Starting phenix.real_space_refine on Wed Feb 4 10:58:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mks_48336/02_2026/9mks_48336.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mks_48336/02_2026/9mks_48336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mks_48336/02_2026/9mks_48336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mks_48336/02_2026/9mks_48336.map" model { file = "/net/cci-nas-00/data/ceres_data/9mks_48336/02_2026/9mks_48336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mks_48336/02_2026/9mks_48336.cif" } resolution = 3.13 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6276 2.51 5 N 1830 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10116 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1686 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 204} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.58, per 1000 atoms: 0.16 Number of scatterers: 10116 At special positions: 0 Unit cell: (126.67, 116.07, 72.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1938 8.00 N 1830 7.00 C 6276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 188 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 188 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 188 " - pdb=" SG CYS F 212 " distance=2.03 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: 1.00 Conformation dependent library (CDL) restraints added in 407.6 milliseconds 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 77.0% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.567A pdb=" N HIS A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 49 through 60 removed outlier: 3.581A pdb=" N LEU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 85 Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 110 through 135 removed outlier: 3.977A pdb=" N GLN A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'A' and resid 168 through 183 removed outlier: 3.772A pdb=" N TYR A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 203 removed outlier: 6.821A pdb=" N THR A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ARG A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'B' and resid 16 through 30 removed outlier: 3.567A pdb=" N HIS B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.581A pdb=" N LEU B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 85 Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 110 through 135 removed outlier: 3.977A pdb=" N GLN B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.772A pdb=" N TYR B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 182 " --> pdb=" O THR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 203 removed outlier: 6.822A pdb=" N THR B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ARG B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'C' and resid 16 through 30 removed outlier: 3.567A pdb=" N HIS C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 45 Processing helix chain 'C' and resid 49 through 60 removed outlier: 3.581A pdb=" N LEU C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 85 Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 110 through 135 removed outlier: 3.977A pdb=" N GLN C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 134 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.772A pdb=" N TYR C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR C 181 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 182 " --> pdb=" O THR C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 203 removed outlier: 6.821A pdb=" N THR C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ARG C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.567A pdb=" N HIS D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 45 Processing helix chain 'D' and resid 49 through 60 removed outlier: 3.581A pdb=" N LEU D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 57 " --> pdb=" O ILE D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 85 Processing helix chain 'D' and resid 93 through 98 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 110 through 135 removed outlier: 3.977A pdb=" N GLN D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.772A pdb=" N TYR D 174 " --> pdb=" O PRO D 170 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 182 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 203 removed outlier: 6.821A pdb=" N THR D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ARG D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 212 Processing helix chain 'E' and resid 16 through 30 removed outlier: 3.567A pdb=" N HIS E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 45 Processing helix chain 'E' and resid 49 through 60 removed outlier: 3.581A pdb=" N LEU E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU E 57 " --> pdb=" O ILE E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 85 Processing helix chain 'E' and resid 93 through 98 Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 110 through 135 removed outlier: 3.977A pdb=" N GLN E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA E 115 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 150 through 165 Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.772A pdb=" N TYR E 174 " --> pdb=" O PRO E 170 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR E 181 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR E 182 " --> pdb=" O THR E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 203 removed outlier: 6.822A pdb=" N THR E 198 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ARG E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 212 Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.567A pdb=" N HIS F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 45 Processing helix chain 'F' and resid 49 through 60 removed outlier: 3.581A pdb=" N LEU F 54 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU F 57 " --> pdb=" O ILE F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 85 Processing helix chain 'F' and resid 93 through 98 Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 110 through 135 removed outlier: 3.977A pdb=" N GLN F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 143 Processing helix chain 'F' and resid 150 through 165 Processing helix chain 'F' and resid 168 through 183 removed outlier: 3.772A pdb=" N TYR F 174 " --> pdb=" O PRO F 170 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR F 181 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR F 182 " --> pdb=" O THR F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 203 removed outlier: 6.821A pdb=" N THR F 198 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ARG F 199 " --> pdb=" O THR F 195 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 212 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=6, first strand: chain 'F' and resid 2 through 4 630 hydrogen bonds defined for protein. 1890 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: 1.27 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2240 1.33 - 1.45: 2034 1.45 - 1.57: 5878 1.57 - 1.69: 0 1.69 - 1.82: 126 Bond restraints: 10278 Sorted by residual: bond pdb=" N ILE C 70 " pdb=" CA ILE C 70 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.17e-02 7.31e+03 1.42e+01 bond pdb=" N ILE B 70 " pdb=" CA ILE B 70 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" N ILE E 70 " pdb=" CA ILE E 70 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" N ILE F 70 " pdb=" CA ILE F 70 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" N ILE D 70 " pdb=" CA ILE D 70 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.17e-02 7.31e+03 1.40e+01 ... (remaining 10273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 9138 1.65 - 3.30: 3871 3.30 - 4.95: 750 4.95 - 6.60: 131 6.60 - 8.25: 30 Bond angle restraints: 13920 Sorted by residual: angle pdb=" O ARG F 128 " pdb=" C ARG F 128 " pdb=" N SER F 129 " ideal model delta sigma weight residual 122.12 129.29 -7.17 1.06e+00 8.90e-01 4.58e+01 angle pdb=" O ARG C 128 " pdb=" C ARG C 128 " pdb=" N SER C 129 " ideal model delta sigma weight residual 122.12 129.29 -7.17 1.06e+00 8.90e-01 4.58e+01 angle pdb=" O ARG E 128 " pdb=" C ARG E 128 " pdb=" N SER E 129 " ideal model delta sigma weight residual 122.12 129.28 -7.16 1.06e+00 8.90e-01 4.57e+01 angle pdb=" O ARG B 128 " pdb=" C ARG B 128 " pdb=" N SER B 129 " ideal model delta sigma weight residual 122.12 129.28 -7.16 1.06e+00 8.90e-01 4.57e+01 angle pdb=" O ARG D 128 " pdb=" C ARG D 128 " pdb=" N SER D 129 " ideal model delta sigma weight residual 122.12 129.28 -7.16 1.06e+00 8.90e-01 4.57e+01 ... (remaining 13915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.28: 5987 12.28 - 24.57: 229 24.57 - 36.85: 90 36.85 - 49.13: 6 49.13 - 61.41: 66 Dihedral angle restraints: 6378 sinusoidal: 2640 harmonic: 3738 Sorted by residual: dihedral pdb=" CA ASN F 139 " pdb=" CB ASN F 139 " pdb=" CG ASN F 139 " pdb=" OD1 ASN F 139 " ideal model delta sinusoidal sigma weight residual 120.00 179.19 -59.19 2 2.00e+01 2.50e-03 8.85e+00 dihedral pdb=" CA ASN D 139 " pdb=" CB ASN D 139 " pdb=" CG ASN D 139 " pdb=" OD1 ASN D 139 " ideal model delta sinusoidal sigma weight residual 120.00 179.16 -59.16 2 2.00e+01 2.50e-03 8.85e+00 dihedral pdb=" CA ASN A 139 " pdb=" CB ASN A 139 " pdb=" CG ASN A 139 " pdb=" OD1 ASN A 139 " ideal model delta sinusoidal sigma weight residual 120.00 179.16 -59.16 2 2.00e+01 2.50e-03 8.85e+00 ... (remaining 6375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 571 0.050 - 0.100: 433 0.100 - 0.149: 408 0.149 - 0.199: 115 0.199 - 0.249: 51 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CG LEU B 142 " pdb=" CB LEU B 142 " pdb=" CD1 LEU B 142 " pdb=" CD2 LEU B 142 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU F 142 " pdb=" CB LEU F 142 " pdb=" CD1 LEU F 142 " pdb=" CD2 LEU F 142 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CG LEU D 142 " pdb=" CB LEU D 142 " pdb=" CD1 LEU D 142 " pdb=" CD2 LEU D 142 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1575 not shown) Planarity restraints: 1824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 128 " -0.014 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C ARG F 128 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG F 128 " -0.020 2.00e-02 2.50e+03 pdb=" N SER F 129 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 128 " 0.014 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C ARG C 128 " -0.052 2.00e-02 2.50e+03 pdb=" O ARG C 128 " 0.020 2.00e-02 2.50e+03 pdb=" N SER C 129 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 128 " 0.014 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C ARG B 128 " -0.052 2.00e-02 2.50e+03 pdb=" O ARG B 128 " 0.020 2.00e-02 2.50e+03 pdb=" N SER B 129 " 0.018 2.00e-02 2.50e+03 ... (remaining 1821 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 4491 2.93 - 3.42: 11600 3.42 - 3.92: 17482 3.92 - 4.41: 20143 4.41 - 4.90: 31204 Nonbonded interactions: 84920 Sorted by model distance: nonbonded pdb=" O ARG A 136 " pdb=" ND2 ASN A 139 " model vdw 2.439 3.120 nonbonded pdb=" O ARG D 136 " pdb=" ND2 ASN D 139 " model vdw 2.439 3.120 nonbonded pdb=" O ARG E 136 " pdb=" ND2 ASN E 139 " model vdw 2.439 3.120 nonbonded pdb=" O ARG B 136 " pdb=" ND2 ASN B 139 " model vdw 2.439 3.120 nonbonded pdb=" O ARG F 136 " pdb=" ND2 ASN F 139 " model vdw 2.439 3.120 ... (remaining 84915 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 5.110 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.550 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 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 : 0.013 0.044 10284 Z= 0.987 Angle : 1.792 8.252 13932 Z= 1.373 Chirality : 0.098 0.249 1578 Planarity : 0.012 0.105 1824 Dihedral : 10.476 61.413 3924 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.32 (0.22), residues: 1266 helix: 0.43 (0.17), residues: 852 sheet: 0.64 (0.88), residues: 54 loop : -0.06 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG C 116 TYR 0.010 0.002 TYR C 44 PHE 0.012 0.003 PHE E 154 TRP 0.028 0.006 TRP B 122 HIS 0.006 0.002 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.01296 (10278) covalent geometry : angle 1.79130 (13920) SS BOND : bond 0.00405 ( 6) SS BOND : angle 2.23057 ( 12) hydrogen bonds : bond 0.24898 ( 630) hydrogen bonds : angle 7.56397 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 264 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 264 average time/residue: 0.1605 time to fit residues: 53.6770 Evaluate side-chains 136 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 66 GLN A 71 GLN A 84 GLN A 96 GLN A 139 ASN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN B 22 GLN B 66 GLN B 71 GLN B 84 GLN B 96 GLN B 139 ASN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN C 22 GLN C 66 GLN C 71 GLN C 84 GLN C 96 GLN C 139 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN D 22 GLN D 66 GLN D 71 GLN D 84 GLN D 96 GLN D 139 ASN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN E 22 GLN E 66 GLN E 71 GLN E 84 GLN E 96 GLN E 139 ASN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN F 22 GLN F 66 GLN F 71 GLN F 84 GLN F 96 GLN F 139 ASN ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.086785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.064819 restraints weight = 38761.971| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 4.92 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10284 Z= 0.183 Angle : 0.762 7.448 13932 Z= 0.398 Chirality : 0.040 0.116 1578 Planarity : 0.006 0.041 1824 Dihedral : 4.117 16.984 1380 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.62 % Allowed : 8.65 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.50 (0.22), residues: 1266 helix: 0.50 (0.16), residues: 930 sheet: 0.64 (0.74), residues: 54 loop : 0.17 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 39 TYR 0.010 0.002 TYR F 151 PHE 0.011 0.003 PHE F 37 TRP 0.019 0.002 TRP F 122 HIS 0.002 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00411 (10278) covalent geometry : angle 0.76047 (13920) SS BOND : bond 0.00174 ( 6) SS BOND : angle 1.85026 ( 12) hydrogen bonds : bond 0.05363 ( 630) hydrogen bonds : angle 4.92190 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7439 (mmm) cc_final: 0.7126 (mmt) REVERT: B 192 MET cc_start: 0.7509 (mmm) cc_final: 0.7179 (mmt) REVERT: C 192 MET cc_start: 0.7539 (mmm) cc_final: 0.7196 (mmt) REVERT: D 192 MET cc_start: 0.7438 (mmm) cc_final: 0.7127 (mmt) REVERT: E 192 MET cc_start: 0.7507 (mmm) cc_final: 0.7177 (mmt) REVERT: F 192 MET cc_start: 0.7522 (mmm) cc_final: 0.7178 (mmt) outliers start: 18 outliers final: 11 residues processed: 158 average time/residue: 0.1124 time to fit residues: 24.8163 Evaluate side-chains 121 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 106 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 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 = 0.4008 r_free = 0.4008 target = 0.083224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.061568 restraints weight = 41048.035| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 4.65 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10284 Z= 0.222 Angle : 0.704 9.890 13932 Z= 0.366 Chirality : 0.041 0.109 1578 Planarity : 0.005 0.034 1824 Dihedral : 4.155 18.650 1380 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.70 % Allowed : 7.39 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.40 (0.23), residues: 1266 helix: 0.57 (0.17), residues: 930 sheet: 0.05 (0.63), residues: 54 loop : -0.33 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 39 TYR 0.020 0.002 TYR C 43 PHE 0.010 0.002 PHE F 37 TRP 0.010 0.002 TRP A 122 HIS 0.003 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00515 (10278) covalent geometry : angle 0.70281 (13920) SS BOND : bond 0.00239 ( 6) SS BOND : angle 1.36818 ( 12) hydrogen bonds : bond 0.04609 ( 630) hydrogen bonds : angle 4.62352 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 ASN cc_start: 0.9219 (t0) cc_final: 0.8710 (t0) REVERT: C 85 ASN cc_start: 0.9214 (t0) cc_final: 0.8730 (t0) REVERT: E 85 ASN cc_start: 0.9223 (t0) cc_final: 0.8708 (t0) REVERT: F 85 ASN cc_start: 0.9215 (t0) cc_final: 0.8735 (t0) outliers start: 30 outliers final: 11 residues processed: 173 average time/residue: 0.0909 time to fit residues: 23.2823 Evaluate side-chains 145 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain F residue 2 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN B 84 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN C 84 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN D 84 GLN D 96 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN E 84 GLN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN F 84 GLN ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.082898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.061449 restraints weight = 41930.454| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 4.57 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10284 Z= 0.188 Angle : 0.715 9.473 13932 Z= 0.373 Chirality : 0.039 0.164 1578 Planarity : 0.004 0.032 1824 Dihedral : 4.169 19.393 1380 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.89 % Allowed : 10.45 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.67 (0.24), residues: 1266 helix: 0.75 (0.18), residues: 918 sheet: -0.14 (0.61), residues: 54 loop : -0.05 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 39 TYR 0.009 0.001 TYR C 43 PHE 0.008 0.002 PHE D 37 TRP 0.006 0.001 TRP E 122 HIS 0.001 0.000 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00434 (10278) covalent geometry : angle 0.70036 (13920) SS BOND : bond 0.01929 ( 6) SS BOND : angle 4.94375 ( 12) hydrogen bonds : bond 0.04232 ( 630) hydrogen bonds : angle 4.63473 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.437 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 84 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8321 (pp30) REVERT: A 133 MET cc_start: 0.8296 (mpp) cc_final: 0.8056 (mtm) REVERT: B 85 ASN cc_start: 0.9021 (t0) cc_final: 0.8779 (t0) REVERT: D 133 MET cc_start: 0.8290 (mpp) cc_final: 0.8051 (mtm) REVERT: E 85 ASN cc_start: 0.9018 (t0) cc_final: 0.8773 (t0) outliers start: 21 outliers final: 6 residues processed: 154 average time/residue: 0.0922 time to fit residues: 21.0051 Evaluate side-chains 133 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 145 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 = 0.4000 r_free = 0.4000 target = 0.082263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.060623 restraints weight = 41752.312| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 4.59 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10284 Z= 0.192 Angle : 0.655 10.705 13932 Z= 0.344 Chirality : 0.039 0.125 1578 Planarity : 0.004 0.032 1824 Dihedral : 4.113 19.103 1380 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.17 % Allowed : 12.07 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.56 (0.24), residues: 1266 helix: 0.70 (0.17), residues: 924 sheet: -0.36 (0.59), residues: 54 loop : -0.16 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 39 TYR 0.009 0.001 TYR C 43 PHE 0.009 0.002 PHE A 37 TRP 0.009 0.001 TRP F 81 HIS 0.001 0.000 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00450 (10278) covalent geometry : angle 0.64973 (13920) SS BOND : bond 0.00851 ( 6) SS BOND : angle 3.01268 ( 12) hydrogen bonds : bond 0.03998 ( 630) hydrogen bonds : angle 4.49370 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.436 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: symmetry clash REVERT: A 133 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8001 (mtm) REVERT: A 168 THR cc_start: 0.8985 (p) cc_final: 0.8767 (t) REVERT: B 168 THR cc_start: 0.9019 (p) cc_final: 0.8803 (t) REVERT: C 192 MET cc_start: 0.6524 (mmt) cc_final: 0.6273 (mmt) REVERT: D 133 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8000 (mtm) REVERT: D 168 THR cc_start: 0.8979 (p) cc_final: 0.8762 (t) REVERT: E 168 THR cc_start: 0.9011 (p) cc_final: 0.8794 (t) REVERT: F 192 MET cc_start: 0.6514 (mmt) cc_final: 0.6264 (mmt) outliers start: 13 outliers final: 10 residues processed: 148 average time/residue: 0.1066 time to fit residues: 22.3424 Evaluate side-chains 142 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 133 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 40.0000 chunk 87 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 79 optimal weight: 40.0000 chunk 37 optimal weight: 40.0000 chunk 113 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.082039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.060215 restraints weight = 41828.918| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.58 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10284 Z= 0.184 Angle : 0.638 11.047 13932 Z= 0.330 Chirality : 0.038 0.109 1578 Planarity : 0.004 0.063 1824 Dihedral : 4.055 19.263 1380 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.35 % Allowed : 13.33 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.69 (0.24), residues: 1266 helix: 0.87 (0.18), residues: 894 sheet: -0.42 (0.59), residues: 54 loop : -0.30 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 83 TYR 0.008 0.001 TYR C 43 PHE 0.009 0.002 PHE D 37 TRP 0.010 0.001 TRP E 81 HIS 0.001 0.000 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00427 (10278) covalent geometry : angle 0.63541 (13920) SS BOND : bond 0.00681 ( 6) SS BOND : angle 2.13536 ( 12) hydrogen bonds : bond 0.03767 ( 630) hydrogen bonds : angle 4.37994 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.444 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: A 133 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7626 (mtt) REVERT: C 133 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7899 (mtm) REVERT: D 133 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7635 (mtt) outliers start: 15 outliers final: 8 residues processed: 143 average time/residue: 0.0967 time to fit residues: 20.1943 Evaluate side-chains 140 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 2 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 92 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 17 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN B 96 GLN B 191 GLN D 191 GLN E 96 GLN E 191 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.082075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.060218 restraints weight = 41453.725| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.56 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10284 Z= 0.160 Angle : 0.623 11.889 13932 Z= 0.321 Chirality : 0.038 0.174 1578 Planarity : 0.004 0.039 1824 Dihedral : 4.065 19.362 1380 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.08 % Allowed : 14.14 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.86 (0.24), residues: 1266 helix: 1.01 (0.18), residues: 894 sheet: -0.11 (0.59), residues: 54 loop : -0.35 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 83 TYR 0.008 0.001 TYR C 43 PHE 0.009 0.001 PHE A 37 TRP 0.010 0.001 TRP F 81 HIS 0.004 0.000 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00364 (10278) covalent geometry : angle 0.62101 (13920) SS BOND : bond 0.00780 ( 6) SS BOND : angle 1.71902 ( 12) hydrogen bonds : bond 0.03567 ( 630) hydrogen bonds : angle 4.34094 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.401 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 75 ASN cc_start: 0.9388 (m-40) cc_final: 0.9140 (m-40) REVERT: A 112 MET cc_start: 0.8191 (mmp) cc_final: 0.7710 (mmp) REVERT: A 133 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7569 (mtt) REVERT: B 133 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7724 (mtm) REVERT: C 112 MET cc_start: 0.8107 (mmp) cc_final: 0.7800 (mmp) REVERT: D 112 MET cc_start: 0.8204 (mmp) cc_final: 0.7718 (mmp) REVERT: D 133 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7569 (mtt) REVERT: E 133 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7729 (mtm) REVERT: F 112 MET cc_start: 0.8112 (mmp) cc_final: 0.7803 (mmp) outliers start: 12 outliers final: 6 residues processed: 129 average time/residue: 0.0918 time to fit residues: 17.1554 Evaluate side-chains 130 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 2 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 50.0000 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN E 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.081603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.059618 restraints weight = 41580.167| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 4.57 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10284 Z= 0.179 Angle : 0.625 10.990 13932 Z= 0.328 Chirality : 0.039 0.145 1578 Planarity : 0.004 0.051 1824 Dihedral : 4.044 19.387 1380 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.44 % Allowed : 14.50 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.82 (0.24), residues: 1266 helix: 0.99 (0.18), residues: 894 sheet: -0.12 (0.59), residues: 54 loop : -0.38 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 83 TYR 0.007 0.001 TYR C 43 PHE 0.010 0.002 PHE A 37 TRP 0.011 0.001 TRP B 81 HIS 0.001 0.000 HIS F 132 Details of bonding type rmsd covalent geometry : bond 0.00411 (10278) covalent geometry : angle 0.62408 (13920) SS BOND : bond 0.00625 ( 6) SS BOND : angle 1.32454 ( 12) hydrogen bonds : bond 0.03562 ( 630) hydrogen bonds : angle 4.35566 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.422 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 75 ASN cc_start: 0.9397 (m-40) cc_final: 0.9153 (m-40) REVERT: A 112 MET cc_start: 0.8242 (mmp) cc_final: 0.7803 (mmp) REVERT: B 133 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7706 (mtt) REVERT: C 112 MET cc_start: 0.8156 (mmp) cc_final: 0.7904 (mmp) REVERT: D 60 MET cc_start: 0.9107 (mmp) cc_final: 0.8867 (mmm) REVERT: D 112 MET cc_start: 0.8267 (mmp) cc_final: 0.7817 (mmp) REVERT: E 133 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7701 (mtt) REVERT: F 112 MET cc_start: 0.8173 (mmp) cc_final: 0.7922 (mmp) outliers start: 16 outliers final: 6 residues processed: 131 average time/residue: 0.0867 time to fit residues: 16.9993 Evaluate side-chains 127 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 2 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN E 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.082438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.060498 restraints weight = 41561.649| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.56 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10284 Z= 0.150 Angle : 0.627 10.376 13932 Z= 0.331 Chirality : 0.039 0.155 1578 Planarity : 0.004 0.046 1824 Dihedral : 4.039 19.461 1380 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.26 % Allowed : 14.68 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.99 (0.23), residues: 1266 helix: 1.15 (0.17), residues: 894 sheet: 0.09 (0.57), residues: 54 loop : -0.44 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 83 TYR 0.007 0.001 TYR C 43 PHE 0.009 0.001 PHE A 37 TRP 0.015 0.001 TRP E 81 HIS 0.003 0.000 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00335 (10278) covalent geometry : angle 0.61296 (13920) SS BOND : bond 0.00461 ( 6) SS BOND : angle 4.46584 ( 12) hydrogen bonds : bond 0.03389 ( 630) hydrogen bonds : angle 4.27492 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.414 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 75 ASN cc_start: 0.9362 (m-40) cc_final: 0.9125 (m-40) REVERT: A 112 MET cc_start: 0.8225 (mmp) cc_final: 0.7834 (mmp) REVERT: D 60 MET cc_start: 0.9067 (mmp) cc_final: 0.8843 (mmm) REVERT: D 75 ASN cc_start: 0.9355 (m-40) cc_final: 0.9125 (m-40) REVERT: D 112 MET cc_start: 0.8249 (mmp) cc_final: 0.7846 (mmp) outliers start: 14 outliers final: 6 residues processed: 136 average time/residue: 0.0901 time to fit residues: 18.3192 Evaluate side-chains 122 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 121 optimal weight: 40.0000 chunk 108 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN B 96 GLN C 191 GLN E 96 GLN F 191 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.082805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.060734 restraints weight = 41327.524| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 4.59 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10284 Z= 0.155 Angle : 0.770 13.248 13932 Z= 0.392 Chirality : 0.039 0.197 1578 Planarity : 0.004 0.039 1824 Dihedral : 4.018 20.841 1380 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.54 % Allowed : 15.50 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.00 (0.23), residues: 1266 helix: 1.07 (0.17), residues: 900 sheet: 0.07 (0.56), residues: 54 loop : -0.16 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 83 TYR 0.012 0.001 TYR D 151 PHE 0.010 0.002 PHE A 37 TRP 0.012 0.001 TRP E 81 HIS 0.001 0.000 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00350 (10278) covalent geometry : angle 0.74635 (13920) SS BOND : bond 0.00971 ( 6) SS BOND : angle 6.49789 ( 12) hydrogen bonds : bond 0.03571 ( 630) hydrogen bonds : angle 4.47702 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.441 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 75 ASN cc_start: 0.9373 (m-40) cc_final: 0.9141 (m-40) REVERT: A 112 MET cc_start: 0.8232 (mmp) cc_final: 0.7855 (mmp) REVERT: B 112 MET cc_start: 0.8385 (mmp) cc_final: 0.7968 (mmp) REVERT: D 75 ASN cc_start: 0.9360 (m-40) cc_final: 0.9140 (m-40) REVERT: D 112 MET cc_start: 0.8272 (mmp) cc_final: 0.7882 (mmp) REVERT: E 112 MET cc_start: 0.8375 (mmp) cc_final: 0.7959 (mmp) outliers start: 6 outliers final: 4 residues processed: 123 average time/residue: 0.0913 time to fit residues: 16.7073 Evaluate side-chains 122 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 2 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 32 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 120 optimal weight: 40.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN F 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.081619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.059648 restraints weight = 41816.616| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 4.58 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10284 Z= 0.201 Angle : 0.730 10.043 13932 Z= 0.381 Chirality : 0.041 0.186 1578 Planarity : 0.004 0.034 1824 Dihedral : 4.135 19.536 1380 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.36 % Allowed : 15.59 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.83 (0.23), residues: 1266 helix: 0.96 (0.17), residues: 894 sheet: 0.10 (0.58), residues: 54 loop : -0.29 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 83 TYR 0.010 0.001 TYR D 151 PHE 0.011 0.002 PHE A 37 TRP 0.011 0.001 TRP E 81 HIS 0.002 0.001 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00462 (10278) covalent geometry : angle 0.71304 (13920) SS BOND : bond 0.01555 ( 6) SS BOND : angle 5.31474 ( 12) hydrogen bonds : bond 0.03790 ( 630) hydrogen bonds : angle 4.59049 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.67 seconds wall clock time: 43 minutes 2.68 seconds (2582.68 seconds total)