Starting phenix.real_space_refine on Tue Mar 3 21:19:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x2v_32972/03_2026/7x2v_32972_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x2v_32972/03_2026/7x2v_32972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x2v_32972/03_2026/7x2v_32972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x2v_32972/03_2026/7x2v_32972.map" model { file = "/net/cci-nas-00/data/ceres_data/7x2v_32972/03_2026/7x2v_32972_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x2v_32972/03_2026/7x2v_32972_neut.cif" } resolution = 3.09 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5599 2.51 5 N 1479 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8755 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1769 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 2, 'TRANS': 217} Chain breaks: 2 Chain: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2179 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Time building chain proxies: 2.05, per 1000 atoms: 0.23 Number of scatterers: 8755 At special positions: 0 Unit cell: (88, 121, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1616 8.00 N 1479 7.00 C 5599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 379.3 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 35.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'D' and resid 5 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'B' and resid 6 through 30 removed outlier: 3.714A pdb=" N LYS B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.999A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 241 through 255 removed outlier: 4.142A pdb=" N GLU B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.841A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.512A pdb=" N ALA B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 350 removed outlier: 4.047A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.559A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 568 through 572 removed outlier: 3.528A pdb=" N ILE R 571 " --> pdb=" O SER R 568 " (cutoff:3.500A) Processing helix chain 'R' and resid 578 through 580 No H-bonds generated for 'chain 'R' and resid 578 through 580' Processing helix chain 'R' and resid 581 through 610 removed outlier: 3.667A pdb=" N LYS R 586 " --> pdb=" O PHE R 582 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TRP R 587 " --> pdb=" O PRO R 583 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY R 598 " --> pdb=" O GLY R 594 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU R 602 " --> pdb=" O GLY R 598 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE R 610 " --> pdb=" O ILE R 606 " (cutoff:3.500A) Processing helix chain 'R' and resid 611 through 614 removed outlier: 3.805A pdb=" N ILE R 614 " --> pdb=" O TRP R 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 611 through 614' Processing helix chain 'R' and resid 617 through 647 removed outlier: 3.719A pdb=" N HIS R 621 " --> pdb=" O SER R 617 " (cutoff:3.500A) Processing helix chain 'R' and resid 655 through 688 removed outlier: 3.736A pdb=" N PHE R 672 " --> pdb=" O TYR R 668 " (cutoff:3.500A) Processing helix chain 'R' and resid 694 through 707 Processing helix chain 'R' and resid 709 through 722 removed outlier: 3.550A pdb=" N SER R 714 " --> pdb=" O PRO R 710 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL R 715 " --> pdb=" O LEU R 711 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE R 718 " --> pdb=" O SER R 714 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA R 719 " --> pdb=" O VAL R 715 " (cutoff:3.500A) Processing helix chain 'R' and resid 723 through 725 No H-bonds generated for 'chain 'R' and resid 723 through 725' Processing helix chain 'R' and resid 743 through 746 Processing helix chain 'R' and resid 747 through 754 removed outlier: 3.773A pdb=" N ILE R 754 " --> pdb=" O PRO R 750 " (cutoff:3.500A) Processing helix chain 'R' and resid 754 through 770 removed outlier: 3.902A pdb=" N LYS R 768 " --> pdb=" O LEU R 764 " (cutoff:3.500A) Processing helix chain 'R' and resid 785 through 797 Processing helix chain 'R' and resid 802 through 810 Processing helix chain 'R' and resid 818 through 828 removed outlier: 3.871A pdb=" N ILE R 822 " --> pdb=" O ALA R 818 " (cutoff:3.500A) Processing helix chain 'R' and resid 829 through 838 Processing helix chain 'R' and resid 842 through 853 Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.723A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 3.634A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.638A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AA5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.612A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E 182 " --> pdb=" O TYR E 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.155A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.415A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.503A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.540A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.710A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.672A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.106A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2789 1.34 - 1.47: 2241 1.47 - 1.59: 3820 1.59 - 1.72: 0 1.72 - 1.84: 89 Bond restraints: 8939 Sorted by residual: bond pdb=" N VAL R 812 " pdb=" CA VAL R 812 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.70e+00 bond pdb=" N ILE R 811 " pdb=" CA ILE R 811 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.41e-02 5.03e+03 7.54e+00 bond pdb=" N ASP R 813 " pdb=" CA ASP R 813 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.92e+00 bond pdb=" N ASN R 816 " pdb=" CA ASN R 816 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.74e+00 bond pdb=" N LEU R 817 " pdb=" CA LEU R 817 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.67e+00 ... (remaining 8934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 11579 2.05 - 4.10: 446 4.10 - 6.16: 71 6.16 - 8.21: 12 8.21 - 10.26: 3 Bond angle restraints: 12111 Sorted by residual: angle pdb=" N ASP B 309 " pdb=" CA ASP B 309 " pdb=" C ASP B 309 " ideal model delta sigma weight residual 111.71 117.95 -6.24 1.15e+00 7.56e-01 2.95e+01 angle pdb=" C LEU B 268 " pdb=" CA LEU B 268 " pdb=" CB LEU B 268 " ideal model delta sigma weight residual 109.48 117.16 -7.68 1.68e+00 3.54e-01 2.09e+01 angle pdb=" N LEU B 268 " pdb=" CA LEU B 268 " pdb=" C LEU B 268 " ideal model delta sigma weight residual 109.76 102.68 7.08 1.64e+00 3.72e-01 1.86e+01 angle pdb=" C VAL E 48 " pdb=" N ALA E 49 " pdb=" CA ALA E 49 " ideal model delta sigma weight residual 121.75 115.08 6.67 1.73e+00 3.34e-01 1.48e+01 angle pdb=" N ASP C 205 " pdb=" CA ASP C 205 " pdb=" C ASP C 205 " ideal model delta sigma weight residual 111.71 106.60 5.11 1.34e+00 5.57e-01 1.46e+01 ... (remaining 12106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 4898 16.66 - 33.31: 315 33.31 - 49.97: 52 49.97 - 66.62: 13 66.62 - 83.28: 3 Dihedral angle restraints: 5281 sinusoidal: 2044 harmonic: 3237 Sorted by residual: dihedral pdb=" CA ASP C 163 " pdb=" C ASP C 163 " pdb=" N THR C 164 " pdb=" CA THR C 164 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ALA C 305 " pdb=" C ALA C 305 " pdb=" N GLY C 306 " pdb=" CA GLY C 306 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP B 309 " pdb=" C ASP B 309 " pdb=" N LEU B 310 " pdb=" CA LEU B 310 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1154 0.070 - 0.140: 214 0.140 - 0.210: 18 0.210 - 0.280: 5 0.280 - 0.350: 1 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CG LEU E 162 " pdb=" CB LEU E 162 " pdb=" CD1 LEU E 162 " pdb=" CD2 LEU E 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA LEU B 283 " pdb=" N LEU B 283 " pdb=" C LEU B 283 " pdb=" CB LEU B 283 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASP C 291 " pdb=" N ASP C 291 " pdb=" C ASP C 291 " pdb=" CB ASP C 291 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1389 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 169 " -0.031 2.00e-02 2.50e+03 2.22e-02 1.24e+01 pdb=" CG TRP C 169 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP C 169 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP C 169 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 169 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 169 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 169 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 169 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 54 " 0.042 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO D 55 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 55 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 55 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 339 " 0.021 2.00e-02 2.50e+03 1.56e-02 6.05e+00 pdb=" CG TRP C 339 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP C 339 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP C 339 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 339 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 339 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 339 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 339 " 0.000 2.00e-02 2.50e+03 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 182 2.67 - 3.23: 8382 3.23 - 3.79: 13474 3.79 - 4.34: 17564 4.34 - 4.90: 29538 Nonbonded interactions: 69140 Sorted by model distance: nonbonded pdb=" O ARG C 219 " pdb=" NE2 GLN C 220 " model vdw 2.115 3.120 nonbonded pdb=" ND2 ASN R 758 " pdb=" O LEU R 800 " model vdw 2.173 3.120 nonbonded pdb=" O CYS C 103 " pdb=" NH2 ARG C 150 " model vdw 2.181 3.120 nonbonded pdb=" N GLY C 144 " pdb=" OD2 ASP C 163 " model vdw 2.209 3.120 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.239 3.040 ... (remaining 69135 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5724 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 : 0.007 0.068 8941 Z= 0.335 Angle : 0.927 10.260 12115 Z= 0.542 Chirality : 0.054 0.350 1392 Planarity : 0.005 0.065 1516 Dihedral : 11.889 83.276 3185 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.10 % Allowed : 2.19 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.89 (0.24), residues: 1104 helix: 0.76 (0.29), residues: 338 sheet: -0.19 (0.29), residues: 294 loop : -1.86 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 624 TYR 0.035 0.004 TYR R 727 PHE 0.032 0.003 PHE C 278 TRP 0.060 0.003 TRP C 169 HIS 0.009 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00714 ( 8939) covalent geometry : angle 0.92688 (12111) SS BOND : bond 0.01056 ( 2) SS BOND : angle 1.15495 ( 4) hydrogen bonds : bond 0.16471 ( 416) hydrogen bonds : angle 6.58395 ( 1149) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.303 Fit side-chains REVERT: E 218 MET cc_start: 0.5067 (ttt) cc_final: 0.4677 (ttt) REVERT: C 50 THR cc_start: 0.8233 (p) cc_final: 0.8015 (p) REVERT: C 325 MET cc_start: 0.5732 (mmm) cc_final: 0.5328 (mmm) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.0932 time to fit residues: 17.0556 Evaluate side-chains 116 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 817 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.0170 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.0070 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 830 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.202791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.174576 restraints weight = 12393.723| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 3.01 r_work: 0.4301 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8941 Z= 0.140 Angle : 0.630 8.186 12115 Z= 0.335 Chirality : 0.045 0.162 1392 Planarity : 0.004 0.059 1516 Dihedral : 5.455 53.700 1201 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.38 % Rotamer: Outliers : 2.08 % Allowed : 5.42 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.29 (0.25), residues: 1104 helix: 1.61 (0.29), residues: 342 sheet: -0.08 (0.30), residues: 279 loop : -1.63 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 52 TYR 0.022 0.002 TYR B 302 PHE 0.014 0.002 PHE C 253 TRP 0.025 0.002 TRP C 339 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8939) covalent geometry : angle 0.63017 (12111) SS BOND : bond 0.00731 ( 2) SS BOND : angle 0.82669 ( 4) hydrogen bonds : bond 0.05634 ( 416) hydrogen bonds : angle 5.18611 ( 1149) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: E 38 ARG cc_start: 0.5768 (ptt180) cc_final: 0.5226 (ptt180) REVERT: E 102 TYR cc_start: 0.7699 (p90) cc_final: 0.7458 (p90) REVERT: E 128 MET cc_start: 0.4293 (ttm) cc_final: 0.3981 (ttm) REVERT: E 210 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6426 (mm-30) REVERT: R 609 LEU cc_start: 0.5891 (tp) cc_final: 0.5607 (tp) REVERT: R 727 TYR cc_start: 0.6764 (t80) cc_final: 0.6438 (t80) REVERT: R 825 LEU cc_start: 0.6404 (tp) cc_final: 0.5947 (pp) REVERT: C 45 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7150 (ttm) REVERT: C 205 ASP cc_start: 0.7374 (t0) cc_final: 0.7121 (t0) REVERT: C 262 MET cc_start: 0.3633 (mmt) cc_final: 0.3293 (mmt) REVERT: C 325 MET cc_start: 0.6416 (mmm) cc_final: 0.5886 (mmm) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.0890 time to fit residues: 15.9780 Evaluate side-chains 134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 671 LEU Chi-restraints excluded: chain R residue 680 ILE Chi-restraints excluded: chain R residue 701 VAL Chi-restraints excluded: chain R residue 769 LEU Chi-restraints excluded: chain R residue 803 THR Chi-restraints excluded: chain R residue 808 ILE Chi-restraints excluded: chain R residue 817 LEU Chi-restraints excluded: chain R residue 835 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 58 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 42 optimal weight: 0.9980 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 HIS ** C 340 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 = 0.4614 r_free = 0.4614 target = 0.197862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.169482 restraints weight = 12341.267| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 2.90 r_work: 0.4200 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8941 Z= 0.228 Angle : 0.687 8.474 12115 Z= 0.368 Chirality : 0.046 0.160 1392 Planarity : 0.005 0.054 1516 Dihedral : 5.432 32.636 1201 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.50 % Allowed : 8.02 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.20 (0.25), residues: 1104 helix: 1.75 (0.29), residues: 345 sheet: 0.04 (0.30), residues: 293 loop : -1.75 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 52 TYR 0.018 0.003 TYR E 95 PHE 0.029 0.003 PHE C 253 TRP 0.031 0.002 TRP C 339 HIS 0.009 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 8939) covalent geometry : angle 0.68734 (12111) SS BOND : bond 0.00954 ( 2) SS BOND : angle 1.01772 ( 4) hydrogen bonds : bond 0.06470 ( 416) hydrogen bonds : angle 5.13767 ( 1149) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: D 21 MET cc_start: 0.0910 (mtm) cc_final: 0.0696 (mtm) REVERT: B 23 LEU cc_start: 0.5212 (OUTLIER) cc_final: 0.4827 (tp) REVERT: B 247 MET cc_start: 0.6048 (mtm) cc_final: 0.5783 (mtm) REVERT: E 128 MET cc_start: 0.4115 (ttm) cc_final: 0.3776 (ttm) REVERT: E 210 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6436 (mm-30) REVERT: R 609 LEU cc_start: 0.5951 (tp) cc_final: 0.5660 (tp) REVERT: R 825 LEU cc_start: 0.6450 (tp) cc_final: 0.5955 (pp) REVERT: C 61 MET cc_start: 0.6704 (ppp) cc_final: 0.6412 (ppp) REVERT: C 205 ASP cc_start: 0.7330 (t0) cc_final: 0.6972 (t0) REVERT: C 262 MET cc_start: 0.3650 (mmt) cc_final: 0.3405 (mmt) REVERT: C 325 MET cc_start: 0.6614 (mmm) cc_final: 0.6106 (mmm) outliers start: 24 outliers final: 13 residues processed: 134 average time/residue: 0.0977 time to fit residues: 18.1355 Evaluate side-chains 139 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain R residue 632 LEU Chi-restraints excluded: chain R residue 671 LEU Chi-restraints excluded: chain R residue 680 ILE Chi-restraints excluded: chain R residue 769 LEU Chi-restraints excluded: chain R residue 803 THR Chi-restraints excluded: chain R residue 808 ILE Chi-restraints excluded: chain C residue 58 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 73 optimal weight: 0.0670 chunk 1 optimal weight: 50.0000 chunk 85 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 691 HIS R 827 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.200975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.172639 restraints weight = 12479.907| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.92 r_work: 0.4272 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8941 Z= 0.148 Angle : 0.597 10.043 12115 Z= 0.317 Chirality : 0.044 0.156 1392 Planarity : 0.004 0.053 1516 Dihedral : 4.952 29.864 1199 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.50 % Allowed : 9.38 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.01 (0.26), residues: 1104 helix: 1.97 (0.29), residues: 350 sheet: -0.01 (0.30), residues: 299 loop : -1.59 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 52 TYR 0.018 0.002 TYR E 95 PHE 0.018 0.002 PHE C 253 TRP 0.018 0.002 TRP C 339 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8939) covalent geometry : angle 0.59711 (12111) SS BOND : bond 0.00728 ( 2) SS BOND : angle 0.74307 ( 4) hydrogen bonds : bond 0.05194 ( 416) hydrogen bonds : angle 4.81658 ( 1149) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: B 198 MET cc_start: 0.6942 (mtm) cc_final: 0.6682 (ttm) REVERT: B 247 MET cc_start: 0.6024 (mtm) cc_final: 0.5816 (mtm) REVERT: E 128 MET cc_start: 0.4043 (ttm) cc_final: 0.3750 (ttm) REVERT: R 609 LEU cc_start: 0.5808 (tp) cc_final: 0.5549 (tp) REVERT: R 825 LEU cc_start: 0.6379 (tp) cc_final: 0.5998 (pp) REVERT: C 178 THR cc_start: 0.3789 (OUTLIER) cc_final: 0.3430 (m) REVERT: C 205 ASP cc_start: 0.7352 (t0) cc_final: 0.7030 (t0) REVERT: C 262 MET cc_start: 0.4095 (mmm) cc_final: 0.3823 (mmt) REVERT: C 325 MET cc_start: 0.6665 (mmm) cc_final: 0.5976 (mmm) outliers start: 24 outliers final: 20 residues processed: 135 average time/residue: 0.0881 time to fit residues: 16.7966 Evaluate side-chains 139 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 680 ILE Chi-restraints excluded: chain R residue 736 ASN Chi-restraints excluded: chain R residue 769 LEU Chi-restraints excluded: chain R residue 796 LEU Chi-restraints excluded: chain R residue 803 THR Chi-restraints excluded: chain R residue 808 ILE Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.0000 chunk 90 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.200297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.172116 restraints weight = 12464.546| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.89 r_work: 0.4276 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8941 Z= 0.149 Angle : 0.589 9.959 12115 Z= 0.312 Chirality : 0.044 0.167 1392 Planarity : 0.004 0.052 1516 Dihedral : 4.831 30.772 1199 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.60 % Allowed : 11.04 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.06 (0.26), residues: 1104 helix: 2.14 (0.29), residues: 346 sheet: -0.01 (0.30), residues: 299 loop : -1.61 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.015 0.002 TYR E 95 PHE 0.019 0.002 PHE C 253 TRP 0.019 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8939) covalent geometry : angle 0.58854 (12111) SS BOND : bond 0.00789 ( 2) SS BOND : angle 0.90770 ( 4) hydrogen bonds : bond 0.05110 ( 416) hydrogen bonds : angle 4.71973 ( 1149) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: D 21 MET cc_start: 0.1821 (mtm) cc_final: 0.1611 (mtt) REVERT: R 693 MET cc_start: 0.6414 (mmm) cc_final: 0.6020 (mmm) REVERT: R 736 ASN cc_start: 0.6733 (OUTLIER) cc_final: 0.5299 (p0) REVERT: R 825 LEU cc_start: 0.6346 (tp) cc_final: 0.5927 (pp) REVERT: C 178 THR cc_start: 0.3696 (OUTLIER) cc_final: 0.3462 (m) REVERT: C 205 ASP cc_start: 0.7378 (t0) cc_final: 0.7113 (t0) REVERT: C 325 MET cc_start: 0.6710 (mmm) cc_final: 0.5977 (mmm) outliers start: 25 outliers final: 22 residues processed: 136 average time/residue: 0.0910 time to fit residues: 17.0654 Evaluate side-chains 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 632 LEU Chi-restraints excluded: chain R residue 680 ILE Chi-restraints excluded: chain R residue 736 ASN Chi-restraints excluded: chain R residue 769 LEU Chi-restraints excluded: chain R residue 796 LEU Chi-restraints excluded: chain R residue 803 THR Chi-restraints excluded: chain R residue 808 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 80 optimal weight: 0.0370 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.201671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.173447 restraints weight = 12476.396| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 2.91 r_work: 0.4252 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8941 Z= 0.140 Angle : 0.580 8.357 12115 Z= 0.307 Chirality : 0.043 0.165 1392 Planarity : 0.004 0.051 1516 Dihedral : 4.704 30.340 1199 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.12 % Allowed : 11.77 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.15 (0.26), residues: 1104 helix: 2.25 (0.29), residues: 346 sheet: 0.03 (0.30), residues: 299 loop : -1.59 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.015 0.002 TYR E 216 PHE 0.018 0.002 PHE C 253 TRP 0.028 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8939) covalent geometry : angle 0.58009 (12111) SS BOND : bond 0.00701 ( 2) SS BOND : angle 0.85958 ( 4) hydrogen bonds : bond 0.04828 ( 416) hydrogen bonds : angle 4.64729 ( 1149) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: D 21 MET cc_start: 0.1994 (mtm) cc_final: 0.1780 (mtt) REVERT: B 186 GLU cc_start: 0.7151 (mp0) cc_final: 0.6923 (mp0) REVERT: B 247 MET cc_start: 0.5997 (mtm) cc_final: 0.5780 (mtm) REVERT: E 47 TRP cc_start: 0.6385 (t60) cc_final: 0.6113 (t60) REVERT: R 693 MET cc_start: 0.6489 (mmm) cc_final: 0.6034 (mmm) REVERT: R 736 ASN cc_start: 0.6753 (OUTLIER) cc_final: 0.5278 (p0) REVERT: R 799 LEU cc_start: 0.8315 (tp) cc_final: 0.8094 (tt) REVERT: R 825 LEU cc_start: 0.6315 (tp) cc_final: 0.5930 (pp) REVERT: C 178 THR cc_start: 0.3617 (OUTLIER) cc_final: 0.3375 (m) REVERT: C 205 ASP cc_start: 0.7368 (t0) cc_final: 0.7081 (t0) REVERT: C 262 MET cc_start: 0.3760 (mmt) cc_final: 0.3421 (mmt) REVERT: C 325 MET cc_start: 0.6648 (mmm) cc_final: 0.5866 (mmm) outliers start: 30 outliers final: 23 residues processed: 139 average time/residue: 0.0940 time to fit residues: 18.1489 Evaluate side-chains 147 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 632 LEU Chi-restraints excluded: chain R residue 680 ILE Chi-restraints excluded: chain R residue 736 ASN Chi-restraints excluded: chain R residue 796 LEU Chi-restraints excluded: chain R residue 803 THR Chi-restraints excluded: chain R residue 808 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 52 optimal weight: 0.0470 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 827 ASN ** C 340 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 = 0.4643 r_free = 0.4643 target = 0.200840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.172374 restraints weight = 12465.813| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 2.93 r_work: 0.4222 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8941 Z= 0.156 Angle : 0.587 8.839 12115 Z= 0.311 Chirality : 0.044 0.196 1392 Planarity : 0.004 0.051 1516 Dihedral : 4.745 30.889 1199 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.92 % Allowed : 12.19 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.16 (0.26), residues: 1104 helix: 2.20 (0.28), residues: 347 sheet: 0.11 (0.30), residues: 297 loop : -1.60 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 52 TYR 0.014 0.002 TYR E 216 PHE 0.019 0.002 PHE C 253 TRP 0.023 0.002 TRP E 47 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8939) covalent geometry : angle 0.58711 (12111) SS BOND : bond 0.00749 ( 2) SS BOND : angle 0.90001 ( 4) hydrogen bonds : bond 0.05016 ( 416) hydrogen bonds : angle 4.63498 ( 1149) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 247 MET cc_start: 0.5992 (mtm) cc_final: 0.5774 (mtm) REVERT: R 693 MET cc_start: 0.6577 (mmm) cc_final: 0.6160 (mmm) REVERT: R 762 VAL cc_start: 0.3245 (t) cc_final: 0.2096 (m) REVERT: R 825 LEU cc_start: 0.6287 (tp) cc_final: 0.6016 (pp) REVERT: C 178 THR cc_start: 0.3869 (OUTLIER) cc_final: 0.3485 (m) REVERT: C 205 ASP cc_start: 0.7433 (t0) cc_final: 0.7206 (t0) REVERT: C 325 MET cc_start: 0.6565 (mmm) cc_final: 0.5892 (mmm) outliers start: 28 outliers final: 24 residues processed: 130 average time/residue: 0.0970 time to fit residues: 17.3912 Evaluate side-chains 138 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 632 LEU Chi-restraints excluded: chain R residue 680 ILE Chi-restraints excluded: chain R residue 736 ASN Chi-restraints excluded: chain R residue 796 LEU Chi-restraints excluded: chain R residue 803 THR Chi-restraints excluded: chain R residue 808 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 101 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.200696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.172560 restraints weight = 12423.971| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.88 r_work: 0.4229 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8941 Z= 0.159 Angle : 0.601 8.778 12115 Z= 0.315 Chirality : 0.044 0.188 1392 Planarity : 0.004 0.051 1516 Dihedral : 4.754 31.401 1199 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.02 % Allowed : 12.50 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.19 (0.26), residues: 1104 helix: 2.17 (0.28), residues: 347 sheet: 0.21 (0.30), residues: 292 loop : -1.58 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.015 0.002 TYR E 216 PHE 0.020 0.002 PHE C 253 TRP 0.036 0.002 TRP E 47 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8939) covalent geometry : angle 0.60089 (12111) SS BOND : bond 0.00747 ( 2) SS BOND : angle 0.93717 ( 4) hydrogen bonds : bond 0.05030 ( 416) hydrogen bonds : angle 4.59082 ( 1149) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.1064 (mtm) cc_final: 0.0126 (mtm) REVERT: R 693 MET cc_start: 0.6598 (mmm) cc_final: 0.6160 (mmm) REVERT: R 698 MET cc_start: 0.7405 (mmp) cc_final: 0.7058 (mpp) REVERT: R 825 LEU cc_start: 0.6305 (tp) cc_final: 0.6035 (pp) REVERT: C 178 THR cc_start: 0.3873 (OUTLIER) cc_final: 0.3403 (m) REVERT: C 205 ASP cc_start: 0.7443 (t0) cc_final: 0.7222 (t0) REVERT: C 262 MET cc_start: 0.3516 (mmt) cc_final: 0.3223 (mmt) REVERT: C 325 MET cc_start: 0.6566 (mmm) cc_final: 0.5905 (mmm) outliers start: 29 outliers final: 25 residues processed: 132 average time/residue: 0.0975 time to fit residues: 17.7951 Evaluate side-chains 137 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 632 LEU Chi-restraints excluded: chain R residue 680 ILE Chi-restraints excluded: chain R residue 736 ASN Chi-restraints excluded: chain R residue 769 LEU Chi-restraints excluded: chain R residue 803 THR Chi-restraints excluded: chain R residue 808 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.201644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.173697 restraints weight = 12460.358| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 2.89 r_work: 0.4254 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8941 Z= 0.142 Angle : 0.599 9.076 12115 Z= 0.312 Chirality : 0.043 0.171 1392 Planarity : 0.004 0.051 1516 Dihedral : 4.684 31.223 1199 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.02 % Allowed : 13.02 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.21 (0.26), residues: 1104 helix: 2.22 (0.28), residues: 346 sheet: 0.22 (0.30), residues: 292 loop : -1.59 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.014 0.002 TYR E 216 PHE 0.016 0.001 PHE C 253 TRP 0.070 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8939) covalent geometry : angle 0.59849 (12111) SS BOND : bond 0.00666 ( 2) SS BOND : angle 0.79929 ( 4) hydrogen bonds : bond 0.04704 ( 416) hydrogen bonds : angle 4.57056 ( 1149) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 693 MET cc_start: 0.6517 (mmm) cc_final: 0.5994 (mmm) REVERT: R 698 MET cc_start: 0.7228 (mmp) cc_final: 0.6791 (mpp) REVERT: R 825 LEU cc_start: 0.6269 (tp) cc_final: 0.5908 (pp) REVERT: C 178 THR cc_start: 0.3627 (OUTLIER) cc_final: 0.3386 (m) REVERT: C 205 ASP cc_start: 0.7370 (t0) cc_final: 0.7086 (t0) REVERT: C 262 MET cc_start: 0.3596 (mmt) cc_final: 0.3205 (mmt) REVERT: C 325 MET cc_start: 0.6678 (mmm) cc_final: 0.5891 (mmm) REVERT: C 332 TRP cc_start: 0.6314 (m-10) cc_final: 0.5999 (m-10) outliers start: 29 outliers final: 25 residues processed: 129 average time/residue: 0.0886 time to fit residues: 15.8956 Evaluate side-chains 134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 632 LEU Chi-restraints excluded: chain R residue 680 ILE Chi-restraints excluded: chain R residue 736 ASN Chi-restraints excluded: chain R residue 769 LEU Chi-restraints excluded: chain R residue 803 THR Chi-restraints excluded: chain R residue 808 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 1 optimal weight: 0.0020 chunk 31 optimal weight: 0.0000 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 2 optimal weight: 0.0070 chunk 22 optimal weight: 0.1980 chunk 9 optimal weight: 0.0370 chunk 39 optimal weight: 2.9990 overall best weight: 0.0488 ------------------------------------------------------------------------------- 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 = 0.4709 r_free = 0.4709 target = 0.207171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.178909 restraints weight = 12521.923| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 3.03 r_work: 0.4351 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8941 Z= 0.105 Angle : 0.563 11.657 12115 Z= 0.289 Chirality : 0.043 0.182 1392 Planarity : 0.004 0.050 1516 Dihedral : 4.346 28.384 1199 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.67 % Allowed : 14.79 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.26), residues: 1104 helix: 2.25 (0.28), residues: 353 sheet: 0.24 (0.30), residues: 292 loop : -1.50 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 52 TYR 0.013 0.001 TYR E 95 PHE 0.016 0.001 PHE C 292 TRP 0.054 0.002 TRP E 47 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8939) covalent geometry : angle 0.56299 (12111) SS BOND : bond 0.00559 ( 2) SS BOND : angle 0.91250 ( 4) hydrogen bonds : bond 0.03455 ( 416) hydrogen bonds : angle 4.34461 ( 1149) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 186 GLU cc_start: 0.7071 (mp0) cc_final: 0.6817 (mp0) REVERT: B 247 MET cc_start: 0.6043 (mtm) cc_final: 0.5799 (mtm) REVERT: R 677 MET cc_start: 0.6054 (tpp) cc_final: 0.5435 (mpp) REVERT: R 693 MET cc_start: 0.6468 (mmm) cc_final: 0.5882 (mmm) REVERT: R 698 MET cc_start: 0.7126 (mmp) cc_final: 0.6702 (mpp) REVERT: R 825 LEU cc_start: 0.6272 (tp) cc_final: 0.5979 (pp) REVERT: C 118 ASP cc_start: 0.6858 (t0) cc_final: 0.6633 (t0) REVERT: C 262 MET cc_start: 0.3418 (mmt) cc_final: 0.3022 (mmt) REVERT: C 325 MET cc_start: 0.6400 (mmm) cc_final: 0.5596 (mmm) outliers start: 16 outliers final: 12 residues processed: 127 average time/residue: 0.1004 time to fit residues: 17.5115 Evaluate side-chains 126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain R residue 627 MET Chi-restraints excluded: chain R residue 736 ASN Chi-restraints excluded: chain R residue 769 LEU Chi-restraints excluded: chain R residue 803 THR Chi-restraints excluded: chain R residue 808 ILE Chi-restraints excluded: chain C residue 58 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 109 optimal weight: 0.5980 chunk 77 optimal weight: 30.0000 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 78 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 827 ASN ** C 340 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 = 0.4653 r_free = 0.4653 target = 0.201767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.173200 restraints weight = 12416.167| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 2.92 r_work: 0.4257 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5712 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8941 Z= 0.158 Angle : 0.620 10.121 12115 Z= 0.320 Chirality : 0.044 0.154 1392 Planarity : 0.004 0.050 1516 Dihedral : 4.543 29.865 1199 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.88 % Allowed : 15.52 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.35 (0.26), residues: 1104 helix: 2.35 (0.29), residues: 347 sheet: 0.33 (0.30), residues: 300 loop : -1.58 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 52 TYR 0.014 0.002 TYR E 216 PHE 0.021 0.002 PHE C 253 TRP 0.059 0.003 TRP E 47 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8939) covalent geometry : angle 0.61983 (12111) SS BOND : bond 0.00666 ( 2) SS BOND : angle 0.79873 ( 4) hydrogen bonds : bond 0.04521 ( 416) hydrogen bonds : angle 4.42335 ( 1149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2551.58 seconds wall clock time: 44 minutes 18.98 seconds (2658.98 seconds total)