Starting phenix.real_space_refine on Tue Dec 31 17:16:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxs_19578/12_2024/8rxs_19578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxs_19578/12_2024/8rxs_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_19578/12_2024/8rxs_19578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxs_19578/12_2024/8rxs_19578.map" model { file = "/net/cci-nas-00/data/ceres_data/8rxs_19578/12_2024/8rxs_19578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxs_19578/12_2024/8rxs_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-5532/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: 10.09, per 1000 atoms: 0.62 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: 4.19 Conformation dependent library (CDL) restraints added in 1.3 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: 1.35 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: 5.81 Time building geometry restraints manager: 5.01 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: 7.360 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: 0.290 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.610 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.520 ------------------------------------------------------------------------------- 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= 0.189 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 *********************** 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 : 1.167 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: 2.5734 time to fit residues: 672.5209 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 : 1.431 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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= 0.199 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 *********************** 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 : 1.289 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 22 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7093 (mt-10) REVERT: A 64 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7771 (tttp) REVERT: B 174 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8141 (mm-40) REVERT: C 64 LYS cc_start: 0.8740 (tttt) cc_final: 0.8408 (ttmm) REVERT: E 17 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8302 (mm-40) REVERT: F 22 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7795 (mt-10) REVERT: F 145 GLU cc_start: 0.7946 (mp0) cc_final: 0.7459 (mp0) outliers start: 16 outliers final: 6 residues processed: 173 average time/residue: 2.3938 time to fit residues: 442.3339 Evaluate side-chains 151 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8160 Z= 0.250 Angle : 0.600 6.620 11100 Z= 0.303 Chirality : 0.041 0.158 1350 Planarity : 0.004 0.040 1446 Dihedral : 4.551 51.762 1116 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.30 % Favored : 92.42 % 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: -1.11 (0.27), residues: 1068 helix: 0.86 (0.30), residues: 366 sheet: -1.50 (0.33), residues: 276 loop : -1.52 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 130 PHE 0.012 0.001 PHE C 5 TYR 0.003 0.001 TYR B 166 ARG 0.003 0.000 ARG E 9 *********************** 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 172 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.431 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 64 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7731 (tttp) REVERT: B 95 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7902 (mt0) REVERT: C 64 LYS cc_start: 0.8795 (tttt) cc_final: 0.8462 (ttmm) REVERT: E 17 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8303 (mm-40) REVERT: F 22 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7851 (mt-10) REVERT: F 145 GLU cc_start: 0.7950 (mp0) cc_final: 0.7513 (mp0) outliers start: 20 outliers final: 9 residues processed: 168 average time/residue: 2.3998 time to fit residues: 430.7953 Evaluate side-chains 156 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 96 ILE Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 158 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 0.0970 chunk 50 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3477 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= 0.180 Angle : 0.577 6.666 11100 Z= 0.288 Chirality : 0.041 0.161 1350 Planarity : 0.004 0.042 1446 Dihedral : 4.350 45.677 1116 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.46 % Favored : 93.26 % Rotamer: Outliers : 1.81 % Allowed : 26.87 % 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: -0.90 (0.28), residues: 1068 helix: 0.92 (0.29), residues: 372 sheet: -1.33 (0.34), residues: 276 loop : -1.36 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 151 PHE 0.004 0.001 PHE F 155 TYR 0.005 0.001 TYR E 166 ARG 0.002 0.000 ARG E 9 *********************** 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 178 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.261 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: 0.8055 (ttmm) cc_final: 0.7760 (tttp) REVERT: C 64 LYS cc_start: 0.8804 (tttt) cc_final: 0.8472 (ttmm) REVERT: D 145 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8385 (mp0) REVERT: E 17 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8300 (mm-40) REVERT: F 22 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7859 (mt-10) REVERT: F 145 GLU cc_start: 0.7946 (mp0) cc_final: 0.7328 (mp0) outliers start: 16 outliers final: 6 residues processed: 174 average time/residue: 2.3934 time to fit residues: 444.7136 Evaluate side-chains 154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 158 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8160 Z= 0.287 Angle : 0.601 7.962 11100 Z= 0.301 Chirality : 0.041 0.163 1350 Planarity : 0.004 0.044 1446 Dihedral : 4.404 42.423 1116 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.77 % Favored : 92.04 % Rotamer: Outliers : 2.49 % Allowed : 25.62 % Favored : 71.88 % 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: -0.83 (0.28), residues: 1068 helix: 0.90 (0.29), residues: 372 sheet: -1.22 (0.34), residues: 276 loop : -1.29 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 151 PHE 0.006 0.001 PHE F 32 TYR 0.003 0.001 TYR E 166 ARG 0.003 0.000 ARG E 9 *********************** 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 177 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.101 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: A 64 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7835 (tttp) REVERT: B 20 SER cc_start: 0.7608 (OUTLIER) cc_final: 0.7329 (t) REVERT: B 95 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: C 64 LYS cc_start: 0.8845 (tttt) cc_final: 0.8501 (ttmm) REVERT: D 145 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8452 (mp0) REVERT: E 17 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8353 (mm-40) REVERT: E 40 THR cc_start: 0.9405 (p) cc_final: 0.9152 (t) REVERT: E 151 HIS cc_start: 0.7830 (t-90) cc_final: 0.7503 (t-90) REVERT: F 22 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7913 (mt-10) REVERT: F 145 GLU cc_start: 0.7937 (mp0) cc_final: 0.7302 (mp0) outliers start: 22 outliers final: 9 residues processed: 173 average time/residue: 2.4117 time to fit residues: 444.8407 Evaluate side-chains 159 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 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 69 LEU Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.0030 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- 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 F 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8160 Z= 0.241 Angle : 0.589 7.858 11100 Z= 0.294 Chirality : 0.041 0.163 1350 Planarity : 0.005 0.062 1446 Dihedral : 4.308 32.784 1116 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.12 % 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: -0.73 (0.28), residues: 1068 helix: 1.02 (0.29), residues: 366 sheet: -1.16 (0.34), residues: 276 loop : -1.24 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 24 PHE 0.004 0.001 PHE C 58 TYR 0.003 0.001 TYR B 166 ARG 0.002 0.000 ARG E 9 *********************** 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 172 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 1.401 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: 0.8410 (t) cc_final: 0.8151 (p) REVERT: A 17 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7866 (mp10) REVERT: A 64 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7819 (tttp) REVERT: A 145 GLU cc_start: 0.7656 (mp0) cc_final: 0.7408 (pm20) REVERT: B 20 SER cc_start: 0.7669 (OUTLIER) cc_final: 0.7318 (t) REVERT: B 95 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7647 (mt0) REVERT: C 1 MET cc_start: 0.6342 (ppp) cc_final: 0.6127 (pp-130) REVERT: C 64 LYS cc_start: 0.8850 (tttt) cc_final: 0.8502 (ttmm) REVERT: E 17 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8261 (mm-40) REVERT: E 39 GLU cc_start: 0.7902 (pt0) cc_final: 0.7643 (pt0) REVERT: E 40 THR cc_start: 0.9412 (p) cc_final: 0.9142 (t) REVERT: E 151 HIS cc_start: 0.7880 (t-90) cc_final: 0.7542 (t-90) REVERT: F 22 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7914 (mt-10) REVERT: F 145 GLU cc_start: 0.7951 (mp0) cc_final: 0.7302 (mp0) outliers start: 19 outliers final: 10 residues processed: 169 average time/residue: 2.4095 time to fit residues: 436.1662 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 : 1.318 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain F residue 158 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8160 Z= 0.268 Angle : 0.585 7.383 11100 Z= 0.292 Chirality : 0.041 0.165 1350 Planarity : 0.004 0.052 1446 Dihedral : 4.300 28.615 1116 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.96 % Favored : 91.85 % Rotamer: Outliers : 1.93 % Allowed : 26.08 % Favored : 72.00 % 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: -0.64 (0.27), residues: 1068 helix: 1.06 (0.29), residues: 366 sheet: -1.09 (0.34), residues: 276 loop : -1.18 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 135 PHE 0.006 0.001 PHE F 32 TYR 0.003 0.001 TYR F 166 ARG 0.002 0.000 ARG A 9 *********************** 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 167 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 VAL cc_start: 0.8373 (t) cc_final: 0.8099 (p) REVERT: A 64 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7815 (tttp) REVERT: B 20 SER cc_start: 0.7675 (OUTLIER) cc_final: 0.7376 (t) REVERT: B 95 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: C 64 LYS cc_start: 0.8856 (tttt) cc_final: 0.8502 (ttmm) REVERT: E 17 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8268 (mm-40) REVERT: E 39 GLU cc_start: 0.7906 (pt0) cc_final: 0.7656 (pt0) REVERT: E 40 THR cc_start: 0.9405 (p) cc_final: 0.9150 (t) REVERT: E 64 LYS cc_start: 0.8871 (ttmm) cc_final: 0.8399 (tttp) REVERT: E 151 HIS cc_start: 0.7940 (t-90) cc_final: 0.7583 (t-90) REVERT: E 179 LYS cc_start: 0.6875 (pttp) cc_final: 0.6354 (mmtt) REVERT: F 22 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7939 (mt-10) REVERT: F 145 GLU cc_start: 0.7944 (mp0) cc_final: 0.7297 (mp0) outliers start: 17 outliers final: 8 residues processed: 166 average time/residue: 2.4349 time to fit residues: 431.9677 Evaluate side-chains 157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** D 17 GLN D 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4367 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= 0.277 Angle : 0.602 8.250 11100 Z= 0.302 Chirality : 0.041 0.164 1350 Planarity : 0.004 0.047 1446 Dihedral : 4.271 23.047 1116 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.49 % Favored : 92.32 % Rotamer: Outliers : 2.27 % Allowed : 25.85 % Favored : 71.88 % 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: -0.58 (0.28), residues: 1068 helix: 1.07 (0.29), residues: 366 sheet: -1.20 (0.33), residues: 294 loop : -0.95 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 135 PHE 0.005 0.001 PHE C 32 TYR 0.004 0.001 TYR F 166 ARG 0.003 0.000 ARG A 9 *********************** 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 171 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.152 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: 0.8386 (t) cc_final: 0.8131 (p) REVERT: A 64 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7817 (tttp) REVERT: A 145 GLU cc_start: 0.7592 (pm20) cc_final: 0.7356 (pm20) REVERT: B 20 SER cc_start: 0.7700 (OUTLIER) cc_final: 0.7353 (t) REVERT: C 64 LYS cc_start: 0.8856 (tttt) cc_final: 0.8498 (ttmm) REVERT: D 17 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8238 (mp10) REVERT: E 17 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8278 (mm-40) REVERT: E 39 GLU cc_start: 0.7914 (pt0) cc_final: 0.7664 (pt0) REVERT: E 40 THR cc_start: 0.9404 (p) cc_final: 0.9147 (t) REVERT: E 151 HIS cc_start: 0.7992 (t-90) cc_final: 0.7639 (t-90) REVERT: E 179 LYS cc_start: 0.6923 (pttp) cc_final: 0.6382 (mmtt) REVERT: F 22 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7941 (mt-10) REVERT: F 145 GLU cc_start: 0.7945 (mp0) cc_final: 0.7304 (mp0) outliers start: 20 outliers final: 12 residues processed: 169 average time/residue: 2.4632 time to fit residues: 444.4058 Evaluate side-chains 162 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 98 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 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 Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** B 17 GLN D 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8160 Z= 0.233 Angle : 0.607 9.262 11100 Z= 0.301 Chirality : 0.041 0.162 1350 Planarity : 0.004 0.044 1446 Dihedral : 4.225 22.531 1116 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.68 % Favored : 92.13 % Rotamer: Outliers : 1.81 % Allowed : 26.42 % Favored : 71.77 % 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: -0.50 (0.28), residues: 1068 helix: 1.11 (0.29), residues: 366 sheet: -1.15 (0.33), residues: 294 loop : -0.89 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 135 PHE 0.005 0.001 PHE A 5 TYR 0.003 0.001 TYR F 166 ARG 0.002 0.000 ARG A 9 *********************** 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 170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.440 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: 0.8173 (t) cc_final: 0.7888 (p) REVERT: A 64 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7808 (tttp) REVERT: A 145 GLU cc_start: 0.7556 (pm20) cc_final: 0.7326 (pm20) REVERT: B 20 SER cc_start: 0.7678 (OUTLIER) cc_final: 0.7374 (t) REVERT: C 64 LYS cc_start: 0.8849 (tttt) cc_final: 0.8489 (ttmm) REVERT: E 17 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8274 (mm-40) REVERT: E 39 GLU cc_start: 0.7921 (pt0) cc_final: 0.7670 (pt0) REVERT: E 40 THR cc_start: 0.9400 (p) cc_final: 0.9150 (t) REVERT: E 64 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8384 (tttp) REVERT: E 151 HIS cc_start: 0.7996 (t-90) cc_final: 0.7641 (t-90) REVERT: E 179 LYS cc_start: 0.6987 (pttp) cc_final: 0.6446 (mmtt) REVERT: F 22 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7939 (mt-10) REVERT: F 145 GLU cc_start: 0.7926 (mp0) cc_final: 0.7275 (mp0) outliers start: 16 outliers final: 12 residues processed: 168 average time/residue: 2.4294 time to fit residues: 435.3145 Evaluate side-chains 165 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.0060 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8160 Z= 0.222 Angle : 0.611 9.294 11100 Z= 0.301 Chirality : 0.041 0.245 1350 Planarity : 0.004 0.043 1446 Dihedral : 4.125 21.199 1116 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.58 % Favored : 92.23 % Rotamer: Outliers : 1.47 % Allowed : 26.76 % Favored : 71.77 % 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: -0.40 (0.28), residues: 1068 helix: 1.08 (0.29), residues: 372 sheet: -1.06 (0.33), residues: 294 loop : -0.75 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 135 PHE 0.004 0.001 PHE F 32 TYR 0.004 0.001 TYR A 166 ARG 0.002 0.000 ARG A 9 ********************** 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 169 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.569 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: 0.8187 (t) cc_final: 0.7938 (p) REVERT: A 64 LYS cc_start: 0.8143 (ttmm) cc_final: 0.7836 (tttp) REVERT: B 20 SER cc_start: 0.7703 (OUTLIER) cc_final: 0.7398 (t) REVERT: C 64 LYS cc_start: 0.8851 (tttt) cc_final: 0.8489 (ttmm) REVERT: D 123 ILE cc_start: 0.9200 (mp) cc_final: 0.8904 (OUTLIER) REVERT: E 17 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8267 (mm-40) REVERT: E 39 GLU cc_start: 0.7929 (pt0) cc_final: 0.7682 (pt0) REVERT: E 40 THR cc_start: 0.9394 (p) cc_final: 0.9144 (t) REVERT: E 64 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8379 (tttp) REVERT: E 151 HIS cc_start: 0.8000 (t-90) cc_final: 0.7637 (t-90) REVERT: F 22 GLU cc_start: 0.8212 (mt-10) cc_final: 0.8009 (mt-10) REVERT: F 145 GLU cc_start: 0.7917 (mp0) cc_final: 0.7261 (mp0) outliers start: 13 outliers final: 11 residues processed: 167 average time/residue: 2.4598 time to fit residues: 438.5322 Evaluate side-chains 163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 176 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN D 103 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 = 0.3128 r_free = 0.3128 target = 0.072871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.058067 restraints weight = 52914.914| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.48 r_work: 0.2720 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8160 Z= 0.231 Angle : 0.601 8.842 11100 Z= 0.297 Chirality : 0.041 0.161 1350 Planarity : 0.004 0.041 1446 Dihedral : 4.081 19.961 1116 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.77 % Favored : 92.04 % Rotamer: Outliers : 1.36 % Allowed : 26.98 % Favored : 71.66 % 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: -0.34 (0.28), residues: 1068 helix: 1.09 (0.29), residues: 372 sheet: -0.98 (0.33), residues: 294 loop : -0.73 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 135 PHE 0.004 0.001 PHE F 32 TYR 0.004 0.001 TYR A 166 ARG 0.003 0.000 ARG A 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7798.82 seconds wall clock time: 139 minutes 30.09 seconds (8370.09 seconds total)