Starting phenix.real_space_refine on Fri Sep 11 20:23:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jca_6441/09_2026/3jca_6441.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jca_6441/09_2026/3jca_6441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jca_6441/09_2026/3jca_6441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jca_6441/09_2026/3jca_6441.map" restraint_files = "/net/cci-nas-00/data/ceres_data/3jca_6441/09_2026/3jca_6441.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jca_6441/09_2026/3jca_6441.cif" model { file = "/net/cci-nas-00/data/ceres_data/3jca_6441/09_2026/3jca_6441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jca_6441/09_2026/3jca_6441.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.044 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 78 5.49 5 S 44 5.16 5 C 7086 2.51 5 N 2076 2.21 5 O 2178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11466 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2096 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 243} Chain breaks: 1 Chain: "B" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2031 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 236} Chain breaks: 1 Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "D" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "E" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2096 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 243} Chain breaks: 1 Chain: "F" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2031 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 236} Chain breaks: 1 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "H" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "I" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "K" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "L" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 299 SG CYS A 37 50.219 31.097 35.214 1.00117.64 S ATOM 320 SG CYS A 40 50.724 33.076 35.605 1.00129.65 S ATOM 2395 SG CYS B 37 120.732 24.422 25.373 1.00177.75 S ATOM 2416 SG CYS B 40 121.081 26.218 26.600 1.00174.63 S ATOM 5212 SG CYS E 37 91.196 65.853 35.151 1.00117.34 S ATOM 5233 SG CYS E 40 90.593 63.888 35.391 1.00131.03 S ATOM 7308 SG CYS F 37 20.729 72.530 25.394 1.00178.00 S ATOM 7329 SG CYS F 40 20.380 70.736 26.617 1.00174.87 S Time building chain proxies: 2.92, per 1000 atoms: 0.25 Number of scatterers: 11466 At special positions: 0 Unit cell: (142.79, 98.25, 94.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 44 16.00 P 78 15.00 O 2178 8.00 N 2076 7.00 C 7086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 487.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 13 " pdb="ZN ZN A 500 " - pdb=" NE2 HIS A 9 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 37 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 9 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 13 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 13 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 9 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 37 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 40 " pdb=" ZN F 500 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 40 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 37 " pdb="ZN ZN F 500 " - pdb=" NE2 HIS F 9 " pdb="ZN ZN F 500 " - pdb=" ND1 HIS F 13 " Number of angles added : 6 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 39.2% alpha, 21.0% beta 36 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 69 through 76 removed outlier: 7.147A pdb=" N LYS A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 154 through 174 Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 202 through 209 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 15 through 24 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 150 through 171 Processing helix chain 'B' and resid 172 through 175 removed outlier: 4.134A pdb=" N GLY B 175 " --> pdb=" O GLN B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 69 through 76 removed outlier: 7.143A pdb=" N LYS E 74 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 129 through 140 Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 154 through 174 Processing helix chain 'E' and resid 179 through 194 Processing helix chain 'E' and resid 202 through 209 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 15 through 24 Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 129 through 139 Processing helix chain 'F' and resid 150 through 171 Processing helix chain 'F' and resid 172 through 175 removed outlier: 4.085A pdb=" N GLY F 175 " --> pdb=" O GLN F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 179 through 194 Processing helix chain 'F' and resid 202 through 209 Processing sheet with id=A, first strand: chain 'A' and resid 88 through 94 removed outlier: 3.547A pdb=" N TYR A 77 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP A 62 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 254 through 257 removed outlier: 5.629A pdb=" N VAL A 219 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 89 through 94 removed outlier: 6.545A pdb=" N TRP B 62 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE B 119 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 254 through 257 removed outlier: 5.600A pdb=" N VAL B 219 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N MET B 218 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'C' and resid 254 through 257 removed outlier: 5.370A pdb=" N VAL C 219 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'D' and resid 254 through 257 removed outlier: 6.598A pdb=" N TYR D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA D 238 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS D 244 " --> pdb=" O ILE D 236 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY D 231 " --> pdb=" O TRP D 221 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TRP D 221 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'E' and resid 88 through 94 removed outlier: 3.543A pdb=" N TYR E 77 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'E' and resid 254 through 257 removed outlier: 5.646A pdb=" N VAL E 219 " --> pdb=" O PRO E 232 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'F' and resid 89 through 94 removed outlier: 6.548A pdb=" N TRP F 62 " --> pdb=" O LYS F 120 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE F 119 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'F' and resid 254 through 257 removed outlier: 5.595A pdb=" N VAL F 219 " --> pdb=" O PRO F 232 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N MET F 218 " --> pdb=" O PHE F 264 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'G' and resid 254 through 257 removed outlier: 5.364A pdb=" N VAL G 219 " --> pdb=" O PRO G 232 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'H' and resid 254 through 257 removed outlier: 6.606A pdb=" N TYR H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA H 238 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS H 244 " --> pdb=" O ILE H 236 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY H 231 " --> pdb=" O TRP H 221 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP H 221 " --> pdb=" O GLY H 231 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2604 1.33 - 1.45: 3657 1.45 - 1.58: 5483 1.58 - 1.70: 154 1.70 - 1.82: 72 Bond restraints: 11970 Sorted by residual: bond pdb=" CA ASP G 223 " pdb=" C ASP G 223 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.30e-02 5.92e+03 1.33e+01 bond pdb=" N9 DA L 12 " pdb=" C4 DA L 12 " ideal model delta sigma weight residual 1.374 1.352 0.022 6.00e-03 2.78e+04 1.32e+01 bond pdb=" CA ASP C 223 " pdb=" C ASP C 223 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.29e-02 6.01e+03 1.29e+01 bond pdb=" CA TRP A 208 " pdb=" CB TRP A 208 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.51e-02 4.39e+03 1.28e+01 bond pdb=" CA ARG A 27 " pdb=" C ARG A 27 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.30e-02 5.92e+03 1.09e+01 ... (remaining 11965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 15189 2.50 - 5.00: 1204 5.00 - 7.51: 193 7.51 - 10.01: 34 10.01 - 12.51: 4 Bond angle restraints: 16624 Sorted by residual: angle pdb=" C PHE E 246 " pdb=" N PRO E 247 " pdb=" CA PRO E 247 " ideal model delta sigma weight residual 119.78 130.02 -10.24 1.03e+00 9.43e-01 9.88e+01 angle pdb=" C PHE A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta sigma weight residual 119.78 129.93 -10.15 1.03e+00 9.43e-01 9.71e+01 angle pdb=" C PHE F 246 " pdb=" N PRO F 247 " pdb=" CA PRO F 247 " ideal model delta sigma weight residual 119.78 129.04 -9.26 1.03e+00 9.43e-01 8.09e+01 angle pdb=" C PHE B 246 " pdb=" N PRO B 247 " pdb=" CA PRO B 247 " ideal model delta sigma weight residual 119.78 128.99 -9.21 1.03e+00 9.43e-01 8.00e+01 angle pdb=" C LYS E 216 " pdb=" N PRO E 217 " pdb=" CA PRO E 217 " ideal model delta sigma weight residual 120.31 128.93 -8.62 9.80e-01 1.04e+00 7.74e+01 ... (remaining 16619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.88: 6304 31.88 - 63.77: 492 63.77 - 95.65: 18 95.65 - 127.54: 0 127.54 - 159.42: 2 Dihedral angle restraints: 6816 sinusoidal: 3254 harmonic: 3562 Sorted by residual: dihedral pdb=" C4' DA K 1 " pdb=" C3' DA K 1 " pdb=" O3' DA K 1 " pdb=" P DA K 2 " ideal model delta sinusoidal sigma weight residual 220.00 60.58 159.42 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' DA I 1 " pdb=" C3' DA I 1 " pdb=" O3' DA I 1 " pdb=" P DA I 2 " ideal model delta sinusoidal sigma weight residual 220.00 64.50 155.50 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C HIS A 13 " pdb=" N HIS A 13 " pdb=" CA HIS A 13 " pdb=" CB HIS A 13 " ideal model delta harmonic sigma weight residual -122.60 -131.24 8.64 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 6813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1287 0.073 - 0.147: 462 0.147 - 0.220: 39 0.220 - 0.293: 1 0.293 - 0.367: 1 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CA HIS A 13 " pdb=" N HIS A 13 " pdb=" C HIS A 13 " pdb=" CB HIS A 13 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA TRP E 208 " pdb=" N TRP E 208 " pdb=" C TRP E 208 " pdb=" CB TRP E 208 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA TRP A 208 " pdb=" N TRP A 208 " pdb=" C TRP A 208 " pdb=" CB TRP A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1787 not shown) Planarity restraints: 1856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 40 " -0.101 5.00e-02 4.00e+02 1.54e-01 3.82e+01 pdb=" N PRO E 41 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO E 41 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO E 41 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 40 " 0.091 5.00e-02 4.00e+02 1.36e-01 2.94e+01 pdb=" N PRO A 41 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 265 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C THR A 265 " -0.063 2.00e-02 2.50e+03 pdb=" O THR A 265 " 0.023 2.00e-02 2.50e+03 pdb=" OXT THR A 265 " 0.022 2.00e-02 2.50e+03 ... (remaining 1853 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 4253 2.88 - 3.38: 11041 3.38 - 3.89: 22227 3.89 - 4.39: 26011 4.39 - 4.90: 38001 Nonbonded interactions: 101533 Sorted by model distance: nonbonded pdb=" N GLU B 71 " pdb=" OE1 GLU B 71 " model vdw 2.370 3.120 nonbonded pdb=" N GLU F 71 " pdb=" OE1 GLU F 71 " model vdw 2.373 3.120 nonbonded pdb=" O5' DA K 2 " pdb=" O4' DA K 2 " model vdw 2.459 2.432 nonbonded pdb=" O PHE H 264 " pdb=" OG1 THR H 265 " model vdw 2.479 3.040 nonbonded pdb=" O PHE D 264 " pdb=" OG1 THR D 265 " model vdw 2.481 3.040 ... (remaining 101528 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 41 or resid 54 through 500)) selection = chain 'B' selection = (chain 'E' and (resid 1 through 41 or resid 54 through 500)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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 group one per residue 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: 1.420 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.300 Find NCS groups from input model: 0.250 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.017 0.740 11986 Z= 0.860 Angle : 1.819 68.485 16630 Z= 1.114 Chirality : 0.067 0.367 1790 Planarity : 0.011 0.154 1856 Dihedral : 18.843 159.419 4504 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.87 (0.21), residues: 1202 helix: -0.84 (0.21), residues: 440 sheet: 0.23 (0.42), residues: 146 loop : -1.93 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 59 TYR 0.040 0.006 TYR E 177 PHE 0.021 0.005 PHE A 110 TRP 0.040 0.009 TRP A 221 HIS 0.008 0.002 HIS B 13 Details of bonding type rmsd/Z covalent geometry : bond 0.01183 / 0.79 (11970) covalent geometry : angle 1.50410 / 1.09 (16624) hydrogen bonds : bond 0.14423 / 10.03 ( 556) hydrogen bonds : angle 8.43256 / 5.92 ( 1484) metal coordination : bond 0.33731 / 24.03 ( 16) metal coordination : angle 53.84415 / 31.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.403 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9405 (mt) cc_final: 0.9059 (tt) REVERT: A 71 GLU cc_start: 0.7546 (tt0) cc_final: 0.6999 (tt0) REVERT: A 79 HIS cc_start: 0.8690 (m-70) cc_final: 0.8019 (m170) REVERT: A 90 PHE cc_start: 0.8938 (t80) cc_final: 0.8054 (t80) REVERT: A 105 HIS cc_start: 0.8914 (t70) cc_final: 0.7271 (t70) REVERT: A 118 LYS cc_start: 0.8574 (ptpt) cc_final: 0.8090 (tttp) REVERT: A 119 ILE cc_start: 0.8954 (tt) cc_final: 0.8672 (pt) REVERT: A 260 PHE cc_start: 0.8769 (m-80) cc_final: 0.8344 (m-10) REVERT: B 6 GLN cc_start: 0.8911 (mt0) cc_final: 0.8441 (tm-30) REVERT: B 25 ILE cc_start: 0.7929 (mt) cc_final: 0.7714 (mt) REVERT: B 168 LEU cc_start: 0.9302 (mt) cc_final: 0.9010 (mt) REVERT: B 169 ASN cc_start: 0.8805 (m-40) cc_final: 0.7777 (t0) REVERT: B 181 HIS cc_start: 0.8320 (m170) cc_final: 0.8091 (m170) REVERT: B 195 ASN cc_start: 0.8332 (m-40) cc_final: 0.8056 (t0) REVERT: B 261 ILE cc_start: 0.8754 (mm) cc_final: 0.8517 (pt) REVERT: C 242 TYR cc_start: 0.7899 (m-80) cc_final: 0.7573 (m-80) REVERT: C 255 TRP cc_start: 0.7736 (m100) cc_final: 0.7305 (m100) REVERT: E 19 LEU cc_start: 0.9381 (mt) cc_final: 0.9072 (tt) REVERT: E 39 ASN cc_start: 0.8959 (m-40) cc_final: 0.8745 (m110) REVERT: E 71 GLU cc_start: 0.7544 (tt0) cc_final: 0.7123 (tt0) REVERT: E 79 HIS cc_start: 0.8697 (m-70) cc_final: 0.8111 (m170) REVERT: E 94 ARG cc_start: 0.8790 (mmm160) cc_final: 0.8192 (mmt180) REVERT: E 105 HIS cc_start: 0.8941 (t70) cc_final: 0.7741 (t70) REVERT: E 119 ILE cc_start: 0.8895 (tt) cc_final: 0.8404 (pt) REVERT: E 144 VAL cc_start: 0.6543 (t) cc_final: 0.6195 (t) REVERT: E 220 MET cc_start: 0.8440 (mmm) cc_final: 0.8019 (mmm) REVERT: F 6 GLN cc_start: 0.8947 (mt0) cc_final: 0.8454 (tm-30) REVERT: F 168 LEU cc_start: 0.9313 (mt) cc_final: 0.9030 (mt) REVERT: F 169 ASN cc_start: 0.8779 (m-40) cc_final: 0.7768 (t0) REVERT: F 181 HIS cc_start: 0.8319 (m170) cc_final: 0.7926 (m170) REVERT: F 261 ILE cc_start: 0.8549 (mm) cc_final: 0.8248 (tp) REVERT: G 224 LEU cc_start: 0.8655 (mt) cc_final: 0.8320 (mp) REVERT: G 228 SER cc_start: 0.8164 (t) cc_final: 0.7914 (p) REVERT: G 233 ASP cc_start: 0.8046 (t0) cc_final: 0.7347 (t0) REVERT: G 242 TYR cc_start: 0.8053 (m-80) cc_final: 0.7523 (m-80) REVERT: G 255 TRP cc_start: 0.7572 (m100) cc_final: 0.6992 (m100) REVERT: H 242 TYR cc_start: 0.8028 (p90) cc_final: 0.7770 (p90) REVERT: H 258 ASP cc_start: 0.9334 (p0) cc_final: 0.8872 (p0) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.1101 time to fit residues: 62.2539 Evaluate side-chains 226 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS B 39 ASN B 63 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN E 68 HIS ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 192 ASN F 195 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.075555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.063079 restraints weight = 58055.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.065074 restraints weight = 34063.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.066343 restraints weight = 22766.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.067383 restraints weight = 17077.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067969 restraints weight = 13575.137| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 11986 Z= 0.176 Angle : 0.748 9.118 16630 Z= 0.406 Chirality : 0.049 0.250 1790 Planarity : 0.007 0.056 1856 Dihedral : 23.984 149.704 2160 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.91 (0.23), residues: 1202 helix: 0.00 (0.23), residues: 422 sheet: 0.18 (0.43), residues: 144 loop : -1.19 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 206 TYR 0.016 0.002 TYR A 77 PHE 0.022 0.002 PHE B 246 TRP 0.013 0.002 TRP A 221 HIS 0.013 0.002 HIS B 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (11970) covalent geometry : angle 0.74030 / 0.41 (16624) hydrogen bonds : bond 0.06277 / 4.29 ( 556) hydrogen bonds : angle 7.08514 / 4.91 ( 1484) metal coordination : bond 0.03583 / 2.74 ( 16) metal coordination : angle 5.76176 / 3.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.379 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: 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 19 LEU cc_start: 0.9379 (mt) cc_final: 0.9038 (tt) REVERT: A 25 ILE cc_start: 0.8558 (pt) cc_final: 0.8149 (pt) REVERT: A 29 GLN cc_start: 0.9009 (mt0) cc_final: 0.8250 (mm-40) REVERT: A 79 HIS cc_start: 0.8011 (m-70) cc_final: 0.7804 (m170) REVERT: A 90 PHE cc_start: 0.8688 (t80) cc_final: 0.7427 (t80) REVERT: A 105 HIS cc_start: 0.8039 (t70) cc_final: 0.7105 (t70) REVERT: A 113 MET cc_start: 0.9019 (mtp) cc_final: 0.8499 (mtp) REVERT: A 118 LYS cc_start: 0.8222 (ptpt) cc_final: 0.7649 (tttm) REVERT: A 119 ILE cc_start: 0.8876 (tt) cc_final: 0.8536 (tt) REVERT: A 144 VAL cc_start: 0.6482 (t) cc_final: 0.6231 (t) REVERT: A 218 MET cc_start: 0.6843 (mtp) cc_final: 0.6536 (ptm) REVERT: A 220 MET cc_start: 0.8565 (tpp) cc_final: 0.8219 (tpp) REVERT: A 260 PHE cc_start: 0.8936 (m-80) cc_final: 0.8606 (m-80) REVERT: B 6 GLN cc_start: 0.8613 (mt0) cc_final: 0.8323 (tm-30) REVERT: B 97 GLU cc_start: 0.8352 (pm20) cc_final: 0.7785 (mm-30) REVERT: B 141 ILE cc_start: 0.9104 (mt) cc_final: 0.8806 (mm) REVERT: B 168 LEU cc_start: 0.9247 (mt) cc_final: 0.8949 (mt) REVERT: B 169 ASN cc_start: 0.8482 (m-40) cc_final: 0.8142 (t0) REVERT: C 255 TRP cc_start: 0.7863 (m100) cc_final: 0.7384 (m100) REVERT: C 258 ASP cc_start: 0.7534 (p0) cc_final: 0.7320 (p0) REVERT: E 19 LEU cc_start: 0.9294 (mt) cc_final: 0.8978 (tt) REVERT: E 25 ILE cc_start: 0.8759 (pt) cc_final: 0.8291 (pt) REVERT: E 29 GLN cc_start: 0.9153 (mt0) cc_final: 0.8472 (mm-40) REVERT: E 39 ASN cc_start: 0.8837 (m-40) cc_final: 0.8496 (m110) REVERT: E 87 HIS cc_start: 0.7988 (t-90) cc_final: 0.7488 (t70) REVERT: E 90 PHE cc_start: 0.8705 (t80) cc_final: 0.7656 (t80) REVERT: E 105 HIS cc_start: 0.7973 (t70) cc_final: 0.7541 (t70) REVERT: E 106 LEU cc_start: 0.9178 (mt) cc_final: 0.8962 (mt) REVERT: E 113 MET cc_start: 0.9028 (mtp) cc_final: 0.8559 (mtp) REVERT: E 134 GLU cc_start: 0.8853 (tt0) cc_final: 0.8598 (tm-30) REVERT: E 218 MET cc_start: 0.6809 (mtp) cc_final: 0.6497 (ptm) REVERT: E 220 MET cc_start: 0.8541 (mmm) cc_final: 0.8065 (mmm) REVERT: E 221 TRP cc_start: 0.7036 (t60) cc_final: 0.6604 (t60) REVERT: E 260 PHE cc_start: 0.8919 (m-80) cc_final: 0.8677 (m-80) REVERT: F 6 GLN cc_start: 0.8699 (mt0) cc_final: 0.8295 (tm-30) REVERT: F 115 ILE cc_start: 0.6875 (mt) cc_final: 0.6361 (mt) REVERT: F 141 ILE cc_start: 0.9036 (mt) cc_final: 0.8661 (mm) REVERT: F 168 LEU cc_start: 0.9189 (mt) cc_final: 0.8859 (mt) REVERT: F 169 ASN cc_start: 0.8495 (m-40) cc_final: 0.8129 (t0) REVERT: G 224 LEU cc_start: 0.8049 (mt) cc_final: 0.7676 (mp) REVERT: G 228 SER cc_start: 0.8239 (t) cc_final: 0.7886 (p) REVERT: G 234 VAL cc_start: 0.8597 (t) cc_final: 0.8202 (t) REVERT: G 242 TYR cc_start: 0.7755 (m-80) cc_final: 0.7438 (m-80) REVERT: G 255 TRP cc_start: 0.7697 (m100) cc_final: 0.7199 (m100) REVERT: H 242 TYR cc_start: 0.7153 (p90) cc_final: 0.6781 (p90) REVERT: H 258 ASP cc_start: 0.9194 (p0) cc_final: 0.8713 (p0) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.0825 time to fit residues: 40.1936 Evaluate side-chains 209 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 48 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 167 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS B 192 ASN B 201 HIS ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS E 123 ASN E 133 GLN F 39 ASN F 108 GLN F 181 HIS F 192 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059690 restraints weight = 60634.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061556 restraints weight = 35584.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.062875 restraints weight = 23671.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.063696 restraints weight = 17378.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064368 restraints weight = 13941.314| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 11986 Z= 0.248 Angle : 0.767 9.343 16630 Z= 0.420 Chirality : 0.047 0.224 1790 Planarity : 0.006 0.055 1856 Dihedral : 23.843 148.797 2160 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.87 (0.23), residues: 1202 helix: -0.00 (0.24), residues: 424 sheet: -0.24 (0.39), residues: 156 loop : -1.04 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 206 TYR 0.033 0.003 TYR F 112 PHE 0.024 0.003 PHE B 88 TRP 0.026 0.002 TRP F 208 HIS 0.011 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.25 (11970) covalent geometry : angle 0.76482 / 0.42 (16624) hydrogen bonds : bond 0.06137 / 4.12 ( 556) hydrogen bonds : angle 6.91499 / 4.81 ( 1484) metal coordination : bond 0.01478 / 1.00 ( 16) metal coordination : angle 3.44646 / 2.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.282 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.9047 (mt0) cc_final: 0.8684 (pt0) REVERT: A 19 LEU cc_start: 0.9519 (mt) cc_final: 0.9173 (tt) REVERT: A 79 HIS cc_start: 0.8211 (m-70) cc_final: 0.8007 (m170) REVERT: A 90 PHE cc_start: 0.8584 (t80) cc_final: 0.7497 (t80) REVERT: A 113 MET cc_start: 0.9210 (mtp) cc_final: 0.8706 (mtp) REVERT: A 218 MET cc_start: 0.7012 (mtp) cc_final: 0.6793 (ptm) REVERT: A 220 MET cc_start: 0.8530 (tpp) cc_final: 0.7539 (mmm) REVERT: A 223 ASP cc_start: 0.7696 (t0) cc_final: 0.7411 (t70) REVERT: A 260 PHE cc_start: 0.8843 (m-80) cc_final: 0.8473 (m-80) REVERT: B 6 GLN cc_start: 0.8378 (mt0) cc_final: 0.8176 (tm-30) REVERT: B 7 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8863 (mt-10) REVERT: B 97 GLU cc_start: 0.8403 (pm20) cc_final: 0.8099 (mm-30) REVERT: B 112 TYR cc_start: 0.7512 (m-10) cc_final: 0.7302 (m-10) REVERT: B 141 ILE cc_start: 0.9129 (mt) cc_final: 0.8830 (mm) REVERT: B 168 LEU cc_start: 0.9228 (mt) cc_final: 0.8950 (mt) REVERT: B 169 ASN cc_start: 0.8718 (m-40) cc_final: 0.8032 (t0) REVERT: C 256 VAL cc_start: 0.9336 (t) cc_final: 0.8969 (p) REVERT: D 245 VAL cc_start: 0.8878 (m) cc_final: 0.8407 (p) REVERT: E 19 LEU cc_start: 0.9389 (mt) cc_final: 0.9105 (tt) REVERT: E 25 ILE cc_start: 0.8769 (pt) cc_final: 0.8351 (pt) REVERT: E 29 GLN cc_start: 0.9204 (mt0) cc_final: 0.8639 (mm-40) REVERT: E 39 ASN cc_start: 0.8848 (m-40) cc_final: 0.8512 (m110) REVERT: E 79 HIS cc_start: 0.8386 (m-70) cc_final: 0.8107 (m170) REVERT: E 90 PHE cc_start: 0.8714 (t80) cc_final: 0.7374 (t80) REVERT: E 105 HIS cc_start: 0.8570 (t70) cc_final: 0.8106 (t-90) REVERT: E 106 LEU cc_start: 0.9094 (mt) cc_final: 0.8887 (mt) REVERT: E 110 PHE cc_start: 0.8710 (m-10) cc_final: 0.8280 (m-80) REVERT: E 113 MET cc_start: 0.9139 (mtp) cc_final: 0.8679 (mtp) REVERT: E 218 MET cc_start: 0.7076 (mtp) cc_final: 0.6836 (ptm) REVERT: E 220 MET cc_start: 0.8775 (mmm) cc_final: 0.7845 (mmm) REVERT: E 260 PHE cc_start: 0.8843 (m-80) cc_final: 0.8493 (m-80) REVERT: F 6 GLN cc_start: 0.8274 (mt0) cc_final: 0.8061 (tm-30) REVERT: F 141 ILE cc_start: 0.9111 (mt) cc_final: 0.8809 (mm) REVERT: F 168 LEU cc_start: 0.9210 (mt) cc_final: 0.8935 (mt) REVERT: F 169 ASN cc_start: 0.8738 (m-40) cc_final: 0.8030 (t0) REVERT: G 256 VAL cc_start: 0.9364 (t) cc_final: 0.9048 (p) REVERT: H 242 TYR cc_start: 0.7203 (p90) cc_final: 0.6845 (p90) REVERT: H 258 ASP cc_start: 0.9249 (p0) cc_final: 0.8811 (p0) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.0830 time to fit residues: 33.0294 Evaluate side-chains 189 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS F 12 HIS F 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.061318 restraints weight = 59562.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063256 restraints weight = 35223.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.064616 restraints weight = 23543.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.065452 restraints weight = 17314.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.066119 restraints weight = 13880.364| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11986 Z= 0.149 Angle : 0.658 8.314 16630 Z= 0.360 Chirality : 0.046 0.212 1790 Planarity : 0.005 0.050 1856 Dihedral : 23.518 148.013 2160 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.61 (0.24), residues: 1202 helix: 0.25 (0.24), residues: 422 sheet: -0.29 (0.39), residues: 152 loop : -0.84 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 138 TYR 0.022 0.002 TYR E 178 PHE 0.027 0.002 PHE A 110 TRP 0.026 0.002 TRP A 221 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (11970) covalent geometry : angle 0.65436 / 0.36 (16624) hydrogen bonds : bond 0.05071 / 3.38 ( 556) hydrogen bonds : angle 6.44395 / 4.47 ( 1484) metal coordination : bond 0.00588 / 0.43 ( 16) metal coordination : angle 3.49072 / 2.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.330 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.9010 (mt0) cc_final: 0.8596 (mm110) REVERT: A 19 LEU cc_start: 0.9469 (mt) cc_final: 0.9168 (tt) REVERT: A 25 ILE cc_start: 0.8603 (pt) cc_final: 0.8266 (pt) REVERT: A 29 GLN cc_start: 0.8876 (mt0) cc_final: 0.8240 (mm-40) REVERT: A 79 HIS cc_start: 0.7956 (m-70) cc_final: 0.7684 (m170) REVERT: A 90 PHE cc_start: 0.8454 (t80) cc_final: 0.7427 (t80) REVERT: A 105 HIS cc_start: 0.8179 (t70) cc_final: 0.7436 (t70) REVERT: A 106 LEU cc_start: 0.9174 (mt) cc_final: 0.8879 (mt) REVERT: A 110 PHE cc_start: 0.8798 (m-80) cc_final: 0.7769 (m-80) REVERT: A 113 MET cc_start: 0.9116 (mtp) cc_final: 0.8373 (mtp) REVERT: A 218 MET cc_start: 0.7163 (mtp) cc_final: 0.6767 (ptm) REVERT: A 220 MET cc_start: 0.8986 (tpp) cc_final: 0.8357 (mmm) REVERT: A 223 ASP cc_start: 0.8246 (t0) cc_final: 0.7815 (t70) REVERT: A 260 PHE cc_start: 0.8601 (m-80) cc_final: 0.8367 (m-80) REVERT: B 7 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8714 (mt-10) REVERT: B 110 PHE cc_start: 0.8507 (m-10) cc_final: 0.8272 (m-10) REVERT: B 112 TYR cc_start: 0.7576 (m-10) cc_final: 0.7344 (m-10) REVERT: B 141 ILE cc_start: 0.9002 (mt) cc_final: 0.8700 (mm) REVERT: B 168 LEU cc_start: 0.9204 (mt) cc_final: 0.8930 (mt) REVERT: B 169 ASN cc_start: 0.8759 (m-40) cc_final: 0.8089 (t0) REVERT: B 220 MET cc_start: 0.7421 (mtm) cc_final: 0.6859 (mmm) REVERT: C 224 LEU cc_start: 0.8411 (mp) cc_final: 0.7270 (mp) REVERT: C 256 VAL cc_start: 0.9345 (t) cc_final: 0.8954 (p) REVERT: D 258 ASP cc_start: 0.9118 (p0) cc_final: 0.8887 (p0) REVERT: E 19 LEU cc_start: 0.9308 (mt) cc_final: 0.9085 (tt) REVERT: E 25 ILE cc_start: 0.8787 (pt) cc_final: 0.8388 (pt) REVERT: E 29 GLN cc_start: 0.9107 (mt0) cc_final: 0.8660 (mm-40) REVERT: E 39 ASN cc_start: 0.8895 (m-40) cc_final: 0.8609 (m-40) REVERT: E 90 PHE cc_start: 0.8424 (t80) cc_final: 0.7548 (t80) REVERT: E 110 PHE cc_start: 0.8704 (m-10) cc_final: 0.8239 (m-80) REVERT: E 190 VAL cc_start: 0.9276 (t) cc_final: 0.8996 (t) REVERT: E 218 MET cc_start: 0.6990 (mtp) cc_final: 0.6591 (ptm) REVERT: E 220 MET cc_start: 0.8825 (mmm) cc_final: 0.8531 (tpp) REVERT: E 260 PHE cc_start: 0.8717 (m-80) cc_final: 0.8427 (m-80) REVERT: F 141 ILE cc_start: 0.9007 (mt) cc_final: 0.8697 (mm) REVERT: F 168 LEU cc_start: 0.9182 (mt) cc_final: 0.8914 (mt) REVERT: F 169 ASN cc_start: 0.8735 (m-40) cc_final: 0.8076 (t0) REVERT: G 224 LEU cc_start: 0.8370 (mp) cc_final: 0.8051 (mp) REVERT: G 256 VAL cc_start: 0.9319 (t) cc_final: 0.8874 (p) REVERT: H 242 TYR cc_start: 0.7151 (p90) cc_final: 0.6818 (p90) REVERT: H 258 ASP cc_start: 0.9248 (p0) cc_final: 0.8788 (p0) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.0812 time to fit residues: 32.8189 Evaluate side-chains 185 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 48 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 92 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN A 133 GLN B 6 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 167 GLN F 201 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.073883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.061969 restraints weight = 59173.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063915 restraints weight = 34352.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.065311 restraints weight = 22782.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.066164 restraints weight = 16548.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066825 restraints weight = 13235.299| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11986 Z= 0.141 Angle : 0.639 11.111 16630 Z= 0.352 Chirality : 0.045 0.200 1790 Planarity : 0.008 0.249 1856 Dihedral : 23.392 146.293 2160 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.10 % Allowed : 1.16 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.54 (0.24), residues: 1202 helix: 0.14 (0.24), residues: 424 sheet: -0.17 (0.40), residues: 152 loop : -0.69 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 94 TYR 0.023 0.002 TYR E 85 PHE 0.034 0.002 PHE A 72 TRP 0.044 0.002 TRP B 208 HIS 0.012 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (11970) covalent geometry : angle 0.63666 / 0.35 (16624) hydrogen bonds : bond 0.04819 / 3.21 ( 556) hydrogen bonds : angle 6.35655 / 4.41 ( 1484) metal coordination : bond 0.00523 / 0.38 ( 16) metal coordination : angle 2.70756 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.409 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9435 (mt) cc_final: 0.9114 (tt) REVERT: A 25 ILE cc_start: 0.8627 (pt) cc_final: 0.8332 (pt) REVERT: A 29 GLN cc_start: 0.8848 (mt0) cc_final: 0.8454 (mm-40) REVERT: A 77 TYR cc_start: 0.7914 (m-80) cc_final: 0.7406 (m-10) REVERT: A 90 PHE cc_start: 0.8437 (t80) cc_final: 0.7632 (t80) REVERT: A 105 HIS cc_start: 0.7997 (t70) cc_final: 0.7370 (t70) REVERT: A 106 LEU cc_start: 0.9187 (mt) cc_final: 0.8901 (mt) REVERT: A 110 PHE cc_start: 0.8831 (m-80) cc_final: 0.7868 (m-80) REVERT: A 113 MET cc_start: 0.8888 (mtp) cc_final: 0.8589 (mtp) REVERT: A 196 MET cc_start: 0.8027 (tpp) cc_final: 0.7716 (mmm) REVERT: A 218 MET cc_start: 0.6933 (mtp) cc_final: 0.6608 (ptm) REVERT: A 220 MET cc_start: 0.8907 (tpp) cc_final: 0.7901 (mmm) REVERT: A 223 ASP cc_start: 0.8332 (t0) cc_final: 0.7871 (t70) REVERT: A 260 PHE cc_start: 0.8576 (m-80) cc_final: 0.8262 (m-80) REVERT: B 112 TYR cc_start: 0.7845 (m-10) cc_final: 0.7402 (m-10) REVERT: B 141 ILE cc_start: 0.8959 (mt) cc_final: 0.8707 (mm) REVERT: B 156 ILE cc_start: 0.7521 (mm) cc_final: 0.7196 (mm) REVERT: B 168 LEU cc_start: 0.9238 (mt) cc_final: 0.8993 (mt) REVERT: B 169 ASN cc_start: 0.8593 (m-40) cc_final: 0.8019 (t0) REVERT: C 224 LEU cc_start: 0.8879 (mp) cc_final: 0.8442 (mp) REVERT: C 256 VAL cc_start: 0.9344 (t) cc_final: 0.8939 (p) REVERT: D 258 ASP cc_start: 0.9202 (p0) cc_final: 0.9000 (p0) REVERT: E 19 LEU cc_start: 0.9312 (mt) cc_final: 0.9081 (tt) REVERT: E 25 ILE cc_start: 0.8787 (pt) cc_final: 0.8380 (pt) REVERT: E 29 GLN cc_start: 0.9095 (mt0) cc_final: 0.8663 (mm-40) REVERT: E 77 TYR cc_start: 0.7904 (m-80) cc_final: 0.7405 (m-10) REVERT: E 90 PHE cc_start: 0.8500 (t80) cc_final: 0.7584 (t80) REVERT: E 106 LEU cc_start: 0.9192 (mt) cc_final: 0.8903 (mt) REVERT: E 110 PHE cc_start: 0.8681 (m-10) cc_final: 0.8294 (m-80) REVERT: E 113 MET cc_start: 0.9024 (mtp) cc_final: 0.8475 (mtp) REVERT: E 218 MET cc_start: 0.7006 (mtp) cc_final: 0.6648 (ptm) REVERT: E 220 MET cc_start: 0.8821 (mmm) cc_final: 0.7777 (mmm) REVERT: E 260 PHE cc_start: 0.8710 (m-80) cc_final: 0.8328 (m-80) REVERT: F 75 LEU cc_start: 0.7626 (mt) cc_final: 0.7406 (mp) REVERT: F 141 ILE cc_start: 0.8967 (mt) cc_final: 0.8712 (mm) REVERT: F 168 LEU cc_start: 0.9269 (mt) cc_final: 0.9007 (mt) REVERT: F 169 ASN cc_start: 0.8591 (m-40) cc_final: 0.7996 (t0) REVERT: F 195 ASN cc_start: 0.8625 (t0) cc_final: 0.8417 (t0) REVERT: G 224 LEU cc_start: 0.8295 (mp) cc_final: 0.7964 (mp) REVERT: G 225 LEU cc_start: 0.8813 (mt) cc_final: 0.8598 (mm) REVERT: G 256 VAL cc_start: 0.9330 (t) cc_final: 0.8940 (p) REVERT: H 234 VAL cc_start: 0.9322 (t) cc_final: 0.8777 (m) REVERT: H 242 TYR cc_start: 0.7147 (p90) cc_final: 0.6842 (p90) REVERT: H 258 ASP cc_start: 0.9244 (p0) cc_final: 0.8800 (p0) outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.0857 time to fit residues: 34.4127 Evaluate side-chains 177 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 102 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.061154 restraints weight = 60262.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.063144 restraints weight = 34994.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.064506 restraints weight = 23135.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065318 restraints weight = 16876.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065977 restraints weight = 13556.380| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11986 Z= 0.157 Angle : 0.648 8.094 16630 Z= 0.360 Chirality : 0.045 0.191 1790 Planarity : 0.007 0.179 1856 Dihedral : 23.312 144.576 2160 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.60 (0.24), residues: 1202 helix: 0.17 (0.24), residues: 424 sheet: -0.46 (0.39), residues: 156 loop : -0.71 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 94 TYR 0.027 0.002 TYR E 85 PHE 0.037 0.002 PHE F 135 TRP 0.036 0.002 TRP B 208 HIS 0.011 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (11970) covalent geometry : angle 0.64634 / 0.36 (16624) hydrogen bonds : bond 0.04721 / 3.18 ( 556) hydrogen bonds : angle 6.35422 / 4.40 ( 1484) metal coordination : bond 0.00505 / 0.31 ( 16) metal coordination : angle 2.34159 / 1.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9479 (mt) cc_final: 0.9040 (tt) REVERT: A 77 TYR cc_start: 0.8328 (m-80) cc_final: 0.7655 (m-10) REVERT: A 90 PHE cc_start: 0.8471 (t80) cc_final: 0.7549 (t80) REVERT: A 105 HIS cc_start: 0.8298 (t70) cc_final: 0.7472 (t70) REVERT: A 106 LEU cc_start: 0.9232 (mt) cc_final: 0.8917 (mt) REVERT: A 110 PHE cc_start: 0.8944 (m-80) cc_final: 0.7923 (m-80) REVERT: A 113 MET cc_start: 0.9086 (mtp) cc_final: 0.8616 (mtp) REVERT: A 218 MET cc_start: 0.7013 (mtp) cc_final: 0.6669 (ptm) REVERT: A 220 MET cc_start: 0.8860 (tpp) cc_final: 0.8013 (mmm) REVERT: A 223 ASP cc_start: 0.8367 (t0) cc_final: 0.7889 (t70) REVERT: B 112 TYR cc_start: 0.7865 (m-10) cc_final: 0.7607 (m-10) REVERT: B 141 ILE cc_start: 0.8978 (mt) cc_final: 0.8697 (mm) REVERT: B 156 ILE cc_start: 0.7461 (mm) cc_final: 0.7095 (mm) REVERT: B 168 LEU cc_start: 0.9310 (mt) cc_final: 0.9009 (mt) REVERT: B 169 ASN cc_start: 0.8628 (m-40) cc_final: 0.8012 (t0) REVERT: C 224 LEU cc_start: 0.8497 (mp) cc_final: 0.7664 (mp) REVERT: C 256 VAL cc_start: 0.9381 (t) cc_final: 0.9064 (p) REVERT: C 258 ASP cc_start: 0.7666 (p0) cc_final: 0.7442 (m-30) REVERT: C 261 ILE cc_start: 0.9391 (mm) cc_final: 0.9135 (mm) REVERT: D 258 ASP cc_start: 0.9231 (p0) cc_final: 0.8979 (p0) REVERT: E 19 LEU cc_start: 0.9357 (mt) cc_final: 0.9015 (tt) REVERT: E 25 ILE cc_start: 0.8865 (pt) cc_final: 0.8382 (pt) REVERT: E 29 GLN cc_start: 0.9139 (mt0) cc_final: 0.8642 (mm-40) REVERT: E 77 TYR cc_start: 0.8368 (m-80) cc_final: 0.7678 (m-10) REVERT: E 90 PHE cc_start: 0.8595 (t80) cc_final: 0.7624 (t80) REVERT: E 106 LEU cc_start: 0.9219 (mt) cc_final: 0.8940 (mt) REVERT: E 110 PHE cc_start: 0.8808 (m-10) cc_final: 0.8379 (m-80) REVERT: E 113 MET cc_start: 0.9070 (mtp) cc_final: 0.8584 (mtp) REVERT: E 218 MET cc_start: 0.7119 (mtp) cc_final: 0.6805 (ptm) REVERT: E 220 MET cc_start: 0.8880 (mmm) cc_final: 0.7998 (mmm) REVERT: E 260 PHE cc_start: 0.8734 (m-80) cc_final: 0.8330 (m-80) REVERT: F 139 TRP cc_start: 0.8595 (m-90) cc_final: 0.8018 (m-90) REVERT: F 141 ILE cc_start: 0.9018 (mt) cc_final: 0.8788 (mm) REVERT: F 168 LEU cc_start: 0.9255 (mt) cc_final: 0.8996 (mt) REVERT: F 169 ASN cc_start: 0.8598 (m-40) cc_final: 0.7980 (t0) REVERT: F 195 ASN cc_start: 0.8677 (t0) cc_final: 0.8459 (t0) REVERT: G 224 LEU cc_start: 0.8289 (mp) cc_final: 0.8006 (mp) REVERT: G 225 LEU cc_start: 0.8838 (mt) cc_final: 0.8626 (mm) REVERT: G 256 VAL cc_start: 0.9362 (t) cc_final: 0.8925 (p) REVERT: G 261 ILE cc_start: 0.9346 (mm) cc_final: 0.9145 (mm) REVERT: H 242 TYR cc_start: 0.7209 (p90) cc_final: 0.6897 (p90) REVERT: H 258 ASP cc_start: 0.9244 (p0) cc_final: 0.8817 (p0) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.0792 time to fit residues: 30.2367 Evaluate side-chains 170 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 6 GLN F 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.070773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059110 restraints weight = 60470.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.061016 restraints weight = 35038.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.062330 restraints weight = 23322.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.063263 restraints weight = 17118.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.063795 restraints weight = 13541.470| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11986 Z= 0.209 Angle : 0.711 8.535 16630 Z= 0.389 Chirality : 0.047 0.192 1790 Planarity : 0.007 0.146 1856 Dihedral : 23.344 143.022 2160 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.10 % Allowed : 0.48 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.78 (0.24), residues: 1202 helix: 0.13 (0.24), residues: 420 sheet: -0.51 (0.40), residues: 144 loop : -0.91 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 94 TYR 0.020 0.002 TYR E 85 PHE 0.024 0.002 PHE B 135 TRP 0.037 0.002 TRP B 208 HIS 0.009 0.002 HIS F 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.21 (11970) covalent geometry : angle 0.70826 / 0.39 (16624) hydrogen bonds : bond 0.05211 / 3.48 ( 556) hydrogen bonds : angle 6.60609 / 4.58 ( 1484) metal coordination : bond 0.01207 / 0.75 ( 16) metal coordination : angle 3.23670 / 1.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.485 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 19 LEU cc_start: 0.9504 (mt) cc_final: 0.9079 (tt) REVERT: A 25 ILE cc_start: 0.8603 (pt) cc_final: 0.8077 (pt) REVERT: A 29 GLN cc_start: 0.9011 (mt0) cc_final: 0.8215 (mm-40) REVERT: A 77 TYR cc_start: 0.8586 (m-80) cc_final: 0.7534 (m-10) REVERT: A 90 PHE cc_start: 0.8587 (t80) cc_final: 0.7565 (t80) REVERT: A 113 MET cc_start: 0.9069 (mtp) cc_final: 0.8554 (mtp) REVERT: A 196 MET cc_start: 0.8371 (mmm) cc_final: 0.7696 (tpp) REVERT: A 218 MET cc_start: 0.6928 (mtp) cc_final: 0.6482 (ptm) REVERT: A 220 MET cc_start: 0.8901 (tpp) cc_final: 0.8145 (mmm) REVERT: A 223 ASP cc_start: 0.8525 (t0) cc_final: 0.7913 (t70) REVERT: B 110 PHE cc_start: 0.8579 (m-10) cc_final: 0.8275 (m-10) REVERT: B 112 TYR cc_start: 0.7887 (m-10) cc_final: 0.7663 (m-10) REVERT: B 141 ILE cc_start: 0.9028 (mt) cc_final: 0.8774 (mm) REVERT: B 168 LEU cc_start: 0.9271 (mt) cc_final: 0.8997 (mt) REVERT: B 169 ASN cc_start: 0.8653 (m-40) cc_final: 0.8055 (t0) REVERT: C 256 VAL cc_start: 0.9413 (t) cc_final: 0.9187 (p) REVERT: C 258 ASP cc_start: 0.7738 (p0) cc_final: 0.7533 (m-30) REVERT: D 245 VAL cc_start: 0.9045 (m) cc_final: 0.8310 (p) REVERT: D 258 ASP cc_start: 0.9270 (p0) cc_final: 0.9028 (p0) REVERT: E 6 GLN cc_start: 0.9123 (mt0) cc_final: 0.8735 (mm110) REVERT: E 19 LEU cc_start: 0.9426 (mt) cc_final: 0.9037 (tp) REVERT: E 90 PHE cc_start: 0.8738 (t80) cc_final: 0.7784 (t80) REVERT: E 106 LEU cc_start: 0.9248 (mt) cc_final: 0.8959 (mt) REVERT: E 110 PHE cc_start: 0.8887 (m-10) cc_final: 0.8435 (m-80) REVERT: E 113 MET cc_start: 0.9209 (mtp) cc_final: 0.8788 (mtp) REVERT: E 218 MET cc_start: 0.7231 (mtp) cc_final: 0.6781 (ptm) REVERT: E 220 MET cc_start: 0.8872 (mmm) cc_final: 0.8558 (tpp) REVERT: E 260 PHE cc_start: 0.8609 (m-80) cc_final: 0.8224 (m-80) REVERT: F 141 ILE cc_start: 0.9056 (mt) cc_final: 0.8759 (mm) REVERT: F 168 LEU cc_start: 0.9321 (mt) cc_final: 0.9001 (mt) REVERT: F 169 ASN cc_start: 0.8612 (m-40) cc_final: 0.7996 (t0) REVERT: F 195 ASN cc_start: 0.8671 (t0) cc_final: 0.8446 (t0) REVERT: G 224 LEU cc_start: 0.8313 (mp) cc_final: 0.7801 (mp) REVERT: G 256 VAL cc_start: 0.9424 (t) cc_final: 0.9081 (p) REVERT: G 258 ASP cc_start: 0.7776 (p0) cc_final: 0.7543 (m-30) REVERT: H 234 VAL cc_start: 0.9011 (m) cc_final: 0.8705 (p) REVERT: H 242 TYR cc_start: 0.7278 (p90) cc_final: 0.6949 (p90) REVERT: H 258 ASP cc_start: 0.9313 (p0) cc_final: 0.8870 (p0) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.0801 time to fit residues: 27.7033 Evaluate side-chains 152 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 0.3980 chunk 23 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 0.0970 chunk 118 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** E 105 HIS ** 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 = 0.3403 r_free = 0.3403 target = 0.071914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060455 restraints weight = 59733.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.062295 restraints weight = 35043.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.063577 restraints weight = 23591.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.064338 restraints weight = 17465.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.064984 restraints weight = 14207.604| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11986 Z= 0.156 Angle : 0.637 8.306 16630 Z= 0.353 Chirality : 0.045 0.197 1790 Planarity : 0.006 0.124 1856 Dihedral : 23.240 141.726 2160 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.60 (0.24), residues: 1202 helix: 0.36 (0.24), residues: 422 sheet: -0.44 (0.41), residues: 142 loop : -0.87 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 94 TYR 0.016 0.002 TYR E 85 PHE 0.036 0.002 PHE E 135 TRP 0.034 0.002 TRP B 208 HIS 0.009 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (11970) covalent geometry : angle 0.63509 / 0.35 (16624) hydrogen bonds : bond 0.04754 / 3.20 ( 556) hydrogen bonds : angle 6.39456 / 4.43 ( 1484) metal coordination : bond 0.00634 / 0.43 ( 16) metal coordination : angle 2.90731 / 1.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.384 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 19 LEU cc_start: 0.9509 (mt) cc_final: 0.9133 (tt) REVERT: A 25 ILE cc_start: 0.8540 (pt) cc_final: 0.8206 (pt) REVERT: A 29 GLN cc_start: 0.8902 (mt0) cc_final: 0.8418 (mm-40) REVERT: A 32 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8115 (mm-30) REVERT: A 52 ASN cc_start: 0.7737 (t0) cc_final: 0.7452 (p0) REVERT: A 77 TYR cc_start: 0.8566 (m-80) cc_final: 0.8156 (m-10) REVERT: A 90 PHE cc_start: 0.8567 (t80) cc_final: 0.7451 (t80) REVERT: A 113 MET cc_start: 0.9038 (mtp) cc_final: 0.8554 (mtp) REVERT: A 196 MET cc_start: 0.7986 (mmm) cc_final: 0.7785 (mmm) REVERT: A 218 MET cc_start: 0.7102 (mtp) cc_final: 0.6810 (ptm) REVERT: A 220 MET cc_start: 0.8906 (tpp) cc_final: 0.8117 (mmm) REVERT: B 19 LEU cc_start: 0.7872 (mt) cc_final: 0.7657 (mt) REVERT: B 110 PHE cc_start: 0.8544 (m-10) cc_final: 0.8195 (m-10) REVERT: B 112 TYR cc_start: 0.7825 (m-10) cc_final: 0.7611 (m-10) REVERT: B 141 ILE cc_start: 0.8982 (mt) cc_final: 0.8740 (mm) REVERT: B 168 LEU cc_start: 0.9307 (mt) cc_final: 0.9036 (mt) REVERT: B 169 ASN cc_start: 0.8608 (m-40) cc_final: 0.8032 (t0) REVERT: C 224 LEU cc_start: 0.8337 (mp) cc_final: 0.7617 (mp) REVERT: C 256 VAL cc_start: 0.9374 (t) cc_final: 0.9020 (p) REVERT: E 6 GLN cc_start: 0.9098 (mt0) cc_final: 0.8673 (mm110) REVERT: E 19 LEU cc_start: 0.9477 (mt) cc_final: 0.9033 (tt) REVERT: E 90 PHE cc_start: 0.8530 (t80) cc_final: 0.7684 (t80) REVERT: E 106 LEU cc_start: 0.9253 (mt) cc_final: 0.8889 (mt) REVERT: E 110 PHE cc_start: 0.8830 (m-10) cc_final: 0.8417 (m-80) REVERT: E 113 MET cc_start: 0.9128 (mtp) cc_final: 0.8564 (mtp) REVERT: E 196 MET cc_start: 0.8264 (mmm) cc_final: 0.7451 (tpp) REVERT: E 218 MET cc_start: 0.7259 (mtp) cc_final: 0.6876 (ptm) REVERT: E 220 MET cc_start: 0.8842 (mmm) cc_final: 0.8239 (mmm) REVERT: E 260 PHE cc_start: 0.8458 (m-80) cc_final: 0.8147 (m-80) REVERT: F 139 TRP cc_start: 0.8553 (m-90) cc_final: 0.7887 (m-90) REVERT: F 141 ILE cc_start: 0.8970 (mt) cc_final: 0.8722 (mm) REVERT: F 168 LEU cc_start: 0.9278 (mt) cc_final: 0.9013 (mt) REVERT: F 169 ASN cc_start: 0.8580 (m-40) cc_final: 0.7985 (t0) REVERT: F 195 ASN cc_start: 0.8672 (t0) cc_final: 0.8456 (t0) REVERT: G 224 LEU cc_start: 0.8273 (mp) cc_final: 0.7757 (mp) REVERT: G 256 VAL cc_start: 0.9437 (t) cc_final: 0.9118 (p) REVERT: H 242 TYR cc_start: 0.7132 (p90) cc_final: 0.6835 (p90) REVERT: H 258 ASP cc_start: 0.9292 (p0) cc_final: 0.8866 (p0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.0844 time to fit residues: 28.9179 Evaluate side-chains 154 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 0.0070 chunk 92 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061365 restraints weight = 60101.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063212 restraints weight = 35665.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064487 restraints weight = 23998.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.065385 restraints weight = 17865.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065947 restraints weight = 14279.622| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11986 Z= 0.133 Angle : 0.620 8.091 16630 Z= 0.343 Chirality : 0.045 0.184 1790 Planarity : 0.006 0.125 1856 Dihedral : 23.136 139.994 2160 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.46 (0.24), residues: 1202 helix: 0.55 (0.25), residues: 420 sheet: -0.37 (0.41), residues: 142 loop : -0.84 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 240 TYR 0.018 0.002 TYR E 149 PHE 0.019 0.001 PHE E 135 TRP 0.039 0.002 TRP B 208 HIS 0.010 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (11970) covalent geometry : angle 0.61853 / 0.34 (16624) hydrogen bonds : bond 0.04443 / 3.00 ( 556) hydrogen bonds : angle 6.23882 / 4.32 ( 1484) metal coordination : bond 0.00451 / 0.30 ( 16) metal coordination : angle 2.38602 / 1.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9509 (mt) cc_final: 0.9042 (tt) REVERT: A 25 ILE cc_start: 0.8618 (pt) cc_final: 0.8318 (pt) REVERT: A 29 GLN cc_start: 0.8828 (mt0) cc_final: 0.8393 (mm-40) REVERT: A 32 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8107 (mm-30) REVERT: A 77 TYR cc_start: 0.8530 (m-80) cc_final: 0.8038 (m-10) REVERT: A 79 HIS cc_start: 0.7938 (m170) cc_final: 0.7725 (m170) REVERT: A 90 PHE cc_start: 0.8465 (t80) cc_final: 0.7439 (t80) REVERT: A 113 MET cc_start: 0.8985 (mtp) cc_final: 0.8584 (mtp) REVERT: A 196 MET cc_start: 0.8146 (mmm) cc_final: 0.7558 (mmm) REVERT: A 218 MET cc_start: 0.6988 (mtp) cc_final: 0.6636 (ptm) REVERT: B 110 PHE cc_start: 0.8510 (m-10) cc_final: 0.8178 (m-10) REVERT: B 141 ILE cc_start: 0.8884 (mt) cc_final: 0.8633 (mm) REVERT: B 168 LEU cc_start: 0.9292 (mt) cc_final: 0.9020 (mt) REVERT: B 169 ASN cc_start: 0.8593 (m-40) cc_final: 0.8020 (t0) REVERT: C 224 LEU cc_start: 0.8224 (mp) cc_final: 0.7484 (mp) REVERT: C 256 VAL cc_start: 0.9389 (t) cc_final: 0.9050 (p) REVERT: E 6 GLN cc_start: 0.9109 (mt0) cc_final: 0.8673 (mm110) REVERT: E 19 LEU cc_start: 0.9454 (mt) cc_final: 0.9060 (tt) REVERT: E 25 ILE cc_start: 0.8706 (pt) cc_final: 0.8354 (pt) REVERT: E 29 GLN cc_start: 0.9076 (mt0) cc_final: 0.8705 (mm-40) REVERT: E 90 PHE cc_start: 0.8423 (t80) cc_final: 0.7604 (t80) REVERT: E 106 LEU cc_start: 0.9267 (mt) cc_final: 0.8889 (mt) REVERT: E 110 PHE cc_start: 0.8825 (m-10) cc_final: 0.8431 (m-80) REVERT: E 113 MET cc_start: 0.9066 (mtp) cc_final: 0.8483 (mtp) REVERT: E 196 MET cc_start: 0.8207 (mmm) cc_final: 0.7243 (tpp) REVERT: E 218 MET cc_start: 0.7128 (mtp) cc_final: 0.6837 (ptm) REVERT: E 221 TRP cc_start: 0.8042 (t60) cc_final: 0.7403 (t60) REVERT: E 260 PHE cc_start: 0.8456 (m-80) cc_final: 0.8211 (m-10) REVERT: F 139 TRP cc_start: 0.8563 (m-90) cc_final: 0.7915 (m-90) REVERT: F 141 ILE cc_start: 0.8897 (mt) cc_final: 0.8648 (mm) REVERT: F 156 ILE cc_start: 0.7106 (mm) cc_final: 0.6797 (mm) REVERT: F 168 LEU cc_start: 0.9259 (mt) cc_final: 0.9002 (mt) REVERT: F 169 ASN cc_start: 0.8518 (m-40) cc_final: 0.7950 (t0) REVERT: F 195 ASN cc_start: 0.8682 (t0) cc_final: 0.8429 (t0) REVERT: G 256 VAL cc_start: 0.9462 (t) cc_final: 0.9090 (p) REVERT: H 242 TYR cc_start: 0.7051 (p90) cc_final: 0.6838 (p90) REVERT: H 258 ASP cc_start: 0.9277 (p0) cc_final: 0.8869 (p0) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.0789 time to fit residues: 27.6817 Evaluate side-chains 165 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** 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 = 0.3351 r_free = 0.3351 target = 0.069803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.058337 restraints weight = 61994.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.060125 restraints weight = 35989.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061434 restraints weight = 24058.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.062214 restraints weight = 17707.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.062851 restraints weight = 14261.611| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11986 Z= 0.230 Angle : 0.729 11.249 16630 Z= 0.396 Chirality : 0.047 0.187 1790 Planarity : 0.006 0.084 1856 Dihedral : 23.271 139.322 2160 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.77 (0.24), residues: 1202 helix: 0.31 (0.24), residues: 418 sheet: -0.47 (0.41), residues: 144 loop : -1.05 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 259 TYR 0.026 0.002 TYR E 77 PHE 0.026 0.003 PHE B 189 TRP 0.053 0.003 TRP F 208 HIS 0.008 0.002 HIS F 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.23 (11970) covalent geometry : angle 0.72081 / 0.40 (16624) hydrogen bonds : bond 0.05293 / 3.59 ( 556) hydrogen bonds : angle 6.59082 / 4.56 ( 1484) metal coordination : bond 0.01993 / 1.37 ( 16) metal coordination : angle 5.81632 / 3.35 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.394 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 19 LEU cc_start: 0.9583 (mt) cc_final: 0.9340 (tp) REVERT: A 29 GLN cc_start: 0.8959 (mt0) cc_final: 0.8382 (mm-40) REVERT: A 32 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8172 (mm-30) REVERT: A 77 TYR cc_start: 0.8515 (m-80) cc_final: 0.8102 (m-10) REVERT: A 113 MET cc_start: 0.9034 (mtp) cc_final: 0.8507 (mtp) REVERT: A 196 MET cc_start: 0.7938 (mmm) cc_final: 0.7395 (mmm) REVERT: A 218 MET cc_start: 0.7042 (mtp) cc_final: 0.6613 (ptm) REVERT: B 110 PHE cc_start: 0.8578 (m-10) cc_final: 0.8163 (m-10) REVERT: B 139 TRP cc_start: 0.8435 (m-90) cc_final: 0.8224 (m-90) REVERT: B 141 ILE cc_start: 0.8951 (mt) cc_final: 0.8728 (mm) REVERT: B 168 LEU cc_start: 0.9348 (mt) cc_final: 0.9079 (mt) REVERT: B 169 ASN cc_start: 0.8689 (m-40) cc_final: 0.8098 (t0) REVERT: B 189 PHE cc_start: 0.9005 (t80) cc_final: 0.8593 (t80) REVERT: C 224 LEU cc_start: 0.8360 (mp) cc_final: 0.7669 (mp) REVERT: C 256 VAL cc_start: 0.9433 (t) cc_final: 0.9030 (p) REVERT: D 245 VAL cc_start: 0.9036 (m) cc_final: 0.8350 (p) REVERT: D 258 ASP cc_start: 0.9152 (p0) cc_final: 0.8951 (p0) REVERT: E 6 GLN cc_start: 0.9169 (mt0) cc_final: 0.8768 (mm110) REVERT: E 19 LEU cc_start: 0.9571 (mt) cc_final: 0.9145 (tt) REVERT: E 90 PHE cc_start: 0.8709 (t80) cc_final: 0.7876 (t80) REVERT: E 106 LEU cc_start: 0.9276 (mt) cc_final: 0.8942 (mt) REVERT: E 110 PHE cc_start: 0.9018 (m-10) cc_final: 0.8572 (m-80) REVERT: E 113 MET cc_start: 0.9093 (mtp) cc_final: 0.8393 (mtp) REVERT: E 196 MET cc_start: 0.8205 (mmm) cc_final: 0.7902 (mmm) REVERT: E 220 MET cc_start: 0.8840 (mmm) cc_final: 0.8253 (mpp) REVERT: E 221 TRP cc_start: 0.8030 (t60) cc_final: 0.7415 (t60) REVERT: E 260 PHE cc_start: 0.8484 (m-80) cc_final: 0.8124 (m-80) REVERT: F 139 TRP cc_start: 0.8528 (m-90) cc_final: 0.7973 (m-90) REVERT: F 141 ILE cc_start: 0.8999 (mt) cc_final: 0.8752 (mm) REVERT: F 168 LEU cc_start: 0.9334 (mt) cc_final: 0.9032 (mt) REVERT: F 169 ASN cc_start: 0.8672 (m-40) cc_final: 0.8053 (t0) REVERT: F 196 MET cc_start: 0.7181 (mtt) cc_final: 0.6907 (mtp) REVERT: G 256 VAL cc_start: 0.9430 (t) cc_final: 0.9085 (p) REVERT: H 242 TYR cc_start: 0.7251 (p90) cc_final: 0.7003 (p90) REVERT: H 258 ASP cc_start: 0.9266 (p0) cc_final: 0.8911 (p0) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.0820 time to fit residues: 26.7608 Evaluate side-chains 145 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 54 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.071725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.060160 restraints weight = 60907.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.061972 restraints weight = 36059.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.063290 restraints weight = 24165.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.064181 restraints weight = 17768.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.064698 restraints weight = 14132.796| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11986 Z= 0.144 Angle : 0.637 8.438 16630 Z= 0.350 Chirality : 0.045 0.169 1790 Planarity : 0.005 0.076 1856 Dihedral : 23.181 138.724 2160 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.60 (0.24), residues: 1202 helix: 0.52 (0.25), residues: 418 sheet: -0.46 (0.41), residues: 142 loop : -0.99 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 240 TYR 0.023 0.002 TYR E 77 PHE 0.027 0.002 PHE B 264 TRP 0.047 0.002 TRP E 208 HIS 0.011 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (11970) covalent geometry : angle 0.63172 / 0.35 (16624) hydrogen bonds : bond 0.04552 / 3.07 ( 556) hydrogen bonds : angle 6.31576 / 4.36 ( 1484) metal coordination : bond 0.00664 / 0.43 ( 16) metal coordination : angle 4.20794 / 2.48 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.37 seconds wall clock time: 30 minutes 51.81 seconds (1851.81 seconds total)