Starting phenix.real_space_refine on Sat Jul 26 18:25:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x2v_32972/07_2025/7x2v_32972_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x2v_32972/07_2025/7x2v_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_32972/07_2025/7x2v_32972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x2v_32972/07_2025/7x2v_32972.map" model { file = "/net/cci-nas-00/data/ceres_data/7x2v_32972/07_2025/7x2v_32972_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x2v_32972/07_2025/7x2v_32972_neut.cif" } resolution = 3.09 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.48, per 1000 atoms: 0.63 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: 2.18 Conformation dependent library (CDL) restraints added in 951.2 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: 1.02 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: 2.59 Time building geometry restraints manager: 2.51 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.210 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.040 ------------------------------------------------------------------------------- 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 : 6.17 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 (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: -0.89 (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 TRP 0.060 0.003 TRP C 169 HIS 0.009 0.002 HIS E 35 PHE 0.032 0.003 PHE C 278 TYR 0.035 0.004 TYR R 727 ARG 0.013 0.001 ARG R 624 Details of bonding type rmsd hydrogen bonds : bond 0.16471 ( 416) hydrogen bonds : angle 6.58395 ( 1149) SS BOND : bond 0.01056 ( 2) SS BOND : angle 1.15495 ( 4) covalent geometry : bond 0.00714 ( 8939) covalent geometry : angle 0.92688 (12111) *********************** 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 : 0.806 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: 0.5329 (mmm) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.2149 time to fit residues: 38.9644 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 : 0.905 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.0030 chunk 86 optimal weight: 0.1980 chunk 33 optimal weight: 0.0170 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.0870 chunk 99 optimal weight: 0.6980 overall best weight: 0.1406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 220 GLN ** 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 = 0.4678 r_free = 0.4678 target = 0.203675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.175464 restraints weight = 12317.990| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 3.00 r_work: 0.4317 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8941 Z= 0.135 Angle : 0.618 8.530 12115 Z= 0.328 Chirality : 0.044 0.167 1392 Planarity : 0.004 0.058 1516 Dihedral : 5.391 54.498 1201 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.92 % Rotamer: Outliers : 1.98 % Allowed : 5.31 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.25), residues: 1104 helix: 1.67 (0.29), residues: 342 sheet: -0.07 (0.30), residues: 279 loop : -1.59 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 339 HIS 0.004 0.001 HIS B 322 PHE 0.014 0.001 PHE B 199 TYR 0.020 0.002 TYR E 95 ARG 0.007 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 416) hydrogen bonds : angle 5.14598 ( 1149) SS BOND : bond 0.00685 ( 2) SS BOND : angle 0.89070 ( 4) covalent geometry : bond 0.00265 ( 8939) covalent geometry : angle 0.61821 (12111) *********************** 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 141 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: E 38 ARG cc_start: 0.5742 (ptt180) cc_final: 0.5224 (ptt180) REVERT: E 102 TYR cc_start: 0.7677 (p90) cc_final: 0.7441 (p90) REVERT: E 128 MET cc_start: 0.4187 (ttm) cc_final: 0.3745 (ttm) REVERT: E 210 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6443 (mm-30) REVERT: R 609 LEU cc_start: 0.5967 (tp) cc_final: 0.5692 (tp) REVERT: R 727 TYR cc_start: 0.6746 (t80) cc_final: 0.6443 (t80) REVERT: R 825 LEU cc_start: 0.6423 (tp) cc_final: 0.5998 (pp) REVERT: C 45 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6949 (ttm) REVERT: C 90 VAL cc_start: 0.4938 (t) cc_final: 0.4716 (m) REVERT: C 205 ASP cc_start: 0.7382 (t0) cc_final: 0.7143 (t0) REVERT: C 262 MET cc_start: 0.3586 (mmt) cc_final: 0.3260 (mmt) REVERT: C 325 MET cc_start: 0.6368 (mmm) cc_final: 0.5862 (mmm) outliers start: 19 outliers final: 14 residues processed: 127 average time/residue: 0.2633 time to fit residues: 47.9818 Evaluate side-chains 128 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 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 58 optimal weight: 8.9990 chunk 66 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.4645 r_free = 0.4645 target = 0.200888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.172371 restraints weight = 12471.613| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 2.94 r_work: 0.4266 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8941 Z= 0.168 Angle : 0.616 6.904 12115 Z= 0.330 Chirality : 0.044 0.159 1392 Planarity : 0.004 0.054 1516 Dihedral : 5.131 40.679 1201 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.40 % Allowed : 7.60 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.02 (0.25), residues: 1104 helix: 1.97 (0.29), residues: 343 sheet: 0.04 (0.30), residues: 295 loop : -1.54 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 339 HIS 0.006 0.001 HIS E 35 PHE 0.025 0.002 PHE C 253 TYR 0.019 0.002 TYR E 95 ARG 0.007 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.05548 ( 416) hydrogen bonds : angle 4.94414 ( 1149) SS BOND : bond 0.00816 ( 2) SS BOND : angle 0.77134 ( 4) covalent geometry : bond 0.00369 ( 8939) covalent geometry : angle 0.61639 (12111) *********************** 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 149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.0854 (mtm) cc_final: 0.0629 (mtm) REVERT: B 247 MET cc_start: 0.5994 (mtm) cc_final: 0.5754 (mtm) REVERT: B 349 LYS cc_start: 0.6702 (pttm) cc_final: 0.6498 (ptpp) REVERT: E 128 MET cc_start: 0.4083 (ttm) cc_final: 0.3754 (ttm) REVERT: R 609 LEU cc_start: 0.5975 (tp) cc_final: 0.5699 (tp) REVERT: R 825 LEU cc_start: 0.6402 (tp) cc_final: 0.5968 (pp) REVERT: R 835 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6799 (tp) REVERT: C 45 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7314 (ttm) REVERT: C 205 ASP cc_start: 0.7402 (t0) cc_final: 0.7058 (t0) REVERT: C 262 MET cc_start: 0.3591 (mmt) cc_final: 0.3332 (mmt) REVERT: C 325 MET cc_start: 0.6663 (mmm) cc_final: 0.6098 (mmm) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 0.2104 time to fit residues: 39.5347 Evaluate side-chains 140 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 53 MET Chi-restraints excluded: chain B residue 184 ILE 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 R residue 627 MET 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 796 LEU Chi-restraints excluded: chain R residue 803 THR Chi-restraints excluded: chain R residue 808 ILE Chi-restraints excluded: chain R residue 835 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 51 optimal weight: 0.0040 chunk 107 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.4648 r_free = 0.4648 target = 0.200950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.172459 restraints weight = 12363.637| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 2.91 r_work: 0.4258 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8941 Z= 0.152 Angle : 0.595 8.414 12115 Z= 0.316 Chirality : 0.044 0.157 1392 Planarity : 0.004 0.053 1516 Dihedral : 4.866 28.122 1199 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % 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 (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: 0.16 (0.26), residues: 1104 helix: 2.17 (0.29), residues: 345 sheet: 0.06 (0.30), residues: 297 loop : -1.52 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 339 HIS 0.005 0.001 HIS E 35 PHE 0.021 0.002 PHE C 253 TYR 0.017 0.002 TYR E 95 ARG 0.006 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.05115 ( 416) hydrogen bonds : angle 4.79134 ( 1149) SS BOND : bond 0.00752 ( 2) SS BOND : angle 0.76388 ( 4) covalent geometry : bond 0.00331 ( 8939) covalent geometry : angle 0.59513 (12111) *********************** 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 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 247 MET cc_start: 0.5973 (mtm) cc_final: 0.5761 (mtm) REVERT: E 128 MET cc_start: 0.4007 (ttm) cc_final: 0.3720 (ttm) REVERT: R 736 ASN cc_start: 0.6658 (OUTLIER) cc_final: 0.5324 (p0) REVERT: R 825 LEU cc_start: 0.6320 (tp) cc_final: 0.5948 (pp) REVERT: C 45 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7227 (ttm) REVERT: C 205 ASP cc_start: 0.7340 (t0) cc_final: 0.7015 (t0) REVERT: C 262 MET cc_start: 0.4096 (mmm) cc_final: 0.3825 (mmt) REVERT: C 325 MET cc_start: 0.6628 (mmm) cc_final: 0.6026 (mmm) outliers start: 24 outliers final: 17 residues processed: 132 average time/residue: 0.2097 time to fit residues: 38.5654 Evaluate side-chains 134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 45 MET Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 0.0040 chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.4643 r_free = 0.4643 target = 0.200438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.172060 restraints weight = 12361.921| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.90 r_work: 0.4235 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8941 Z= 0.166 Angle : 0.611 8.334 12115 Z= 0.323 Chirality : 0.044 0.163 1392 Planarity : 0.004 0.052 1516 Dihedral : 4.833 30.328 1199 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % 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 (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: 0.10 (0.26), residues: 1104 helix: 2.14 (0.29), residues: 344 sheet: 0.10 (0.30), residues: 297 loop : -1.62 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 339 HIS 0.006 0.001 HIS E 35 PHE 0.022 0.002 PHE C 253 TYR 0.016 0.002 TYR E 95 ARG 0.006 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.05310 ( 416) hydrogen bonds : angle 4.75979 ( 1149) SS BOND : bond 0.00804 ( 2) SS BOND : angle 0.93402 ( 4) covalent geometry : bond 0.00370 ( 8939) covalent geometry : angle 0.61122 (12111) *********************** 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 145 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: B 186 GLU cc_start: 0.7212 (mp0) cc_final: 0.7000 (mp0) REVERT: R 736 ASN cc_start: 0.6742 (OUTLIER) cc_final: 0.5222 (p0) REVERT: R 799 LEU cc_start: 0.8352 (tp) cc_final: 0.8129 (tt) REVERT: R 825 LEU cc_start: 0.6283 (tp) cc_final: 0.5871 (pp) REVERT: C 178 THR cc_start: 0.3678 (OUTLIER) cc_final: 0.3316 (m) REVERT: C 205 ASP cc_start: 0.7412 (t0) cc_final: 0.7085 (t0) REVERT: C 325 MET cc_start: 0.6687 (mmm) cc_final: 0.6056 (mmm) outliers start: 25 outliers final: 21 residues processed: 131 average time/residue: 0.2134 time to fit residues: 39.1187 Evaluate side-chains 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 184 ILE 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 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 74 SER Chi-restraints excluded: chain C residue 178 THR 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 59 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4645 r_free = 0.4645 target = 0.200685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.172408 restraints weight = 12206.741| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.88 r_work: 0.4290 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8941 Z= 0.163 Angle : 0.616 9.678 12115 Z= 0.323 Chirality : 0.044 0.194 1392 Planarity : 0.004 0.051 1516 Dihedral : 4.818 31.073 1199 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.81 % Allowed : 11.77 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.12 (0.26), residues: 1104 helix: 2.14 (0.29), residues: 346 sheet: 0.11 (0.30), residues: 297 loop : -1.60 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.021 0.002 PHE C 253 TYR 0.015 0.002 TYR E 95 ARG 0.009 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.05165 ( 416) hydrogen bonds : angle 4.69669 ( 1149) SS BOND : bond 0.00783 ( 2) SS BOND : angle 0.93405 ( 4) covalent geometry : bond 0.00364 ( 8939) covalent geometry : angle 0.61573 (12111) *********************** 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 148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: B 186 GLU cc_start: 0.7181 (mp0) cc_final: 0.6966 (mp0) REVERT: B 247 MET cc_start: 0.5969 (mtm) cc_final: 0.5766 (mtm) REVERT: E 47 TRP cc_start: 0.6392 (t60) cc_final: 0.6141 (t60) REVERT: R 799 LEU cc_start: 0.8314 (tp) cc_final: 0.8056 (tt) REVERT: R 825 LEU cc_start: 0.6252 (tp) cc_final: 0.5862 (pp) REVERT: C 178 THR cc_start: 0.3616 (OUTLIER) cc_final: 0.3290 (m) REVERT: C 205 ASP cc_start: 0.7328 (t0) cc_final: 0.7053 (t0) REVERT: C 262 MET cc_start: 0.3822 (mmt) cc_final: 0.3470 (mmt) REVERT: C 325 MET cc_start: 0.6699 (mmm) cc_final: 0.5983 (mmm) outliers start: 27 outliers final: 24 residues processed: 135 average time/residue: 0.2118 time to fit residues: 39.7089 Evaluate side-chains 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 184 ILE 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 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 74 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 67 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4642 r_free = 0.4642 target = 0.200368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.172080 restraints weight = 12404.474| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.88 r_work: 0.4245 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8941 Z= 0.160 Angle : 0.614 10.000 12115 Z= 0.320 Chirality : 0.044 0.187 1392 Planarity : 0.004 0.051 1516 Dihedral : 4.770 31.806 1199 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.60 % Allowed : 11.98 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.11 (0.26), residues: 1104 helix: 1.95 (0.28), residues: 356 sheet: 0.19 (0.30), residues: 292 loop : -1.58 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.019 0.002 PHE C 253 TYR 0.014 0.002 TYR E 95 ARG 0.008 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.05101 ( 416) hydrogen bonds : angle 4.65340 ( 1149) SS BOND : bond 0.00776 ( 2) SS BOND : angle 0.96345 ( 4) covalent geometry : bond 0.00359 ( 8939) covalent geometry : angle 0.61401 (12111) *********************** 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 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: B 198 MET cc_start: 0.6942 (mtm) cc_final: 0.6657 (ttm) REVERT: B 247 MET cc_start: 0.5922 (mtm) cc_final: 0.5700 (mtm) REVERT: R 762 VAL cc_start: 0.3239 (t) cc_final: 0.1972 (m) REVERT: R 825 LEU cc_start: 0.6278 (tp) cc_final: 0.5896 (pp) REVERT: C 178 THR cc_start: 0.3597 (OUTLIER) cc_final: 0.3297 (m) REVERT: C 205 ASP cc_start: 0.7408 (t0) cc_final: 0.7110 (t0) REVERT: C 262 MET cc_start: 0.3809 (mmt) cc_final: 0.3410 (mmt) REVERT: C 325 MET cc_start: 0.6682 (mmm) cc_final: 0.5946 (mmm) outliers start: 25 outliers final: 22 residues processed: 133 average time/residue: 0.2145 time to fit residues: 39.6218 Evaluate side-chains 138 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 184 ILE 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 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 74 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 46 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.200716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.172565 restraints weight = 12517.719| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.88 r_work: 0.4234 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8941 Z= 0.155 Angle : 0.620 13.275 12115 Z= 0.320 Chirality : 0.043 0.158 1392 Planarity : 0.004 0.053 1516 Dihedral : 4.749 31.786 1199 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.81 % Allowed : 12.71 % 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 (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: 0.20 (0.26), residues: 1104 helix: 2.17 (0.28), residues: 347 sheet: 0.20 (0.30), residues: 292 loop : -1.55 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.018 0.002 PHE C 253 TYR 0.014 0.002 TYR E 95 ARG 0.009 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04963 ( 416) hydrogen bonds : angle 4.58193 ( 1149) SS BOND : bond 0.00713 ( 2) SS BOND : angle 0.84953 ( 4) covalent geometry : bond 0.00349 ( 8939) covalent geometry : angle 0.61948 (12111) *********************** 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 139 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 1.765 Fit side-chains revert: symmetry clash REVERT: B 198 MET cc_start: 0.7095 (mtm) cc_final: 0.6815 (ttm) REVERT: R 698 MET cc_start: 0.7454 (mmp) cc_final: 0.7073 (mpp) REVERT: R 825 LEU cc_start: 0.6288 (tp) cc_final: 0.6019 (pp) REVERT: C 178 THR cc_start: 0.3903 (OUTLIER) cc_final: 0.3424 (m) REVERT: C 205 ASP cc_start: 0.7442 (t0) cc_final: 0.7224 (t0) REVERT: C 262 MET cc_start: 0.3528 (mmt) cc_final: 0.3322 (mmt) REVERT: C 325 MET cc_start: 0.6532 (mmm) cc_final: 0.5881 (mmm) outliers start: 27 outliers final: 21 residues processed: 128 average time/residue: 0.2897 time to fit residues: 51.3537 Evaluate side-chains 132 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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 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 44 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4638 r_free = 0.4638 target = 0.200285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.172119 restraints weight = 12575.733| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.90 r_work: 0.4242 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8941 Z= 0.166 Angle : 0.641 12.130 12115 Z= 0.330 Chirality : 0.044 0.158 1392 Planarity : 0.004 0.056 1516 Dihedral : 4.782 31.853 1199 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.92 % Allowed : 12.81 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.17 (0.26), residues: 1104 helix: 2.13 (0.28), residues: 347 sheet: 0.13 (0.30), residues: 299 loop : -1.54 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.019 0.002 PHE C 253 TYR 0.015 0.002 TYR E 95 ARG 0.008 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.05072 ( 416) hydrogen bonds : angle 4.63639 ( 1149) SS BOND : bond 0.00707 ( 2) SS BOND : angle 0.92592 ( 4) covalent geometry : bond 0.00375 ( 8939) covalent geometry : angle 0.64102 (12111) *********************** 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 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: B 186 GLU cc_start: 0.7206 (mp0) cc_final: 0.6996 (mp0) REVERT: B 198 MET cc_start: 0.6977 (mtm) cc_final: 0.6728 (ttm) REVERT: E 34 MET cc_start: 0.4803 (OUTLIER) cc_final: 0.4538 (mmp) REVERT: R 698 MET cc_start: 0.7372 (mmp) cc_final: 0.6922 (mpp) REVERT: R 825 LEU cc_start: 0.6302 (tp) cc_final: 0.5916 (pp) REVERT: C 178 THR cc_start: 0.3650 (OUTLIER) cc_final: 0.3304 (m) REVERT: C 205 ASP cc_start: 0.7421 (t0) cc_final: 0.7131 (t0) REVERT: C 262 MET cc_start: 0.3751 (mmt) cc_final: 0.3382 (mmt) REVERT: C 325 MET cc_start: 0.6688 (mmm) cc_final: 0.5921 (mmm) REVERT: C 332 TRP cc_start: 0.6337 (m-10) cc_final: 0.5958 (m-10) outliers start: 28 outliers final: 21 residues processed: 128 average time/residue: 0.2325 time to fit residues: 40.8315 Evaluate side-chains 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 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 34 MET 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 736 ASN Chi-restraints excluded: chain R residue 793 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 178 THR Chi-restraints excluded: chain C residue 217 MET 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 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 1 optimal weight: 50.0000 chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4642 r_free = 0.4642 target = 0.200522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.172550 restraints weight = 12440.424| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.88 r_work: 0.4249 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8941 Z= 0.156 Angle : 0.620 11.838 12115 Z= 0.321 Chirality : 0.044 0.158 1392 Planarity : 0.004 0.058 1516 Dihedral : 4.739 32.023 1199 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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 (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: 0.17 (0.26), residues: 1104 helix: 2.16 (0.28), residues: 346 sheet: 0.11 (0.30), residues: 299 loop : -1.54 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP E 47 HIS 0.006 0.001 HIS E 35 PHE 0.018 0.002 PHE C 253 TYR 0.017 0.002 TYR E 95 ARG 0.008 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04928 ( 416) hydrogen bonds : angle 4.57267 ( 1149) SS BOND : bond 0.00751 ( 2) SS BOND : angle 0.95272 ( 4) covalent geometry : bond 0.00348 ( 8939) covalent geometry : angle 0.62017 (12111) ********************** 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 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: B 198 MET cc_start: 0.6947 (mtm) cc_final: 0.6705 (ttm) REVERT: B 247 MET cc_start: 0.5935 (mtm) cc_final: 0.5724 (mtm) REVERT: E 34 MET cc_start: 0.4778 (OUTLIER) cc_final: 0.4519 (mmp) REVERT: R 698 MET cc_start: 0.7253 (mmp) cc_final: 0.6804 (mpp) REVERT: R 825 LEU cc_start: 0.6287 (tp) cc_final: 0.5929 (pp) REVERT: C 178 THR cc_start: 0.3620 (OUTLIER) cc_final: 0.3182 (m) REVERT: C 205 ASP cc_start: 0.7365 (t0) cc_final: 0.7086 (t0) REVERT: C 262 MET cc_start: 0.3716 (mmt) cc_final: 0.3354 (mmt) REVERT: C 325 MET cc_start: 0.6673 (mmm) cc_final: 0.5927 (mmm) REVERT: C 332 TRP cc_start: 0.6334 (m-10) cc_final: 0.6001 (m-10) outliers start: 29 outliers final: 23 residues processed: 129 average time/residue: 0.2234 time to fit residues: 39.6079 Evaluate side-chains 140 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 53 MET Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 34 MET 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 686 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 178 THR Chi-restraints excluded: chain C residue 217 MET 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 16 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4653 r_free = 0.4653 target = 0.201665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.173509 restraints weight = 12545.743| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.92 r_work: 0.4247 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8941 Z= 0.149 Angle : 0.616 14.037 12115 Z= 0.317 Chirality : 0.043 0.156 1392 Planarity : 0.004 0.059 1516 Dihedral : 4.694 31.696 1199 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.71 % Allowed : 13.02 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.22 (0.26), residues: 1104 helix: 2.20 (0.29), residues: 347 sheet: 0.14 (0.30), residues: 299 loop : -1.52 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP E 47 HIS 0.006 0.001 HIS E 35 PHE 0.017 0.002 PHE C 253 TYR 0.017 0.002 TYR E 95 ARG 0.008 0.000 ARG C 52 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 416) hydrogen bonds : angle 4.52751 ( 1149) SS BOND : bond 0.00727 ( 2) SS BOND : angle 0.92002 ( 4) covalent geometry : bond 0.00333 ( 8939) covalent geometry : angle 0.61592 (12111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6090.74 seconds wall clock time: 107 minutes 26.55 seconds (6446.55 seconds total)