: 0.8231 (mp0) cc_final: 0.7615 (mp0) outliers start: 16 outliers final: 8 residues processed: 162 average time/residue: 2.4327 time to fit residues: 420.4427 Evaluate side-chains 150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN D 55 ASN F 135 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.071717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.056780 restraints weight = 53431.666| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.49 r_work: 0.2696 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8160 Z= 0.223 Angle : 0.611 8.191 11100 Z= 0.307 Chirality : 0.042 0.166 1350 Planarity : 0.005 0.044 1446 Dihedral : 4.404 24.731 1116 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.96 % Favored : 91.85 % Rotamer: Outliers : 2.04 % Allowed : 25.74 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.67 (0.28), residues: 1068 helix: 0.87 (0.29), residues: 366 sheet: -1.21 (0.32), residues: 294 loop : -0.89 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 24 PHE 0.006 0.001 PHE C 32 TYR 0.005 0.001 TYR A 166 ARG 0.003 0.000 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 314) hydrogen bonds : angle 4.72275 ( 912) covalent geometry : bond 0.00516 ( 8160) covalent geometry : angle 0.61081 (11100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8887 (t) cc_final: 0.8621 (p) REVERT: A 64 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8466 (tttp) REVERT: A 145 GLU cc_start: 0.8229 (mp0) cc_final: 0.8001 (pm20) REVERT: B 20 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.7986 (t) REVERT: C 64 LYS cc_start: 0.8527 (tttt) cc_final: 0.8082 (ttmm) REVERT: D 17 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: D 145 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8706 (mm-30) REVERT: E 17 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8190 (mm-40) REVERT: E 40 THR cc_start: 0.9201 (p) cc_final: 0.8950 (t) REVERT: E 59 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8402 (mp0) REVERT: E 64 LYS cc_start: 0.8440 (ttmm) cc_final: 0.7919 (tttp) REVERT: E 145 GLU cc_start: 0.8975 (tp30) cc_final: 0.8729 (tp30) REVERT: E 151 HIS cc_start: 0.8322 (t-90) cc_final: 0.7901 (t-90) REVERT: E 179 LYS cc_start: 0.6934 (pttp) cc_final: 0.6227 (mmtt) REVERT: F 22 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8414 (mt-10) REVERT: F 145 GLU cc_start: 0.8237 (mp0) cc_final: 0.7821 (mp0) outliers start: 18 outliers final: 10 residues processed: 163 average time/residue: 2.3350 time to fit residues: 406.0601 Evaluate side-chains 158 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN E 135 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.071943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.057309 restraints weight = 53831.577| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.47 r_work: 0.2700 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8160 Z= 0.180 Angle : 0.611 9.472 11100 Z= 0.305 Chirality : 0.042 0.162 1350 Planarity : 0.005 0.044 1446 Dihedral : 4.344 23.115 1116 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.68 % Favored : 92.13 % Rotamer: Outliers : 1.93 % Allowed : 25.85 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.60 (0.28), residues: 1068 helix: 0.90 (0.29), residues: 366 sheet: -1.14 (0.33), residues: 294 loop : -0.86 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 24 PHE 0.009 0.001 PHE F 32 TYR 0.004 0.001 TYR F 166 ARG 0.002 0.000 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 314) hydrogen bonds : angle 4.68139 ( 912) covalent geometry : bond 0.00420 ( 8160) covalent geometry : angle 0.61121 (11100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8873 (t) cc_final: 0.8645 (p) REVERT: A 64 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8456 (tttp) REVERT: A 145 GLU cc_start: 0.8236 (mp0) cc_final: 0.8005 (pm20) REVERT: B 20 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.8005 (t) REVERT: C 64 LYS cc_start: 0.8517 (tttt) cc_final: 0.8072 (ttmm) REVERT: D 123 ILE cc_start: 0.9190 (mp) cc_final: 0.8881 (OUTLIER) REVERT: D 145 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8712 (mm-30) REVERT: E 17 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8189 (mm-40) REVERT: E 40 THR cc_start: 0.9200 (p) cc_final: 0.8946 (t) REVERT: E 59 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8410 (mp0) REVERT: E 64 LYS cc_start: 0.8421 (ttmm) cc_final: 0.7905 (tttp) REVERT: E 145 GLU cc_start: 0.8954 (tp30) cc_final: 0.8733 (tp30) REVERT: E 151 HIS cc_start: 0.8334 (t-90) cc_final: 0.7893 (t-90) REVERT: F 22 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8411 (mt-10) REVERT: F 145 GLU cc_start: 0.8237 (mp0) cc_final: 0.7821 (mp0) outliers start: 17 outliers final: 14 residues processed: 159 average time/residue: 2.3506 time to fit residues: 399.0543 Evaluate side-chains 158 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 158 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.072023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.057399 restraints weight = 53683.053| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.46 r_work: 0.2702 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 8160 Z= 0.202 Angle : 0.921 59.153 11100 Z= 0.530 Chirality : 0.042 0.165 1350 Planarity : 0.005 0.043 1446 Dihedral : 4.345 22.922 1116 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.87 % Favored : 91.95 % Rotamer: Outliers : 1.70 % Allowed : 26.19 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.59 (0.28), residues: 1068 helix: 0.90 (0.29), residues: 366 sheet: -1.14 (0.33), residues: 294 loop : -0.84 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 24 PHE 0.008 0.001 PHE F 32 TYR 0.013 0.002 TYR A 166 ARG 0.002 0.000 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 314) hydrogen bonds : angle 4.68575 ( 912) covalent geometry : bond 0.00455 ( 8160) covalent geometry : angle 0.92080 (11100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8924 (t) cc_final: 0.8699 (p) REVERT: A 17 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8466 (mt0) REVERT: A 64 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8442 (tttp) REVERT: A 145 GLU cc_start: 0.8249 (mp0) cc_final: 0.8015 (pm20) REVERT: B 20 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7982 (t) REVERT: C 64 LYS cc_start: 0.8505 (tttt) cc_final: 0.8059 (ttmm) REVERT: D 123 ILE cc_start: 0.9186 (mp) cc_final: 0.8876 (OUTLIER) REVERT: D 145 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8607 (OUTLIER) REVERT: E 17 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8185 (mm-40) REVERT: E 40 THR cc_start: 0.9188 (p) cc_final: 0.8936 (t) REVERT: E 59 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8398 (mp0) REVERT: E 145 GLU cc_start: 0.8955 (tp30) cc_final: 0.8732 (tp30) REVERT: E 151 HIS cc_start: 0.8338 (t-90) cc_final: 0.7892 (t-90) REVERT: F 22 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8413 (mt-10) REVERT: F 145 GLU cc_start: 0.8233 (mp0) cc_final: 0.7817 (mp0) outliers start: 15 outliers final: 14 residues processed: 156 average time/residue: 2.4220 time to fit residues: 402.7557 Evaluate side-chains 158 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 158 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 102 optimal weight: 0.0050 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.072077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.057371 restraints weight = 53519.840| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.47 r_work: 0.2699 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.480 8160 Z= 0.401 Angle : 0.805 28.522 11100 Z= 0.472 Chirality : 0.042 0.163 1350 Planarity : 0.010 0.330 1446 Dihedral : 4.345 22.923 1116 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.87 % Favored : 91.95 % Rotamer: Outliers : 1.70 % Allowed : 26.19 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.59 (0.28), residues: 1068 helix: 0.90 (0.29), residues: 366 sheet: -1.14 (0.33), residues: 294 loop : -0.84 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 24 PHE 0.008 0.001 PHE F 32 TYR 0.013 0.002 TYR A 166 ARG 0.002 0.000 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 314) hydrogen bonds : angle 4.68570 ( 912) covalent geometry : bond 0.00874 ( 8160) covalent geometry : angle 0.80457 (11100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10702.05 seconds wall clock time: 182 minutes 39.75 seconds (10959.75 seconds total)