Starting phenix.real_space_refine on Tue Nov 19 00:03:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/11_2024/8g02_29642.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/11_2024/8g02_29642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/11_2024/8g02_29642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/11_2024/8g02_29642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/11_2024/8g02_29642.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g02_29642/11_2024/8g02_29642.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 5906 2.51 5 N 1480 2.21 5 O 1536 1.98 5 H 9228 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18194 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 5758 Classifications: {'peptide': 360} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 345} Chain: "E" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 5758 Classifications: {'peptide': 360} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 345} Chain: "B" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1109 Classifications: {'peptide': 65} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 59} Chain: "G" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1109 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "F" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2230 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "H" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2230 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Time building chain proxies: 9.13, per 1000 atoms: 0.50 Number of scatterers: 18194 At special positions: 0 Unit cell: (89.024, 103.168, 119.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1536 8.00 N 1480 7.00 C 5906 6.00 H 9228 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.00 Conformation dependent library (CDL) restraints added in 1.4 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 62.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 4.434A pdb=" N LYS A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 53 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 75 through 91 removed outlier: 4.195A pdb=" N ILE A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 121 removed outlier: 3.665A pdb=" N TRP A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 153 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 174 through 195 removed outlier: 3.881A pdb=" N LEU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 201 through 220 removed outlier: 3.653A pdb=" N THR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 235 through 257 removed outlier: 3.629A pdb=" N LEU A 239 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 removed outlier: 3.706A pdb=" N GLY A 269 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 334 through 360 removed outlier: 3.764A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 21 through 41 Processing helix chain 'E' and resid 42 through 53 removed outlier: 3.566A pdb=" N LEU E 51 " --> pdb=" O HIS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 91 removed outlier: 4.047A pdb=" N ILE E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 122 removed outlier: 3.737A pdb=" N TRP E 99 " --> pdb=" O ASN E 95 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 115 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.738A pdb=" N GLY E 127 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU E 128 " --> pdb=" O THR E 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 128' Processing helix chain 'E' and resid 129 through 152 removed outlier: 3.864A pdb=" N LYS E 133 " --> pdb=" O ILE E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 174 through 195 removed outlier: 3.798A pdb=" N LEU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 220 Processing helix chain 'E' and resid 221 through 229 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 238 through 258 removed outlier: 3.776A pdb=" N PHE E 256 " --> pdb=" O GLY E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 284 removed outlier: 3.731A pdb=" N GLY E 269 " --> pdb=" O MET E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 294 through 314 Processing helix chain 'E' and resid 323 through 332 removed outlier: 3.534A pdb=" N HIS E 327 " --> pdb=" O PRO E 323 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 332 " --> pdb=" O TYR E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 357 removed outlier: 3.812A pdb=" N LEU E 357 " --> pdb=" O GLY E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.511A pdb=" N THR B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) Proline residue: B 21 - end of helix removed outlier: 3.842A pdb=" N ILE B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.056A pdb=" N ARG B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 52 removed outlier: 3.541A pdb=" N ALA B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 25 Proline residue: G 21 - end of helix Processing helix chain 'G' and resid 26 through 28 No H-bonds generated for 'chain 'G' and resid 26 through 28' Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 35 through 51 Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 63 through 68 Processing helix chain 'F' and resid 143 through 149 Processing helix chain 'H' and resid 42 through 50 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 143 through 149 Processing sheet with id=AA1, first strand: chain 'B' and resid 57 through 58 removed outlier: 3.756A pdb=" N THR F 110 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL F 118 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL F 112 " --> pdb=" O HIS F 116 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 57 through 58 removed outlier: 3.825A pdb=" N LYS G 57 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL H 118 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL H 112 " --> pdb=" O HIS H 116 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 22 through 25 removed outlier: 7.747A pdb=" N VAL F 15 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU F 25 " --> pdb=" O TYR F 13 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR F 13 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 22 through 25 removed outlier: 7.747A pdb=" N VAL F 15 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU F 25 " --> pdb=" O TYR F 13 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR F 13 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA F 138 " --> pdb=" O SER F 10 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA F 12 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL F 136 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLN F 14 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL F 134 " --> pdb=" O GLN F 14 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ARG F 16 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE F 132 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 removed outlier: 6.918A pdb=" N LEU H 22 " --> pdb=" O THR H 17 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR H 17 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP H 24 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL H 15 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 22 through 25 removed outlier: 6.918A pdb=" N LEU H 22 " --> pdb=" O THR H 17 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR H 17 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP H 24 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL H 15 " --> pdb=" O ASP H 24 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL H 8 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE H 139 " --> pdb=" O VAL H 8 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER H 10 " --> pdb=" O VAL H 137 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.37 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9222 1.04 - 1.24: 1121 1.24 - 1.44: 2771 1.44 - 1.64: 5220 1.64 - 1.84: 82 Bond restraints: 18416 Sorted by residual: bond pdb=" CB MET H 85 " pdb=" CG MET H 85 " ideal model delta sigma weight residual 1.520 1.594 -0.074 3.00e-02 1.11e+03 6.15e+00 bond pdb=" N GLY G 1 " pdb=" CA GLY G 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.05e+00 bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.03e+00 bond pdb=" CG MET H 85 " pdb=" SD MET H 85 " ideal model delta sigma weight residual 1.803 1.842 -0.039 2.50e-02 1.60e+03 2.43e+00 bond pdb=" N GLY G 1 " pdb=" H GLY G 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 18411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 33274 2.52 - 5.05: 125 5.05 - 7.57: 12 7.57 - 10.09: 2 10.09 - 12.61: 1 Bond angle restraints: 33414 Sorted by residual: angle pdb=" CG MET H 85 " pdb=" SD MET H 85 " pdb=" CE MET H 85 " ideal model delta sigma weight residual 100.90 110.19 -9.29 2.20e+00 2.07e-01 1.78e+01 angle pdb=" CB MET H 85 " pdb=" CG MET H 85 " pdb=" SD MET H 85 " ideal model delta sigma weight residual 112.70 125.31 -12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" N MET H 85 " pdb=" CA MET H 85 " pdb=" CB MET H 85 " ideal model delta sigma weight residual 111.56 117.41 -5.85 1.58e+00 4.01e-01 1.37e+01 angle pdb=" C MET A 203 " pdb=" N PRO A 204 " pdb=" CD PRO A 204 " ideal model delta sigma weight residual 120.60 113.40 7.20 2.20e+00 2.07e-01 1.07e+01 angle pdb=" C MET A 203 " pdb=" N PRO A 204 " pdb=" CA PRO A 204 " ideal model delta sigma weight residual 127.00 134.65 -7.65 2.40e+00 1.74e-01 1.02e+01 ... (remaining 33409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 7447 17.10 - 34.19: 762 34.19 - 51.29: 266 51.29 - 68.39: 98 68.39 - 85.48: 7 Dihedral angle restraints: 8580 sinusoidal: 4602 harmonic: 3978 Sorted by residual: dihedral pdb=" CA LEU B 24 " pdb=" C LEU B 24 " pdb=" N ILE B 25 " pdb=" CA ILE B 25 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ILE A 202 " pdb=" C ILE A 202 " pdb=" N MET A 203 " pdb=" CA MET A 203 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU A 197 " pdb=" C LEU A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 8577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1040 0.035 - 0.071: 288 0.071 - 0.106: 99 0.106 - 0.142: 32 0.142 - 0.177: 3 Chirality restraints: 1462 Sorted by residual: chirality pdb=" CB VAL A 308 " pdb=" CA VAL A 308 " pdb=" CG1 VAL A 308 " pdb=" CG2 VAL A 308 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE A 230 " pdb=" N ILE A 230 " pdb=" C ILE A 230 " pdb=" CB ILE A 230 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA ARG G 55 " pdb=" N ARG G 55 " pdb=" C ARG G 55 " pdb=" CB ARG G 55 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1459 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 255 " 0.025 2.00e-02 2.50e+03 1.79e-02 1.29e+01 pdb=" CG TRP A 255 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 255 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 255 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 255 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 255 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 255 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 255 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 255 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 255 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 255 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 TRP A 255 " 0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP A 255 " -0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 255 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 255 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 255 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 55 " 0.295 9.50e-02 1.11e+02 9.88e-02 1.10e+01 pdb=" NE ARG G 55 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG G 55 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG G 55 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 55 " 0.010 2.00e-02 2.50e+03 pdb="HH11 ARG G 55 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG G 55 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG G 55 " -0.012 2.00e-02 2.50e+03 pdb="HH22 ARG G 55 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 335 " 0.049 5.00e-02 4.00e+02 7.37e-02 8.68e+00 pdb=" N PRO A 336 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.041 5.00e-02 4.00e+02 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1308 2.20 - 2.80: 38234 2.80 - 3.40: 52285 3.40 - 4.00: 65943 4.00 - 4.60: 102050 Nonbonded interactions: 259820 Sorted by model distance: nonbonded pdb=" OE1 GLU A 287 " pdb=" H GLU A 287 " model vdw 1.605 2.450 nonbonded pdb=" O MET E 40 " pdb=" H MET E 44 " model vdw 1.641 2.450 nonbonded pdb=" O LEU B 19 " pdb=" HG SER B 22 " model vdw 1.654 2.450 nonbonded pdb="HE22 GLN E 307 " pdb=" O PHE E 319 " model vdw 1.680 2.450 nonbonded pdb="HH12 ARG E 314 " pdb=" OE1 GLN E 316 " model vdw 1.681 2.450 ... (remaining 259815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 0.940 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: 0.310 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 41.190 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9188 Z= 0.199 Angle : 0.614 12.613 12508 Z= 0.312 Chirality : 0.040 0.177 1462 Planarity : 0.007 0.128 1546 Dihedral : 15.732 84.149 3236 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.10 % Allowed : 19.52 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1136 helix: 1.11 (0.21), residues: 630 sheet: 0.53 (0.57), residues: 92 loop : -0.10 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 255 HIS 0.004 0.001 HIS A 8 PHE 0.023 0.001 PHE A 319 TYR 0.018 0.001 TYR E 176 ARG 0.009 0.001 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 1.290 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: A 307 GLN cc_start: 0.7369 (tp40) cc_final: 0.7154 (tp40) REVERT: A 329 GLU cc_start: 0.7078 (tp30) cc_final: 0.6797 (tp30) outliers start: 1 outliers final: 1 residues processed: 296 average time/residue: 0.5134 time to fit residues: 205.8956 Evaluate side-chains 293 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9188 Z= 0.226 Angle : 0.574 6.573 12508 Z= 0.298 Chirality : 0.040 0.178 1462 Planarity : 0.006 0.117 1546 Dihedral : 4.670 43.527 1235 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.88 % Allowed : 18.27 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1136 helix: 1.09 (0.20), residues: 656 sheet: 0.38 (0.55), residues: 90 loop : -0.34 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 255 HIS 0.004 0.001 HIS A 325 PHE 0.018 0.001 PHE F 96 TYR 0.011 0.001 TYR A 97 ARG 0.007 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 319 time to evaluate : 1.448 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: A 307 GLN cc_start: 0.7498 (tp40) cc_final: 0.7292 (tp40) REVERT: A 329 GLU cc_start: 0.6945 (tp30) cc_final: 0.6645 (tp30) REVERT: E 119 LYS cc_start: 0.7891 (tptt) cc_final: 0.7648 (tptt) REVERT: E 149 TYR cc_start: 0.8289 (t80) cc_final: 0.7984 (t80) REVERT: F 102 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7688 (tm-30) REVERT: H 77 GLN cc_start: 0.6859 (mm-40) cc_final: 0.6511 (mm110) outliers start: 18 outliers final: 13 residues processed: 323 average time/residue: 0.5050 time to fit residues: 220.5254 Evaluate side-chains 327 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 314 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 69 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 0.2980 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9188 Z= 0.230 Angle : 0.562 6.642 12508 Z= 0.291 Chirality : 0.040 0.182 1462 Planarity : 0.005 0.093 1546 Dihedral : 4.443 31.077 1232 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.57 % Allowed : 19.83 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1136 helix: 1.04 (0.20), residues: 666 sheet: 0.47 (0.52), residues: 94 loop : -0.39 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 39 HIS 0.005 0.001 HIS A 325 PHE 0.014 0.001 PHE A 253 TYR 0.009 0.001 TYR A 149 ARG 0.013 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 314 time to evaluate : 1.370 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: A 162 VAL cc_start: 0.8691 (t) cc_final: 0.8487 (t) REVERT: A 283 LEU cc_start: 0.8223 (mp) cc_final: 0.8014 (mt) REVERT: A 329 GLU cc_start: 0.6932 (tp30) cc_final: 0.6657 (tp30) REVERT: E 321 MET cc_start: 0.6180 (mtp) cc_final: 0.5901 (mtp) REVERT: F 102 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7767 (tm-30) outliers start: 15 outliers final: 13 residues processed: 317 average time/residue: 0.5078 time to fit residues: 218.0792 Evaluate side-chains 321 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 308 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9188 Z= 0.361 Angle : 0.610 6.731 12508 Z= 0.328 Chirality : 0.042 0.195 1462 Planarity : 0.005 0.083 1546 Dihedral : 4.760 28.902 1232 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.82 % Allowed : 19.42 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1136 helix: 0.70 (0.20), residues: 668 sheet: 0.15 (0.51), residues: 94 loop : -0.52 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 255 HIS 0.009 0.001 HIS A 325 PHE 0.019 0.002 PHE F 96 TYR 0.016 0.002 TYR F 71 ARG 0.007 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 332 time to evaluate : 1.582 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: A 2 LEU cc_start: 0.8237 (mt) cc_final: 0.7986 (mp) REVERT: A 36 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7935 (mt) REVERT: A 162 VAL cc_start: 0.8767 (t) cc_final: 0.8453 (m) REVERT: E 321 MET cc_start: 0.6443 (mtp) cc_final: 0.6207 (mtp) REVERT: G 55 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.5705 (mtp85) outliers start: 27 outliers final: 21 residues processed: 341 average time/residue: 0.5223 time to fit residues: 239.3416 Evaluate side-chains 342 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 319 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 74 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9188 Z= 0.225 Angle : 0.561 6.847 12508 Z= 0.290 Chirality : 0.040 0.177 1462 Planarity : 0.005 0.088 1546 Dihedral : 4.559 33.997 1232 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.82 % Allowed : 20.77 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1136 helix: 0.90 (0.20), residues: 668 sheet: 0.05 (0.51), residues: 94 loop : -0.46 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 255 HIS 0.004 0.001 HIS A 325 PHE 0.015 0.001 PHE A 24 TYR 0.016 0.001 TYR A 232 ARG 0.004 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 317 time to evaluate : 1.495 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: A 2 LEU cc_start: 0.8222 (mt) cc_final: 0.8003 (mp) REVERT: E 142 LEU cc_start: 0.8309 (mt) cc_final: 0.8083 (mp) REVERT: E 321 MET cc_start: 0.6482 (mtp) cc_final: 0.6022 (mtp) REVERT: B 42 ARG cc_start: 0.6837 (tmm-80) cc_final: 0.6324 (tmm-80) REVERT: G 55 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6138 (mtp85) REVERT: H 85 MET cc_start: 0.2788 (ptt) cc_final: 0.2256 (pmm) outliers start: 27 outliers final: 20 residues processed: 325 average time/residue: 0.5241 time to fit residues: 229.8445 Evaluate side-chains 338 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 317 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 0.0030 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN H 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9188 Z= 0.203 Angle : 0.543 6.780 12508 Z= 0.280 Chirality : 0.040 0.172 1462 Planarity : 0.005 0.076 1546 Dihedral : 4.474 34.531 1232 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.51 % Allowed : 20.77 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1136 helix: 1.03 (0.20), residues: 668 sheet: 0.01 (0.50), residues: 94 loop : -0.45 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 39 HIS 0.004 0.001 HIS A 325 PHE 0.012 0.001 PHE E 165 TYR 0.016 0.001 TYR A 232 ARG 0.004 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 314 time to evaluate : 1.550 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: A 2 LEU cc_start: 0.8196 (mt) cc_final: 0.7984 (mp) REVERT: A 36 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7891 (mt) REVERT: E 142 LEU cc_start: 0.8283 (mt) cc_final: 0.8065 (mp) REVERT: E 317 ARG cc_start: 0.7455 (mmm-85) cc_final: 0.7222 (mmt90) REVERT: E 321 MET cc_start: 0.6408 (mtp) cc_final: 0.5971 (mtp) REVERT: B 42 ARG cc_start: 0.6865 (tmm-80) cc_final: 0.6411 (tmm-80) REVERT: G 55 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6084 (mtp85) REVERT: H 85 MET cc_start: 0.2717 (ptt) cc_final: 0.2244 (pmm) outliers start: 24 outliers final: 20 residues processed: 322 average time/residue: 0.5192 time to fit residues: 226.8758 Evaluate side-chains 331 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 309 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 3 ARG Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9188 Z= 0.291 Angle : 0.572 6.753 12508 Z= 0.302 Chirality : 0.041 0.203 1462 Planarity : 0.005 0.076 1546 Dihedral : 4.616 36.050 1232 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.65 % Allowed : 20.25 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1136 helix: 0.94 (0.20), residues: 667 sheet: -0.06 (0.50), residues: 94 loop : -0.51 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 255 HIS 0.007 0.001 HIS A 325 PHE 0.017 0.001 PHE E 165 TYR 0.014 0.001 TYR A 232 ARG 0.004 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 322 time to evaluate : 1.503 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 2 LEU cc_start: 0.8224 (mt) cc_final: 0.8013 (mp) REVERT: A 36 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7929 (mt) REVERT: A 329 GLU cc_start: 0.6989 (tp30) cc_final: 0.6716 (tp30) REVERT: E 321 MET cc_start: 0.6411 (mtp) cc_final: 0.6025 (mtp) REVERT: B 42 ARG cc_start: 0.6853 (tmm-80) cc_final: 0.6442 (tmm-80) REVERT: G 23 LEU cc_start: 0.8229 (tp) cc_final: 0.8021 (tt) REVERT: G 55 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6141 (mtp85) REVERT: H 85 MET cc_start: 0.2620 (ptt) cc_final: 0.2123 (pmm) REVERT: H 133 ASN cc_start: 0.3050 (OUTLIER) cc_final: 0.2559 (p0) outliers start: 35 outliers final: 27 residues processed: 334 average time/residue: 0.5136 time to fit residues: 231.1901 Evaluate side-chains 347 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 317 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 3 ARG Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9188 Z= 0.298 Angle : 0.581 6.856 12508 Z= 0.307 Chirality : 0.042 0.186 1462 Planarity : 0.005 0.075 1546 Dihedral : 4.701 42.198 1232 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.13 % Allowed : 21.50 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1136 helix: 0.86 (0.20), residues: 667 sheet: -0.18 (0.51), residues: 94 loop : -0.61 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 255 HIS 0.006 0.001 HIS A 325 PHE 0.018 0.001 PHE E 165 TYR 0.018 0.002 TYR E 181 ARG 0.004 0.001 ARG E 285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 319 time to evaluate : 1.421 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: A 2 LEU cc_start: 0.8236 (mt) cc_final: 0.8029 (mp) REVERT: A 36 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7965 (mt) REVERT: A 98 VAL cc_start: 0.8722 (t) cc_final: 0.8427 (p) REVERT: A 329 GLU cc_start: 0.6970 (tp30) cc_final: 0.6679 (tp30) REVERT: E 181 TYR cc_start: 0.8646 (t80) cc_final: 0.8350 (t80) REVERT: B 42 ARG cc_start: 0.6827 (tmm-80) cc_final: 0.6531 (tmm-80) REVERT: G 55 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6102 (mtp85) REVERT: H 85 MET cc_start: 0.2608 (ptt) cc_final: 0.2063 (pmm) outliers start: 30 outliers final: 24 residues processed: 329 average time/residue: 0.5166 time to fit residues: 228.8766 Evaluate side-chains 345 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 319 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9188 Z= 0.216 Angle : 0.559 6.882 12508 Z= 0.289 Chirality : 0.040 0.188 1462 Planarity : 0.005 0.074 1546 Dihedral : 4.592 42.735 1232 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.71 % Allowed : 22.34 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1136 helix: 1.00 (0.20), residues: 667 sheet: -0.17 (0.52), residues: 94 loop : -0.59 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 39 HIS 0.004 0.001 HIS A 325 PHE 0.018 0.001 PHE H 96 TYR 0.022 0.001 TYR A 232 ARG 0.003 0.000 ARG E 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 312 time to evaluate : 1.464 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: A 2 LEU cc_start: 0.8208 (mt) cc_final: 0.7988 (mp) REVERT: A 36 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7945 (mt) REVERT: A 98 VAL cc_start: 0.8717 (t) cc_final: 0.8405 (p) REVERT: A 329 GLU cc_start: 0.6904 (tp30) cc_final: 0.6618 (tp30) REVERT: G 55 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6121 (mtp85) REVERT: H 85 MET cc_start: 0.2485 (ptt) cc_final: 0.1995 (pmm) outliers start: 26 outliers final: 20 residues processed: 318 average time/residue: 0.5126 time to fit residues: 220.8966 Evaluate side-chains 334 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 312 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9188 Z= 0.183 Angle : 0.543 7.191 12508 Z= 0.276 Chirality : 0.040 0.179 1462 Planarity : 0.005 0.068 1546 Dihedral : 4.434 41.671 1232 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.30 % Allowed : 22.34 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1136 helix: 1.14 (0.20), residues: 668 sheet: -0.12 (0.52), residues: 94 loop : -0.53 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 39 HIS 0.003 0.001 HIS F 116 PHE 0.020 0.001 PHE H 96 TYR 0.021 0.001 TYR A 232 ARG 0.003 0.000 ARG E 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 305 time to evaluate : 1.405 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: A 2 LEU cc_start: 0.8174 (mt) cc_final: 0.7960 (mp) REVERT: A 98 VAL cc_start: 0.8715 (t) cc_final: 0.8383 (p) REVERT: G 24 LEU cc_start: 0.8539 (mt) cc_final: 0.8238 (mp) REVERT: G 55 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6135 (mtp85) REVERT: H 85 MET cc_start: 0.2325 (ptt) cc_final: 0.1849 (pmm) outliers start: 22 outliers final: 19 residues processed: 312 average time/residue: 0.5134 time to fit residues: 217.2723 Evaluate side-chains 324 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 304 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.0070 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.154206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120126 restraints weight = 40971.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125388 restraints weight = 13979.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128348 restraints weight = 7110.587| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9188 Z= 0.176 Angle : 0.541 6.810 12508 Z= 0.275 Chirality : 0.040 0.179 1462 Planarity : 0.005 0.063 1546 Dihedral : 4.387 42.421 1232 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.30 % Allowed : 22.65 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1136 helix: 1.38 (0.20), residues: 651 sheet: -0.08 (0.52), residues: 94 loop : -0.48 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 39 HIS 0.004 0.001 HIS E 325 PHE 0.021 0.001 PHE H 96 TYR 0.019 0.001 TYR A 232 ARG 0.007 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5230.65 seconds wall clock time: 93 minutes 29.26 seconds (5609.26 seconds total)