Starting phenix.real_space_refine on Tue Jan 21 03:53:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxs_19578/01_2025/8rxs_19578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxs_19578/01_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_19578/01_2025/8rxs_19578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxs_19578/01_2025/8rxs_19578.map" model { file = "/net/cci-nas-00/data/ceres_data/8rxs_19578/01_2025/8rxs_19578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxs_19578/01_2025/8rxs_19578.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 5070 2.51 5 N 1404 2.21 5 O 1518 1.98 5 H 8245 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.86, per 1000 atoms: 0.61 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: 4.26 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: 1.32 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: 5.96 Time building geometry restraints manager: 5.04 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.280 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.600 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.020 ------------------------------------------------------------------------------- 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 : 1.265 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: 2.5632 time to fit residues: 669.7481 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 : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.0970 chunk 45 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS B 57 GLN D 135 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.079988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.065521 restraints weight = 52676.901| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.43 r_work: 0.2859 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8160 Z= 0.199 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 : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8468 (tttp) REVERT: C 29 LEU cc_start: 0.8427 (mt) cc_final: 0.8171 (mm) REVERT: C 64 LYS cc_start: 0.8466 (tttt) cc_final: 0.8043 (ttmm) REVERT: D 47 ASP cc_start: 0.8807 (m-30) cc_final: 0.8588 (m-30) REVERT: E 17 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8270 (mm-40) REVERT: E 59 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8180 (mp0) REVERT: E 145 GLU cc_start: 0.9025 (tp30) cc_final: 0.8748 (tp30) REVERT: F 22 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8348 (mt-10) REVERT: F 145 GLU cc_start: 0.8288 (mp0) cc_final: 0.7822 (mp0) outliers start: 16 outliers final: 6 residues processed: 173 average time/residue: 2.4144 time to fit residues: 446.3431 Evaluate side-chains 150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.0170 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 GLN D 103 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.078758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.064111 restraints weight = 52468.543| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.42 r_work: 0.2841 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3209 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= 0.183 Angle : 0.580 6.744 11100 Z= 0.291 Chirality : 0.041 0.159 1350 Planarity : 0.004 0.039 1446 Dihedral : 4.443 49.599 1116 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.02 % Favored : 92.70 % Rotamer: Outliers : 2.15 % Allowed : 26.53 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.27), residues: 1068 helix: 0.91 (0.30), residues: 366 sheet: -1.16 (0.35), residues: 246 loop : -1.77 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 130 PHE 0.011 0.001 PHE C 5 TYR 0.006 0.001 TYR A 166 ARG 0.002 0.000 ARG 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 175 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.250 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: 0.8657 (ttmm) cc_final: 0.8314 (tttp) REVERT: C 5 PHE cc_start: 0.8492 (m-80) cc_final: 0.8283 (m-80) REVERT: C 29 LEU cc_start: 0.8303 (mt) cc_final: 0.8061 (mm) REVERT: C 64 LYS cc_start: 0.8435 (tttt) cc_final: 0.8016 (ttmm) REVERT: D 47 ASP cc_start: 0.8744 (m-30) cc_final: 0.8542 (m-30) REVERT: E 17 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8205 (mm-40) REVERT: E 59 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8156 (mp0) REVERT: E 145 GLU cc_start: 0.9013 (tp30) cc_final: 0.8783 (tp30) REVERT: F 22 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8290 (mt-10) REVERT: F 94 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8414 (tm-30) REVERT: F 145 GLU cc_start: 0.8248 (mp0) cc_final: 0.7798 (mp0) outliers start: 19 outliers final: 7 residues processed: 169 average time/residue: 2.3772 time to fit residues: 428.9581 Evaluate side-chains 154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 120 SER Chi-restraints excluded: chain F residue 132 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.076266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.061439 restraints weight = 53217.133| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.48 r_work: 0.2790 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8160 Z= 0.243 Angle : 0.583 6.546 11100 Z= 0.292 Chirality : 0.041 0.162 1350 Planarity : 0.004 0.041 1446 Dihedral : 4.397 47.356 1116 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.12 % Favored : 92.60 % Rotamer: Outliers : 2.27 % Allowed : 25.96 % Favored : 71.77 % 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: -0.87 (0.28), residues: 1068 helix: 0.92 (0.29), residues: 372 sheet: -1.28 (0.34), residues: 276 loop : -1.35 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 151 PHE 0.010 0.001 PHE C 5 TYR 0.004 0.001 TYR E 166 ARG 0.003 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 177 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.298 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: 0.8676 (ttmm) cc_final: 0.8438 (tttp) REVERT: A 162 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8443 (mt-10) REVERT: B 95 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8088 (mt0) REVERT: C 29 LEU cc_start: 0.8303 (mt) cc_final: 0.8069 (mm) REVERT: C 64 LYS cc_start: 0.8476 (tttt) cc_final: 0.8059 (ttmm) REVERT: D 145 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8646 (mp0) REVERT: E 17 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8227 (mm-40) REVERT: E 59 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8228 (mp0) REVERT: E 145 GLU cc_start: 0.9022 (tp30) cc_final: 0.8765 (tp30) REVERT: F 22 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8397 (mt-10) REVERT: F 145 GLU cc_start: 0.8260 (mp0) cc_final: 0.7661 (mp0) outliers start: 20 outliers final: 11 residues processed: 172 average time/residue: 2.4613 time to fit residues: 451.4306 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 : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN D 17 GLN D 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.075398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.060542 restraints weight = 53651.678| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.46 r_work: 0.2769 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8160 Z= 0.232 Angle : 0.582 7.871 11100 Z= 0.290 Chirality : 0.041 0.162 1350 Planarity : 0.004 0.041 1446 Dihedral : 4.298 39.050 1116 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.12 % Favored : 92.70 % Rotamer: Outliers : 2.15 % Allowed : 25.40 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.28), residues: 1068 helix: 1.03 (0.29), residues: 366 sheet: -1.18 (0.34), residues: 276 loop : -1.30 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 151 PHE 0.004 0.001 PHE E 58 TYR 0.003 0.001 TYR B 166 ARG 0.002 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 171 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8490 (mp10) REVERT: A 64 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8460 (tttp) REVERT: B 20 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7945 (t) REVERT: B 95 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: C 7 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8407 (mtpp) REVERT: C 29 LEU cc_start: 0.8256 (mt) cc_final: 0.8024 (mm) REVERT: C 64 LYS cc_start: 0.8491 (tttt) cc_final: 0.8059 (ttmm) REVERT: D 145 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8668 (mm-30) REVERT: E 17 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8225 (mm-40) REVERT: E 40 THR cc_start: 0.9178 (p) cc_final: 0.8904 (t) REVERT: E 59 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8291 (mp0) REVERT: E 145 GLU cc_start: 0.9015 (tp30) cc_final: 0.8727 (tp30) REVERT: E 151 HIS cc_start: 0.8065 (t-90) cc_final: 0.7722 (t-90) REVERT: F 22 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8408 (mt-10) REVERT: F 145 GLU cc_start: 0.8245 (mp0) cc_final: 0.7624 (mp0) outliers start: 19 outliers final: 10 residues processed: 168 average time/residue: 2.3905 time to fit residues: 428.8726 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 : 1.400 ------------------------------------------------------------------------------- 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 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 132 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.074337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.059460 restraints weight = 53356.552| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.46 r_work: 0.2757 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4080 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= 0.247 Angle : 0.586 8.685 11100 Z= 0.290 Chirality : 0.041 0.172 1350 Planarity : 0.005 0.056 1446 Dihedral : 4.271 29.317 1116 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.84 % Favored : 92.98 % Rotamer: Outliers : 2.38 % Allowed : 25.06 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.28), residues: 1068 helix: 0.93 (0.29), residues: 372 sheet: -1.11 (0.34), residues: 276 loop : -1.25 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 151 PHE 0.006 0.001 PHE F 32 TYR 0.004 0.001 TYR A 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: 21 poor density : 151 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8439 (mp10) REVERT: A 64 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8449 (tttp) REVERT: A 145 GLU cc_start: 0.8252 (mp0) cc_final: 0.7983 (pm20) REVERT: B 20 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.7940 (t) REVERT: B 95 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: C 7 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8412 (mtpp) REVERT: C 29 LEU cc_start: 0.8265 (mt) cc_final: 0.8035 (mm) REVERT: C 64 LYS cc_start: 0.8486 (tttt) cc_final: 0.8049 (ttmm) REVERT: C 134 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8269 (mm-40) REVERT: D 145 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8634 (mm-30) REVERT: E 17 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8148 (mm-40) REVERT: E 40 THR cc_start: 0.9170 (p) cc_final: 0.8906 (t) REVERT: E 59 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8371 (mp0) REVERT: E 64 LYS cc_start: 0.8392 (ttmm) cc_final: 0.7871 (tttp) REVERT: E 145 GLU cc_start: 0.9021 (tp30) cc_final: 0.8755 (tp30) REVERT: E 151 HIS cc_start: 0.8176 (t-90) cc_final: 0.7772 (t-90) REVERT: E 179 LYS cc_start: 0.6731 (pttp) cc_final: 0.6063 (mmtt) REVERT: F 22 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8379 (mt-10) REVERT: F 145 GLU cc_start: 0.8223 (mp0) cc_final: 0.7584 (mp0) outliers start: 21 outliers final: 11 residues processed: 168 average time/residue: 2.4348 time to fit residues: 436.1672 Evaluate side-chains 158 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 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 96 ILE Chi-restraints excluded: chain F residue 132 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 D 55 ASN D 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.074348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.059675 restraints weight = 53638.217| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.45 r_work: 0.2757 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8160 Z= 0.212 Angle : 0.572 8.755 11100 Z= 0.283 Chirality : 0.041 0.162 1350 Planarity : 0.004 0.053 1446 Dihedral : 4.173 26.481 1116 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.84 % Favored : 92.98 % Rotamer: Outliers : 2.04 % Allowed : 25.40 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.28), residues: 1068 helix: 0.97 (0.29), residues: 372 sheet: -1.07 (0.34), residues: 276 loop : -1.12 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 24 PHE 0.004 0.001 PHE F 155 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 169 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8417 (tttp) REVERT: A 145 GLU cc_start: 0.8215 (mp0) cc_final: 0.7937 (pm20) REVERT: B 20 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7911 (t) REVERT: B 95 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: C 29 LEU cc_start: 0.8221 (mt) cc_final: 0.7990 (mm) REVERT: C 64 LYS cc_start: 0.8469 (tttt) cc_final: 0.8026 (ttmm) REVERT: D 145 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8632 (mm-30) REVERT: E 17 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8130 (mm-40) REVERT: E 40 THR cc_start: 0.9155 (p) cc_final: 0.8887 (t) REVERT: E 59 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8384 (mp0) REVERT: E 145 GLU cc_start: 0.9010 (tp30) cc_final: 0.8765 (tp30) REVERT: E 151 HIS cc_start: 0.8208 (t-90) cc_final: 0.7793 (t-90) REVERT: E 179 LYS cc_start: 0.6776 (pttp) cc_final: 0.6106 (mmtt) REVERT: F 22 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8362 (mt-10) REVERT: F 145 GLU cc_start: 0.8200 (mp0) cc_final: 0.7541 (mp0) outliers start: 18 outliers final: 11 residues processed: 167 average time/residue: 2.4438 time to fit residues: 435.5785 Evaluate side-chains 157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 132 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.071726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.056981 restraints weight = 53879.725| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.46 r_work: 0.2693 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8160 Z= 0.392 Angle : 0.620 7.545 11100 Z= 0.313 Chirality : 0.042 0.167 1350 Planarity : 0.005 0.046 1446 Dihedral : 4.394 24.763 1116 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.71 % Favored : 91.10 % Rotamer: Outliers : 2.04 % Allowed : 25.85 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.28), residues: 1068 helix: 0.89 (0.29), residues: 366 sheet: -1.20 (0.32), residues: 294 loop : -0.92 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 24 PHE 0.009 0.001 PHE C 32 TYR 0.007 0.001 TYR A 166 ARG 0.004 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 163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8462 (tttp) REVERT: A 145 GLU cc_start: 0.8205 (mp0) cc_final: 0.7990 (pm20) REVERT: B 20 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.8000 (t) REVERT: C 64 LYS cc_start: 0.8511 (tttt) cc_final: 0.8070 (ttmm) REVERT: D 17 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8039 (mp10) REVERT: D 145 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8709 (mm-30) REVERT: E 17 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8163 (mm-40) REVERT: E 40 THR cc_start: 0.9189 (p) cc_final: 0.8940 (t) REVERT: E 59 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8392 (mp0) REVERT: E 64 LYS cc_start: 0.8402 (ttmm) cc_final: 0.7880 (tttp) REVERT: E 145 GLU cc_start: 0.8990 (tp30) cc_final: 0.8728 (tp30) REVERT: E 151 HIS cc_start: 0.8333 (t-90) cc_final: 0.7903 (t-90) REVERT: E 179 LYS cc_start: 0.6917 (pttp) cc_final: 0.6213 (mmtt) REVERT: F 22 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8421 (mt-10) REVERT: F 145 GLU cc_start: 0.8239 (mp0) cc_final: 0.7810 (mp0) outliers start: 18 outliers final: 10 residues processed: 160 average time/residue: 2.5181 time to fit residues: 428.9173 Evaluate side-chains 151 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** 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 = 0.3133 r_free = 0.3133 target = 0.072805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.058271 restraints weight = 53549.387| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.44 r_work: 0.2721 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8160 Z= 0.208 Angle : 0.595 9.447 11100 Z= 0.297 Chirality : 0.041 0.162 1350 Planarity : 0.005 0.045 1446 Dihedral : 4.252 22.136 1116 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.84 % Favored : 92.98 % Rotamer: Outliers : 1.70 % Allowed : 26.19 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.28), residues: 1068 helix: 0.98 (0.29), residues: 366 sheet: -1.10 (0.33), residues: 294 loop : -0.83 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 151 PHE 0.005 0.001 PHE A 5 TYR 0.004 0.001 TYR A 166 ARG 0.003 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 160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 1.219 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: 0.8772 (ttmm) cc_final: 0.8450 (tttp) REVERT: A 145 GLU cc_start: 0.8218 (mp0) cc_final: 0.8003 (pm20) REVERT: B 20 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.7992 (t) REVERT: C 64 LYS cc_start: 0.8513 (tttt) cc_final: 0.8066 (ttmm) REVERT: D 123 ILE cc_start: 0.9165 (mp) cc_final: 0.8859 (mm) REVERT: D 145 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8679 (mm-30) REVERT: E 17 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8169 (mm-40) REVERT: E 40 THR cc_start: 0.9179 (p) cc_final: 0.8924 (t) REVERT: E 59 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8406 (mp0) REVERT: E 64 LYS cc_start: 0.8369 (ttmm) cc_final: 0.7855 (tttp) REVERT: E 145 GLU cc_start: 0.8954 (tp30) cc_final: 0.8697 (tp30) REVERT: E 151 HIS cc_start: 0.8286 (t-90) cc_final: 0.7844 (t-90) REVERT: F 22 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8400 (mt-10) REVERT: F 145 GLU cc_start: 0.8203 (mp0) cc_final: 0.7580 (mp0) outliers start: 15 outliers final: 11 residues processed: 159 average time/residue: 2.4126 time to fit residues: 409.1499 Evaluate side-chains 156 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 38 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 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** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.072118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.057291 restraints weight = 53781.576| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.51 r_work: 0.2688 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8160 Z= 0.295 Angle : 0.604 8.699 11100 Z= 0.301 Chirality : 0.041 0.164 1350 Planarity : 0.004 0.042 1446 Dihedral : 4.264 21.770 1116 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.61 % Favored : 91.20 % 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 (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: 0.98 (0.29), residues: 366 sheet: -1.07 (0.33), residues: 294 loop : -0.81 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 151 PHE 0.008 0.001 PHE F 32 TYR 0.008 0.001 TYR A 166 ARG 0.002 0.000 ARG B 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 157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8448 (tttp) REVERT: A 145 GLU cc_start: 0.8251 (mp0) cc_final: 0.8034 (pm20) REVERT: B 20 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.8011 (t) REVERT: C 64 LYS cc_start: 0.8512 (tttt) cc_final: 0.8065 (ttmm) REVERT: D 123 ILE cc_start: 0.9197 (mp) cc_final: 0.8910 (OUTLIER) REVERT: D 145 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8707 (mm-30) REVERT: E 17 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8163 (mm-40) REVERT: E 40 THR cc_start: 0.9176 (p) cc_final: 0.8933 (t) REVERT: E 59 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8402 (mp0) REVERT: E 145 GLU cc_start: 0.8951 (tp30) cc_final: 0.8719 (tp30) REVERT: E 151 HIS cc_start: 0.8354 (t-90) cc_final: 0.7910 (t-90) REVERT: F 22 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8416 (mt-10) REVERT: F 145 GLU cc_start: 0.8246 (mp0) cc_final: 0.7826 (mp0) outliers start: 13 outliers final: 10 residues processed: 156 average time/residue: 2.4866 time to fit residues: 415.6889 Evaluate side-chains 152 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 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 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 102 optimal weight: 0.0040 chunk 88 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.6894 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.073007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.058420 restraints weight = 53209.243| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.48 r_work: 0.2718 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8160 Z= 0.197 Angle : 0.587 8.573 11100 Z= 0.289 Chirality : 0.041 0.161 1350 Planarity : 0.004 0.042 1446 Dihedral : 4.098 19.273 1116 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.02 % Favored : 92.79 % Rotamer: Outliers : 1.25 % Allowed : 26.76 % 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: -0.35 (0.28), residues: 1068 helix: 1.11 (0.29), residues: 366 sheet: -0.98 (0.33), residues: 294 loop : -0.74 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 151 PHE 0.005 0.001 PHE A 5 TYR 0.003 0.001 TYR B 166 ARG 0.002 0.000 ARG D 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10820.69 seconds wall clock time: 190 minutes 44.82 seconds (11444.82 seconds total)