Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 19:22:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/08_2023/6lni_0931.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/08_2023/6lni_0931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.702 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/08_2023/6lni_0931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/08_2023/6lni_0931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/08_2023/6lni_0931.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lni_0931/08_2023/6lni_0931.pdb" } resolution = 2.702 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= 0.000 sd= 0.003 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 50 5.16 5 C 2990 2.51 5 N 870 2.21 5 O 1010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 208": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "F ARG 208": "NH1" <-> "NH2" Residue "G ARG 208": "NH1" <-> "NH2" Residue "H ARG 208": "NH1" <-> "NH2" Residue "I ARG 208": "NH1" <-> "NH2" Residue "J ARG 208": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 4920 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "B" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "C" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "D" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "E" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "F" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "G" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "H" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "I" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "J" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Time building chain proxies: 2.55, per 1000 atoms: 0.52 Number of scatterers: 4920 At special positions: 0 Unit cell: (145.002, 122.694, 44.616, 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 50 16.00 O 1010 8.00 N 870 7.00 C 2990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 214 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 179 " - pdb=" SG CYS G 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 179 " - pdb=" SG CYS I 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 179 " - pdb=" SG CYS J 214 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.88 Conformation dependent library (CDL) restraints added in 630.1 milliseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 178 Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 185 removed outlier: 6.240A pdb=" N THR A 183 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 183 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR C 183 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR D 183 " --> pdb=" O ILE E 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 192 Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 202 removed outlier: 6.356A pdb=" N ASN A 197 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU B 200 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR A 199 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP B 202 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N THR A 201 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN B 197 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N GLU C 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N THR B 199 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP C 202 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N THR B 201 " --> pdb=" O ASP C 202 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE C 198 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR D 199 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU C 200 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN D 197 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU E 200 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR D 199 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASP E 202 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N THR D 201 " --> pdb=" O ASP E 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 210 removed outlier: 8.802A pdb=" N GLU A 207 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N VAL B 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL A 209 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N GLU B 207 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N VAL C 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL B 209 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N GLU C 207 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 9.920A pdb=" N VAL D 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL C 209 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLU D 207 " --> pdb=" O ARG E 208 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N VAL E 210 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL D 209 " --> pdb=" O VAL E 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 223 through 225 removed outlier: 6.697A pdb=" N ALA A 224 " --> pdb=" O TYR B 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 173 through 178 Processing sheet with id=AA8, first strand: chain 'F' and resid 182 through 185 removed outlier: 6.258A pdb=" N THR F 183 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR G 183 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR H 183 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR I 183 " --> pdb=" O ILE J 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 189 through 192 Processing sheet with id=AB1, first strand: chain 'F' and resid 197 through 202 removed outlier: 6.899A pdb=" N PHE F 198 " --> pdb=" O ASN G 197 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR G 199 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU F 200 " --> pdb=" O THR G 199 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE G 198 " --> pdb=" O ASN H 197 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR H 199 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU G 200 " --> pdb=" O THR H 199 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE H 198 " --> pdb=" O ASN I 197 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR I 199 " --> pdb=" O PHE H 198 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU H 200 " --> pdb=" O THR I 199 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN I 197 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU J 200 " --> pdb=" O ASN I 197 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N THR I 199 " --> pdb=" O GLU J 200 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP J 202 " --> pdb=" O THR I 199 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR I 201 " --> pdb=" O ASP J 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 206 through 210 removed outlier: 8.779A pdb=" N GLU F 207 " --> pdb=" O ARG G 208 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N VAL G 210 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL F 209 " --> pdb=" O VAL G 210 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLU G 207 " --> pdb=" O ARG H 208 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N VAL H 210 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL G 209 " --> pdb=" O VAL H 210 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N GLU H 207 " --> pdb=" O ARG I 208 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL I 210 " --> pdb=" O GLU H 207 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL H 209 " --> pdb=" O VAL I 210 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N GLU I 207 " --> pdb=" O ARG J 208 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N VAL J 210 " --> pdb=" O GLU I 207 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL I 209 " --> pdb=" O VAL J 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 79 hydrogen bonds defined for protein. 237 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: 1.13 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1700 1.34 - 1.46: 947 1.46 - 1.58: 2253 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 4980 Sorted by residual: bond pdb=" CB CYS B 214 " pdb=" SG CYS B 214 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.40e-01 bond pdb=" CB CYS I 214 " pdb=" SG CYS I 214 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.39e-01 bond pdb=" CB CYS D 214 " pdb=" SG CYS D 214 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.35e-01 bond pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.31e-01 bond pdb=" CB CYS J 214 " pdb=" SG CYS J 214 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.30e-01 ... (remaining 4975 not shown) Histogram of bond angle deviations from ideal: 100.40 - 106.56: 60 106.56 - 112.73: 2648 112.73 - 118.90: 1352 118.90 - 125.07: 2630 125.07 - 131.24: 20 Bond angle restraints: 6710 Sorted by residual: angle pdb=" C ARG H 220 " pdb=" N GLU H 221 " pdb=" CA GLU H 221 " ideal model delta sigma weight residual 122.08 125.05 -2.97 1.47e+00 4.63e-01 4.09e+00 angle pdb=" C ARG D 220 " pdb=" N GLU D 221 " pdb=" CA GLU D 221 " ideal model delta sigma weight residual 122.08 125.05 -2.97 1.47e+00 4.63e-01 4.09e+00 angle pdb=" C ARG F 220 " pdb=" N GLU F 221 " pdb=" CA GLU F 221 " ideal model delta sigma weight residual 122.08 125.04 -2.96 1.47e+00 4.63e-01 4.07e+00 angle pdb=" C ARG J 220 " pdb=" N GLU J 221 " pdb=" CA GLU J 221 " ideal model delta sigma weight residual 122.08 125.04 -2.96 1.47e+00 4.63e-01 4.05e+00 angle pdb=" C ARG B 220 " pdb=" N GLU B 221 " pdb=" CA GLU B 221 " ideal model delta sigma weight residual 122.08 125.04 -2.96 1.47e+00 4.63e-01 4.05e+00 ... (remaining 6705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.13: 2550 13.13 - 26.26: 350 26.26 - 39.39: 100 39.39 - 52.52: 40 52.52 - 65.66: 20 Dihedral angle restraints: 3060 sinusoidal: 1280 harmonic: 1780 Sorted by residual: dihedral pdb=" CA CYS B 214 " pdb=" C CYS B 214 " pdb=" N ILE B 215 " pdb=" CA ILE B 215 " ideal model delta harmonic sigma weight residual -180.00 -161.04 -18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA CYS G 214 " pdb=" C CYS G 214 " pdb=" N ILE G 215 " pdb=" CA ILE G 215 " ideal model delta harmonic sigma weight residual 180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA CYS A 214 " pdb=" C CYS A 214 " pdb=" N ILE A 215 " pdb=" CA ILE A 215 " ideal model delta harmonic sigma weight residual 180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 3057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 353 0.024 - 0.047: 221 0.047 - 0.071: 89 0.071 - 0.095: 56 0.095 - 0.118: 41 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA ILE H 182 " pdb=" N ILE H 182 " pdb=" C ILE H 182 " pdb=" CB ILE H 182 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE D 182 " pdb=" N ILE D 182 " pdb=" C ILE D 182 " pdb=" CB ILE D 182 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 757 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 226 " -0.007 2.00e-02 2.50e+03 4.67e-03 4.36e-01 pdb=" CG TYR E 226 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR E 226 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR E 226 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 226 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 226 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 226 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 226 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 226 " -0.007 2.00e-02 2.50e+03 4.64e-03 4.30e-01 pdb=" CG TYR A 226 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 226 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 226 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 226 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 226 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 226 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 226 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 226 " 0.007 2.00e-02 2.50e+03 4.63e-03 4.29e-01 pdb=" CG TYR F 226 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR F 226 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR F 226 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 226 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 226 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 226 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 226 " 0.001 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 311 2.74 - 3.28: 4447 3.28 - 3.82: 7759 3.82 - 4.36: 9521 4.36 - 4.90: 17980 Nonbonded interactions: 40018 Sorted by model distance: nonbonded pdb=" NZ LYS E 194 " pdb=" OE2 GLU J 196 " model vdw 2.200 2.520 nonbonded pdb=" NZ LYS C 194 " pdb=" OE2 GLU H 196 " model vdw 2.220 2.520 nonbonded pdb=" NZ LYS D 194 " pdb=" OE2 GLU I 196 " model vdw 2.236 2.520 nonbonded pdb=" NZ LYS B 194 " pdb=" OE2 GLU G 196 " model vdw 2.243 2.520 nonbonded pdb=" OE2 GLU C 196 " pdb=" NZ LYS G 194 " model vdw 2.267 2.520 ... (remaining 40013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.630 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: 0.010 Extract box with map and model: 12.670 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.360 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 0.004 0.024 4980 Z= 0.276 Angle : 0.554 3.752 6710 Z= 0.347 Chirality : 0.044 0.118 760 Planarity : 0.002 0.006 880 Dihedral : 14.813 65.656 1870 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.05 (0.19), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.14), residues: 580 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.602 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 182 average time/residue: 1.6033 time to fit residues: 299.5116 Evaluate side-chains 148 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1698 time to fit residues: 0.9537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.0770 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 174 ASN A 177 HIS A 187 HIS A 227 GLN B 173 ASN B 174 ASN B 177 HIS B 217 GLN C 173 ASN C 174 ASN C 177 HIS C 187 HIS D 173 ASN D 174 ASN D 177 HIS E 173 ASN E 174 ASN E 187 HIS F 173 ASN F 174 ASN F 187 HIS G 173 ASN G 174 ASN G 177 HIS G 187 HIS H 173 ASN H 174 ASN H 177 HIS I 173 ASN I 174 ASN I 177 HIS I 187 HIS J 173 ASN J 174 ASN J 187 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.045 4980 Z= 0.479 Angle : 0.655 5.872 6710 Z= 0.386 Chirality : 0.048 0.154 760 Planarity : 0.004 0.031 880 Dihedral : 6.089 24.422 650 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.12 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.17), residues: 580 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 0.611 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 150 average time/residue: 1.9316 time to fit residues: 296.4626 Evaluate side-chains 149 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 3 average time/residue: 0.6127 time to fit residues: 2.7753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS E 172 GLN ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.041 4980 Z= 0.470 Angle : 0.647 5.910 6710 Z= 0.382 Chirality : 0.047 0.158 760 Planarity : 0.004 0.037 880 Dihedral : 6.130 24.101 650 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.71 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.19), residues: 580 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 0.597 Fit side-chains outliers start: 21 outliers final: 7 residues processed: 147 average time/residue: 1.8468 time to fit residues: 278.0198 Evaluate side-chains 146 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 3 average time/residue: 0.8528 time to fit residues: 3.3939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 HIS F 177 HIS I 174 ASN ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.033 4980 Z= 0.373 Angle : 0.592 5.281 6710 Z= 0.350 Chirality : 0.046 0.119 760 Planarity : 0.003 0.036 880 Dihedral : 5.912 22.385 650 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer Outliers : 4.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.48 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.19), residues: 580 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 0.615 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 153 average time/residue: 1.8564 time to fit residues: 290.7794 Evaluate side-chains 155 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 6 average time/residue: 1.0294 time to fit residues: 7.1989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 GLN ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 4980 Z= 0.281 Angle : 0.550 4.580 6710 Z= 0.324 Chirality : 0.045 0.139 760 Planarity : 0.004 0.039 880 Dihedral : 5.662 20.860 650 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.25 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.20), residues: 580 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 0.634 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 154 average time/residue: 1.8994 time to fit residues: 299.4238 Evaluate side-chains 151 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 3 average time/residue: 1.0029 time to fit residues: 3.9662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4980 Z= 0.220 Angle : 0.527 5.022 6710 Z= 0.309 Chirality : 0.044 0.155 760 Planarity : 0.003 0.038 880 Dihedral : 5.485 18.949 650 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer Outliers : 4.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.06 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.20), residues: 580 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 0.624 Fit side-chains outliers start: 25 outliers final: 6 residues processed: 158 average time/residue: 1.8047 time to fit residues: 292.1603 Evaluate side-chains 150 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 0.599 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 0.6228 time to fit residues: 2.1563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 174 ASN H 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.052 4980 Z= 0.630 Angle : 0.750 6.764 6710 Z= 0.438 Chirality : 0.051 0.175 760 Planarity : 0.004 0.040 880 Dihedral : 6.239 23.647 650 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.16 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.20), residues: 580 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 0.633 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 162 average time/residue: 1.8796 time to fit residues: 311.6945 Evaluate side-chains 157 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 2 average time/residue: 0.1625 time to fit residues: 1.0770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 174 ASN E 172 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4980 Z= 0.222 Angle : 0.591 6.850 6710 Z= 0.344 Chirality : 0.046 0.196 760 Planarity : 0.004 0.039 880 Dihedral : 5.797 21.405 650 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.01 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.608 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 154 average time/residue: 1.8532 time to fit residues: 292.1858 Evaluate side-chains 151 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 0.642 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.7395 time to fit residues: 2.3983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 172 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 4980 Z= 0.295 Angle : 0.628 7.489 6710 Z= 0.364 Chirality : 0.047 0.205 760 Planarity : 0.004 0.037 880 Dihedral : 5.889 19.969 650 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.01 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 580 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 0.572 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 156 average time/residue: 1.8589 time to fit residues: 296.9164 Evaluate side-chains 156 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 3 average time/residue: 0.5737 time to fit residues: 2.6466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 172 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.029 4980 Z= 0.352 Angle : 0.681 7.923 6710 Z= 0.396 Chirality : 0.049 0.217 760 Planarity : 0.004 0.043 880 Dihedral : 6.231 24.813 650 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.04 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.20), residues: 580 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.589 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 153 average time/residue: 1.9128 time to fit residues: 299.5758 Evaluate side-chains 152 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 0.585 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 1 average time/residue: 0.1940 time to fit residues: 1.2817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.131786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.113369 restraints weight = 5191.051| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.12 r_work: 0.3693 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4980 Z= 0.199 Angle : 0.617 8.591 6710 Z= 0.355 Chirality : 0.047 0.215 760 Planarity : 0.003 0.042 880 Dihedral : 6.073 27.878 650 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.97 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.21), residues: 580 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4185.28 seconds wall clock time: 73 minutes 47.39 seconds (4427.39 seconds total)