Starting phenix.real_space_refine on Thu Sep 18 11:07:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxs_19578/09_2025/8rxs_19578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxs_19578/09_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_19578/09_2025/8rxs_19578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxs_19578/09_2025/8rxs_19578.map" model { file = "/net/cci-nas-00/data/ceres_data/8rxs_19578/09_2025/8rxs_19578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxs_19578/09_2025/8rxs_19578.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.80, per 1000 atoms: 0.17 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: 1.40 Conformation dependent library (CDL) restraints added in 483.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.52 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: 3.38 Time building geometry restraints manager: 1.91 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: 7.800 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: 0.090 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.940 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (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 ARG 0.004 0.000 ARG B 117 TYR 0.003 0.001 TYR F 166 PHE 0.007 0.001 PHE B 58 HIS 0.007 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8160) covalent geometry : angle 0.60900 (11100) hydrogen bonds : bond 0.19584 ( 314) hydrogen bonds : angle 7.89912 ( 912) *********************** 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 : 0.451 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: 1.2736 time to fit residues: 331.4633 Evaluate side-chains 154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS B 27 ASN B 57 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.078770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.064290 restraints weight = 52504.934| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.43 r_work: 0.2840 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8160 Z= 0.147 Angle : 0.634 6.730 11100 Z= 0.321 Chirality : 0.042 0.160 1350 Planarity : 0.005 0.045 1446 Dihedral : 5.594 103.330 1119 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.02 % Favored : 92.70 % Rotamer: Outliers : 2.27 % Allowed : 26.87 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.27), residues: 1068 helix: 0.63 (0.29), residues: 366 sheet: -1.45 (0.34), residues: 246 loop : -1.89 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 9 TYR 0.008 0.001 TYR E 166 PHE 0.013 0.001 PHE C 5 HIS 0.005 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8160) covalent geometry : angle 0.63383 (11100) hydrogen bonds : bond 0.04288 ( 314) hydrogen bonds : angle 5.75000 ( 912) *********************** 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 182 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.454 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: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8681 (ttmm) cc_final: 0.8402 (tttp) REVERT: C 29 LEU cc_start: 0.8411 (mt) cc_final: 0.8150 (mm) REVERT: C 64 LYS cc_start: 0.8421 (tttt) cc_final: 0.7998 (ttmm) REVERT: D 47 ASP cc_start: 0.8797 (m-30) cc_final: 0.8560 (m-30) REVERT: E 17 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8228 (mm-40) REVERT: E 59 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8155 (mp0) REVERT: E 115 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8286 (tt0) REVERT: E 145 GLU cc_start: 0.9027 (tp30) cc_final: 0.8742 (tp30) REVERT: F 22 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8322 (mt-10) REVERT: F 145 GLU cc_start: 0.8269 (mp0) cc_final: 0.7808 (mp0) outliers start: 20 outliers final: 10 residues processed: 179 average time/residue: 1.1152 time to fit residues: 212.8628 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 : 0.417 ------------------------------------------------------------------------------- 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 40 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain E residue 112 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 158 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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** F 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.074818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.060158 restraints weight = 54047.601| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.47 r_work: 0.2744 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8160 Z= 0.185 Angle : 0.605 6.742 11100 Z= 0.307 Chirality : 0.042 0.162 1350 Planarity : 0.004 0.040 1446 Dihedral : 4.652 52.390 1116 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.12 % Favored : 92.60 % Rotamer: Outliers : 2.72 % Allowed : 24.60 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.27), residues: 1068 helix: 0.76 (0.29), residues: 372 sheet: -1.44 (0.34), residues: 276 loop : -1.44 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 9 TYR 0.004 0.001 TYR E 166 PHE 0.014 0.001 PHE C 5 HIS 0.005 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8160) covalent geometry : angle 0.60501 (11100) hydrogen bonds : bond 0.03824 ( 314) hydrogen bonds : angle 5.21474 ( 912) *********************** 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 181 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.443 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: 0.8758 (ttmm) cc_final: 0.8506 (tttp) REVERT: B 20 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8073 (t) REVERT: B 95 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8095 (mt0) REVERT: C 29 LEU cc_start: 0.8415 (mt) cc_final: 0.8182 (mm) REVERT: C 64 LYS cc_start: 0.8542 (tttt) cc_final: 0.8125 (ttmm) REVERT: C 145 GLU cc_start: 0.8173 (mp0) cc_final: 0.7936 (mp0) REVERT: D 47 ASP cc_start: 0.8797 (m-30) cc_final: 0.8587 (m-30) REVERT: D 145 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8659 (mm-30) REVERT: E 17 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8284 (mm-40) REVERT: E 59 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8244 (mp0) REVERT: E 115 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8283 (tt0) REVERT: E 145 GLU cc_start: 0.9015 (tp30) cc_final: 0.8774 (tp30) REVERT: E 151 HIS cc_start: 0.8070 (t70) cc_final: 0.7815 (t-90) REVERT: F 22 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8408 (mt-10) REVERT: F 145 GLU cc_start: 0.8286 (mp0) cc_final: 0.7861 (mp0) outliers start: 24 outliers final: 10 residues processed: 176 average time/residue: 1.0640 time to fit residues: 199.8456 Evaluate side-chains 155 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 C residue 40 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.074330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.059413 restraints weight = 53576.383| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.53 r_work: 0.2742 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3734 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= 0.157 Angle : 0.586 6.748 11100 Z= 0.294 Chirality : 0.041 0.166 1350 Planarity : 0.004 0.042 1446 Dihedral : 4.507 46.558 1116 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.93 % Favored : 92.88 % Rotamer: Outliers : 1.59 % Allowed : 25.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.27), residues: 1068 helix: 0.93 (0.29), residues: 366 sheet: -1.29 (0.34), residues: 276 loop : -1.35 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 9 TYR 0.004 0.001 TYR E 166 PHE 0.004 0.001 PHE C 5 HIS 0.005 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8160) covalent geometry : angle 0.58637 (11100) hydrogen bonds : bond 0.03356 ( 314) hydrogen bonds : angle 4.99917 ( 912) *********************** 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 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.342 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 15 VAL cc_start: 0.8903 (t) cc_final: 0.8697 (p) REVERT: A 17 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8469 (mp10) REVERT: A 64 LYS cc_start: 0.8752 (ttmm) cc_final: 0.8487 (tttp) REVERT: B 95 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: C 29 LEU cc_start: 0.8326 (mt) cc_final: 0.8086 (mm) REVERT: C 64 LYS cc_start: 0.8509 (tttt) cc_final: 0.8081 (ttmm) REVERT: C 145 GLU cc_start: 0.8205 (mp0) cc_final: 0.7927 (mp0) REVERT: D 145 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8652 (mp0) REVERT: E 17 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8231 (mm-40) REVERT: E 40 THR cc_start: 0.9183 (p) cc_final: 0.8917 (t) REVERT: E 59 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8270 (mp0) REVERT: E 115 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8266 (tt0) REVERT: E 145 GLU cc_start: 0.9021 (tp30) cc_final: 0.8739 (tp30) REVERT: E 151 HIS cc_start: 0.8188 (t70) cc_final: 0.7910 (t-90) REVERT: F 22 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8427 (mt-10) REVERT: F 145 GLU cc_start: 0.8224 (mp0) cc_final: 0.7847 (mp0) outliers start: 14 outliers final: 8 residues processed: 171 average time/residue: 1.0996 time to fit residues: 200.3396 Evaluate side-chains 155 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3171 r_free = 0.3171 target = 0.074835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.059926 restraints weight = 53451.302| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.51 r_work: 0.2748 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3936 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= 0.126 Angle : 0.572 6.940 11100 Z= 0.284 Chirality : 0.041 0.164 1350 Planarity : 0.004 0.061 1446 Dihedral : 4.333 37.799 1116 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.28), residues: 1068 helix: 0.95 (0.29), residues: 372 sheet: -1.21 (0.34), residues: 276 loop : -1.20 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 9 TYR 0.005 0.001 TYR E 166 PHE 0.004 0.001 PHE F 155 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8160) covalent geometry : angle 0.57191 (11100) hydrogen bonds : bond 0.03068 ( 314) hydrogen bonds : angle 4.83660 ( 912) *********************** 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 170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.391 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 15 VAL cc_start: 0.8865 (t) cc_final: 0.8623 (p) REVERT: A 64 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8441 (tttp) REVERT: B 95 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: C 29 LEU cc_start: 0.8262 (mt) cc_final: 0.8034 (mm) REVERT: C 64 LYS cc_start: 0.8463 (tttt) cc_final: 0.8029 (ttmm) REVERT: C 145 GLU cc_start: 0.8237 (mp0) cc_final: 0.7934 (mp0) REVERT: D 145 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8662 (mm-30) REVERT: E 17 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8142 (mm-40) REVERT: E 40 THR cc_start: 0.9158 (p) cc_final: 0.8891 (t) REVERT: E 59 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8328 (mp0) REVERT: E 115 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8221 (tt0) REVERT: E 145 GLU cc_start: 0.9021 (tp30) cc_final: 0.8770 (tp30) REVERT: E 151 HIS cc_start: 0.8193 (t70) cc_final: 0.7905 (t-90) REVERT: E 179 LYS cc_start: 0.6680 (pttp) cc_final: 0.6009 (mmtt) REVERT: F 22 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8376 (mt-10) REVERT: F 145 GLU cc_start: 0.8223 (mp0) cc_final: 0.7620 (mp0) outliers start: 17 outliers final: 9 residues processed: 168 average time/residue: 1.1144 time to fit residues: 199.5827 Evaluate side-chains 155 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 0.0000 chunk 34 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- 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 F 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.073676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.058841 restraints weight = 53136.018| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.51 r_work: 0.2721 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4112 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= 0.161 Angle : 0.578 7.713 11100 Z= 0.287 Chirality : 0.041 0.166 1350 Planarity : 0.004 0.054 1446 Dihedral : 4.311 31.479 1116 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.68 % Favored : 92.13 % Rotamer: Outliers : 1.93 % Allowed : 25.40 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.27), residues: 1068 helix: 0.97 (0.29), residues: 372 sheet: -1.14 (0.34), residues: 276 loop : -1.15 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 9 TYR 0.003 0.001 TYR A 166 PHE 0.005 0.001 PHE F 32 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8160) covalent geometry : angle 0.57784 (11100) hydrogen bonds : bond 0.03191 ( 314) hydrogen bonds : angle 4.73628 ( 912) *********************** 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 171 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.458 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: 0.8879 (t) cc_final: 0.8640 (p) REVERT: A 64 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8428 (tttp) REVERT: A 145 GLU cc_start: 0.8179 (mp0) cc_final: 0.7886 (pm20) REVERT: B 95 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: C 29 LEU cc_start: 0.8259 (mt) cc_final: 0.8024 (mm) REVERT: C 64 LYS cc_start: 0.8475 (tttt) cc_final: 0.8034 (ttmm) REVERT: C 145 GLU cc_start: 0.8264 (mp0) cc_final: 0.7963 (mp0) REVERT: D 145 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8678 (mm-30) REVERT: E 17 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8144 (mm-40) REVERT: E 40 THR cc_start: 0.9164 (p) cc_final: 0.8910 (t) REVERT: E 59 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8390 (mp0) REVERT: E 115 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8207 (tt0) REVERT: E 145 GLU cc_start: 0.9018 (tp30) cc_final: 0.8803 (tp30) REVERT: E 151 HIS cc_start: 0.8265 (t70) cc_final: 0.7892 (t-90) REVERT: F 22 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8386 (mt-10) REVERT: F 145 GLU cc_start: 0.8228 (mp0) cc_final: 0.7619 (mp0) outliers start: 17 outliers final: 9 residues processed: 168 average time/residue: 1.2152 time to fit residues: 217.1553 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 : 0.569 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** D 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.073371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.058563 restraints weight = 52954.032| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.49 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: 0.8238 moved from start: 0.4281 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= 0.171 Angle : 0.583 8.237 11100 Z= 0.290 Chirality : 0.041 0.167 1350 Planarity : 0.004 0.045 1446 Dihedral : 4.309 26.956 1116 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.96 % Favored : 91.85 % Rotamer: Outliers : 1.93 % Allowed : 25.28 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.28), residues: 1068 helix: 1.10 (0.29), residues: 366 sheet: -1.25 (0.32), residues: 294 loop : -0.96 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 9 TYR 0.004 0.001 TYR A 166 PHE 0.005 0.001 PHE C 32 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8160) covalent geometry : angle 0.58282 (11100) hydrogen bonds : bond 0.03198 ( 314) hydrogen bonds : angle 4.68090 ( 912) *********************** 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 169 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.545 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 15 VAL cc_start: 0.8870 (t) cc_final: 0.8634 (p) REVERT: A 64 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8469 (tttp) REVERT: A 145 GLU cc_start: 0.8201 (mp0) cc_final: 0.7908 (pm20) REVERT: B 95 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7733 (mt0) REVERT: C 3 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9047 (pt) REVERT: C 29 LEU cc_start: 0.8262 (mt) cc_final: 0.8025 (mm) REVERT: C 64 LYS cc_start: 0.8491 (tttt) cc_final: 0.8048 (ttmm) REVERT: C 145 GLU cc_start: 0.8312 (mp0) cc_final: 0.8015 (mp0) REVERT: D 145 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8701 (mm-30) REVERT: E 17 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8178 (mm-40) REVERT: E 40 THR cc_start: 0.9175 (p) cc_final: 0.8923 (t) REVERT: E 59 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8418 (mp0) REVERT: E 64 LYS cc_start: 0.8386 (ttmm) cc_final: 0.7886 (tttp) REVERT: E 115 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8235 (tt0) REVERT: E 145 GLU cc_start: 0.8998 (tp30) cc_final: 0.8763 (tp30) REVERT: E 151 HIS cc_start: 0.8317 (t70) cc_final: 0.7965 (t-90) REVERT: E 179 LYS cc_start: 0.6878 (pttp) cc_final: 0.6171 (mmtt) REVERT: F 22 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8390 (mt-10) REVERT: F 145 GLU cc_start: 0.8215 (mp0) cc_final: 0.7791 (mp0) outliers start: 17 outliers final: 11 residues processed: 167 average time/residue: 1.2097 time to fit residues: 215.0579 Evaluate side-chains 160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 95 GLN Chi-restraints excluded: chain C residue 3 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 F 135 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.072605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.057772 restraints weight = 53842.556| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.51 r_work: 0.2692 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4389 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= 0.179 Angle : 0.590 9.330 11100 Z= 0.293 Chirality : 0.041 0.163 1350 Planarity : 0.004 0.046 1446 Dihedral : 4.293 23.477 1116 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.87 % Favored : 91.95 % Rotamer: Outliers : 1.70 % Allowed : 25.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.28), residues: 1068 helix: 1.09 (0.29), residues: 366 sheet: -1.23 (0.32), residues: 294 loop : -0.92 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 9 TYR 0.004 0.001 TYR F 166 PHE 0.008 0.001 PHE F 32 HIS 0.005 0.001 HIS F 151 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8160) covalent geometry : angle 0.58956 (11100) hydrogen bonds : bond 0.03267 ( 314) hydrogen bonds : angle 4.65942 ( 912) *********************** 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: 15 poor density : 150 time to evaluate : 0.490 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 15 VAL cc_start: 0.8732 (t) cc_final: 0.8453 (p) REVERT: A 64 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8439 (tttp) REVERT: A 145 GLU cc_start: 0.8195 (mp0) cc_final: 0.7878 (pm20) REVERT: B 95 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: C 64 LYS cc_start: 0.8482 (tttt) cc_final: 0.8039 (ttmm) REVERT: C 145 GLU cc_start: 0.8351 (mp0) cc_final: 0.8041 (mp0) REVERT: E 17 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8169 (mm-40) REVERT: E 40 THR cc_start: 0.9176 (p) cc_final: 0.8934 (t) REVERT: E 59 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8413 (mp0) REVERT: E 64 LYS cc_start: 0.8355 (ttmm) cc_final: 0.7852 (tttp) REVERT: E 115 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8220 (tt0) REVERT: E 145 GLU cc_start: 0.8975 (tp30) cc_final: 0.8726 (tp30) REVERT: E 151 HIS cc_start: 0.8347 (t70) cc_final: 0.7969 (t-90) REVERT: F 22 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8386 (mt-10) REVERT: F 145 GLU cc_start: 0.8219 (mp0) cc_final: 0.7798 (mp0) outliers start: 15 outliers final: 11 residues processed: 164 average time/residue: 1.1400 time to fit residues: 199.0790 Evaluate side-chains 160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** D 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.073173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.058562 restraints weight = 52960.244| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.47 r_work: 0.2725 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8160 Z= 0.134 Angle : 0.582 8.913 11100 Z= 0.288 Chirality : 0.041 0.162 1350 Planarity : 0.004 0.043 1446 Dihedral : 4.173 22.478 1116 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.02 % Favored : 92.79 % Rotamer: Outliers : 1.70 % Allowed : 25.85 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.28), residues: 1068 helix: 1.18 (0.29), residues: 366 sheet: -1.12 (0.33), residues: 294 loop : -0.80 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 48 TYR 0.003 0.001 TYR E 166 PHE 0.005 0.001 PHE F 32 HIS 0.004 0.001 HIS F 151 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8160) covalent geometry : angle 0.58248 (11100) hydrogen bonds : bond 0.03001 ( 314) hydrogen bonds : angle 4.55083 ( 912) *********************** 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 165 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.467 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 15 VAL cc_start: 0.8727 (t) cc_final: 0.8455 (p) REVERT: A 64 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8444 (tttp) REVERT: A 134 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8048 (mm-40) REVERT: A 145 GLU cc_start: 0.8267 (mp0) cc_final: 0.7962 (pm20) REVERT: C 7 LYS cc_start: 0.8724 (mtmm) cc_final: 0.8420 (mtpp) REVERT: C 64 LYS cc_start: 0.8492 (tttt) cc_final: 0.8044 (ttmm) REVERT: C 145 GLU cc_start: 0.8380 (mp0) cc_final: 0.8071 (mp0) REVERT: D 17 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: D 123 ILE cc_start: 0.9176 (mp) cc_final: 0.8872 (OUTLIER) REVERT: E 17 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8164 (mm-40) REVERT: E 40 THR cc_start: 0.9174 (p) cc_final: 0.8933 (t) REVERT: E 59 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8410 (mp0) REVERT: E 115 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8308 (tt0) REVERT: E 145 GLU cc_start: 0.8957 (tp30) cc_final: 0.8718 (tp30) REVERT: E 151 HIS cc_start: 0.8329 (t70) cc_final: 0.7940 (t-90) REVERT: F 22 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8377 (mt-10) REVERT: F 145 GLU cc_start: 0.8197 (mp0) cc_final: 0.7767 (mp0) outliers start: 15 outliers final: 12 residues processed: 163 average time/residue: 1.2335 time to fit residues: 213.8150 Evaluate side-chains 160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 C residue 98 LEU Chi-restraints excluded: chain D residue 17 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN E 135 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.073033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.058427 restraints weight = 53403.327| |-----------------------------------------------------------------------------| r_work (start): 0.2859 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: 0.8230 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 8160 Z= 0.178 Angle : 0.909 59.170 11100 Z= 0.522 Chirality : 0.041 0.160 1350 Planarity : 0.004 0.043 1446 Dihedral : 4.174 22.216 1116 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.12 % Favored : 92.70 % Rotamer: Outliers : 1.47 % Allowed : 26.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.28), residues: 1068 helix: 1.18 (0.29), residues: 366 sheet: -1.12 (0.32), residues: 294 loop : -0.80 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 48 TYR 0.003 0.001 TYR B 166 PHE 0.005 0.001 PHE F 32 HIS 0.003 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8160) covalent geometry : angle 0.90889 (11100) hydrogen bonds : bond 0.03031 ( 314) hydrogen bonds : angle 4.55827 ( 912) ********************** 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 161 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.476 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 15 VAL cc_start: 0.8732 (t) cc_final: 0.8459 (p) REVERT: A 64 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8432 (tttp) REVERT: A 145 GLU cc_start: 0.8257 (mp0) cc_final: 0.7951 (pm20) REVERT: C 7 LYS cc_start: 0.8724 (mtmm) cc_final: 0.8418 (mtpp) REVERT: C 64 LYS cc_start: 0.8491 (tttt) cc_final: 0.8043 (ttmm) REVERT: C 145 GLU cc_start: 0.8380 (mp0) cc_final: 0.8070 (mp0) REVERT: D 123 ILE cc_start: 0.9171 (mp) cc_final: 0.8871 (OUTLIER) REVERT: E 17 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8168 (mm-40) REVERT: E 40 THR cc_start: 0.9176 (p) cc_final: 0.8935 (t) REVERT: E 59 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8409 (mp0) REVERT: E 115 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8308 (tt0) REVERT: E 145 GLU cc_start: 0.8953 (tp30) cc_final: 0.8714 (tp30) REVERT: E 151 HIS cc_start: 0.8332 (t70) cc_final: 0.7941 (t-90) REVERT: F 22 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8379 (mt-10) REVERT: F 145 GLU cc_start: 0.8199 (mp0) cc_final: 0.7767 (mp0) outliers start: 13 outliers final: 13 residues processed: 159 average time/residue: 1.2779 time to fit residues: 215.7855 Evaluate side-chains 159 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.073020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.058452 restraints weight = 53242.822| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.47 r_work: 0.2720 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8160 Z= 0.160 Angle : 0.911 59.196 11100 Z= 0.522 Chirality : 0.040 0.156 1350 Planarity : 0.004 0.043 1446 Dihedral : 4.172 22.220 1116 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.60 % Rotamer: Outliers : 1.70 % Allowed : 26.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.28), residues: 1068 helix: 1.18 (0.29), residues: 366 sheet: -1.12 (0.33), residues: 294 loop : -0.80 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 48 TYR 0.004 0.001 TYR B 166 PHE 0.005 0.001 PHE A 5 HIS 0.003 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8160) covalent geometry : angle 0.91060 (11100) hydrogen bonds : bond 0.03014 ( 314) hydrogen bonds : angle 4.55287 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5568.89 seconds wall clock time: 95 minutes 0.36 seconds (5700.36 seconds total)