Starting phenix.real_space_refine on Thu Aug 6 22:30:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwi_47249/08_2026/9dwi_47249.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwi_47249/08_2026/9dwi_47249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dwi_47249/08_2026/9dwi_47249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwi_47249/08_2026/9dwi_47249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwi_47249/08_2026/9dwi_47249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwi_47249/08_2026/9dwi_47249.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 1.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4192 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 293 5.49 5 S 19 5.16 5 C 8313 2.51 5 N 2722 2.21 5 O 3314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14661 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 733 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 727 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 818 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 807 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Conformer: "B" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} bond proxies already assigned to first conformer: 738 Chain: "I" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2383 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 595 Classifications: {'DNA': 29} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 28} Chain: "L" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2591 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 308} Chain breaks: 1 Time building chain proxies: 3.55, per 1000 atoms: 0.24 Number of scatterers: 14661 At special positions: 0 Unit cell: (98.707, 152.397, 130.921, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 293 15.00 O 3314 8.00 N 2722 7.00 C 8313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 474.6 milliseconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 68.3% alpha, 4.5% beta 142 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.848A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.567A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.758A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.531A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.602A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.547A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.538A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.798A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.551A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.270A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.637A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.511A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.628A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 29 removed outlier: 3.995A pdb=" N GLU L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU L 22 " --> pdb=" O MET L 18 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN L 24 " --> pdb=" O THR L 20 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE L 25 " --> pdb=" O GLU L 21 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 49 removed outlier: 4.278A pdb=" N ALA L 38 " --> pdb=" O HIS L 34 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR L 49 " --> pdb=" O VAL L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 Processing helix chain 'L' and resid 66 through 80 Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'L' and resid 91 through 102 Processing helix chain 'L' and resid 107 through 117 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 129 through 132 Processing helix chain 'L' and resid 133 through 142 Processing helix chain 'L' and resid 142 through 147 removed outlier: 3.541A pdb=" N GLU L 147 " --> pdb=" O PHE L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 170 Processing helix chain 'L' and resid 209 through 221 removed outlier: 3.663A pdb=" N VAL L 214 " --> pdb=" O LEU L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 274 removed outlier: 4.606A pdb=" N TYR L 266 " --> pdb=" O LYS L 262 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N CYS L 267 " --> pdb=" O ASP L 263 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY L 274 " --> pdb=" O LEU L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 289 Processing helix chain 'L' and resid 315 through 323 removed outlier: 3.536A pdb=" N ILE L 323 " --> pdb=" O ILE L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.153A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.355A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.588A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.210A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.691A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'L' and resid 150 through 151 removed outlier: 3.604A pdb=" N ILE L 150 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER L 188 " --> pdb=" O ILE L 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'L' and resid 174 through 177 removed outlier: 3.733A pdb=" N ILE L 174 " --> pdb=" O THR L 196 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL L 238 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR L 227 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 291 through 293 527 hydrogen bonds defined for protein. 1553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.60 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: 3527 1.34 - 1.46: 4367 1.46 - 1.58: 7009 1.58 - 1.70: 584 1.70 - 1.82: 35 Bond restraints: 15522 Sorted by residual: bond pdb=" P DC K 119 " pdb=" OP3 DC K 119 " ideal model delta sigma weight residual 1.480 1.619 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C3' DA J 12 " pdb=" C2' DA J 12 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DG J 136 " pdb=" C2' DG J 136 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC J 114 " pdb=" C2' DC J 114 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG J 97 " pdb=" C2' DG J 97 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 15517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 22125 3.39 - 6.78: 62 6.78 - 10.17: 8 10.17 - 13.56: 1 13.56 - 16.95: 2 Bond angle restraints: 22198 Sorted by residual: angle pdb=" C LYS L 87 " pdb=" CA LYS L 87 " pdb=" CB LYS L 87 " ideal model delta sigma weight residual 110.88 93.93 16.95 1.57e+00 4.06e-01 1.17e+02 angle pdb=" CB LYS L 87 " pdb=" CG LYS L 87 " pdb=" CD LYS L 87 " ideal model delta sigma weight residual 111.30 94.87 16.43 2.30e+00 1.89e-01 5.10e+01 angle pdb=" C ASP G 72 " pdb=" N ASN G 73 " pdb=" CA ASN G 73 " ideal model delta sigma weight residual 122.83 115.63 7.20 1.54e+00 4.22e-01 2.19e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT I 35 " pdb=" C4 DT I 35 " pdb=" O4 DT I 35 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.03e+01 ... (remaining 22193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.34: 6844 28.34 - 56.68: 1607 56.68 - 85.02: 167 85.02 - 113.36: 5 113.36 - 141.70: 4 Dihedral angle restraints: 8627 sinusoidal: 5476 harmonic: 3151 Sorted by residual: dihedral pdb=" C LYS L 87 " pdb=" N LYS L 87 " pdb=" CA LYS L 87 " pdb=" CB LYS L 87 " ideal model delta harmonic sigma weight residual -122.60 -101.49 -21.11 0 2.50e+00 1.60e-01 7.13e+01 dihedral pdb=" N LYS L 87 " pdb=" C LYS L 87 " pdb=" CA LYS L 87 " pdb=" CB LYS L 87 " ideal model delta harmonic sigma weight residual 122.80 111.47 11.33 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 8624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 2492 0.126 - 0.253: 10 0.253 - 0.379: 1 0.379 - 0.506: 2 0.506 - 0.632: 2 Chirality restraints: 2507 Sorted by residual: chirality pdb=" P DG J 30 " pdb=" OP1 DG J 30 " pdb=" OP2 DG J 30 " pdb=" O5' DG J 30 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 9.99e+00 chirality pdb=" P DC K 119 " pdb=" OP1 DC K 119 " pdb=" OP2 DC K 119 " pdb=" O5' DC K 119 " both_signs ideal model delta sigma weight residual True 2.34 2.97 -0.63 2.00e-01 2.50e+01 9.97e+00 chirality pdb=" CA LYS L 87 " pdb=" N LYS L 87 " pdb=" C LYS L 87 " pdb=" CB LYS L 87 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 2504 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 71 " -0.647 9.50e-02 1.11e+02 2.90e-01 5.14e+01 pdb=" NE ARG G 71 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG G 71 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 71 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 71 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 68 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C ASN G 68 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN G 68 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA G 69 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " 0.018 2.00e-02 2.50e+03 1.69e-02 5.70e+00 pdb=" CG TYR D 83 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.000 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3218 2.81 - 3.33: 13195 3.33 - 3.85: 28520 3.85 - 4.38: 31766 4.38 - 4.90: 46425 Nonbonded interactions: 123124 Sorted by model distance: nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.286 3.040 nonbonded pdb=" OE2 GLU C 41 " pdb=" OG SER D 87 " model vdw 2.302 3.040 nonbonded pdb=" O ASP L 17 " pdb=" OG1 THR L 20 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 71 " model vdw 2.307 3.040 nonbonded pdb=" OG SER C 18 " pdb=" O LEU C 23 " model vdw 2.317 3.040 ... (remaining 123119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 32 or resid 34 through 81 or resid 83 through 124)) selection = (chain 'H' and (resid 32 or resid 34 through 81 or resid 83 through 124)) } 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=0.50 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: 19.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.950 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.400 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 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 : 0.005 0.139 15522 Z= 0.475 Angle : 0.775 16.954 22198 Z= 0.644 Chirality : 0.050 0.632 2507 Planarity : 0.008 0.290 1802 Dihedral : 25.838 141.698 6597 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.11 % Allowed : 0.98 % Favored : 98.91 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.26), residues: 1067 helix: 1.89 (0.20), residues: 702 sheet: 1.41 (0.88), residues: 29 loop : -0.28 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 79 TYR 0.042 0.002 TYR D 83 PHE 0.009 0.001 PHE D 65 TRP 0.003 0.001 TRP L 325 HIS 0.010 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.47 (15522) covalent geometry : angle 0.77511 / 0.64 (22198) hydrogen bonds : bond 0.11620 / 7.96 ( 892) hydrogen bonds : angle 4.01131 / 2.87 ( 2283) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8036 (mt-10) REVERT: A 120 MET cc_start: 0.7920 (mtm) cc_final: 0.7309 (mtp) REVERT: C 36 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8590 (ttmt) REVERT: C 61 GLU cc_start: 0.8133 (tp30) cc_final: 0.7861 (tp30) REVERT: G 110 ASN cc_start: 0.8874 (t0) cc_final: 0.8649 (t0) REVERT: L 72 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8330 (mptt) REVERT: L 135 HIS cc_start: 0.8523 (t70) cc_final: 0.8303 (t-170) REVERT: L 282 MET cc_start: -0.1462 (mmp) cc_final: -0.1741 (mmp) REVERT: L 325 TRP cc_start: 0.7697 (t-100) cc_final: 0.7371 (t-100) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1605 time to fit residues: 35.0114 Evaluate side-chains 127 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.0370 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.2980 overall best weight: 1.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.095112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.056968 restraints weight = 63459.415| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.70 r_work: 0.2798 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15522 Z= 0.158 Angle : 0.587 8.504 22198 Z= 0.353 Chirality : 0.042 0.222 2507 Planarity : 0.004 0.053 1802 Dihedral : 29.006 143.756 4410 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.54 % Favored : 97.37 % Rotamer: Outliers : 0.65 % Allowed : 6.41 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.12 (0.26), residues: 1067 helix: 2.16 (0.19), residues: 720 sheet: 1.18 (0.86), residues: 29 loop : -0.31 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 40 TYR 0.035 0.002 TYR H 83 PHE 0.006 0.001 PHE D 65 TRP 0.003 0.001 TRP L 325 HIS 0.006 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (15522) covalent geometry : angle 0.58713 / 0.35 (22198) hydrogen bonds : bond 0.04703 / 3.15 ( 892) hydrogen bonds : angle 3.38318 / 2.42 ( 2283) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8688 (mt-10) REVERT: A 120 MET cc_start: 0.8645 (mtm) cc_final: 0.8354 (mtp) REVERT: C 36 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8864 (ttmt) REVERT: C 61 GLU cc_start: 0.8868 (tp30) cc_final: 0.8534 (tp30) REVERT: E 59 GLU cc_start: 0.8247 (pm20) cc_final: 0.8042 (pm20) REVERT: G 110 ASN cc_start: 0.8991 (t0) cc_final: 0.8652 (t0) REVERT: H 83 TYR cc_start: 0.8552 (m-10) cc_final: 0.8186 (m-80) REVERT: L 72 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8445 (mptt) REVERT: L 282 MET cc_start: -0.1103 (mmp) cc_final: -0.1360 (mmp) REVERT: L 325 TRP cc_start: 0.7797 (t-100) cc_final: 0.7489 (t-100) outliers start: 6 outliers final: 4 residues processed: 133 average time/residue: 0.1544 time to fit residues: 28.4842 Evaluate side-chains 124 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain L residue 72 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 122 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 87 optimal weight: 40.0000 chunk 85 optimal weight: 30.0000 chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 50.0000 chunk 116 optimal weight: 40.0000 chunk 83 optimal weight: 50.0000 overall best weight: 4.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN D 67 ASN E 39 HIS L 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.092235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053660 restraints weight = 84561.305| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.02 r_work: 0.2688 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15522 Z= 0.268 Angle : 0.660 6.859 22198 Z= 0.375 Chirality : 0.044 0.245 2507 Planarity : 0.004 0.048 1802 Dihedral : 29.393 145.876 4410 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 1.41 % Allowed : 8.26 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.00 (0.26), residues: 1067 helix: 2.08 (0.19), residues: 725 sheet: 1.33 (0.86), residues: 29 loop : -0.47 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 254 TYR 0.028 0.002 TYR D 83 PHE 0.009 0.001 PHE C 25 TRP 0.002 0.001 TRP L 325 HIS 0.006 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.27 (15522) covalent geometry : angle 0.66046 / 0.38 (22198) hydrogen bonds : bond 0.05049 / 3.45 ( 892) hydrogen bonds : angle 3.37115 / 2.41 ( 2283) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8737 (mt-10) REVERT: A 120 MET cc_start: 0.8746 (mtm) cc_final: 0.8466 (mtp) REVERT: C 36 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8900 (ttmt) REVERT: C 61 GLU cc_start: 0.8985 (tp30) cc_final: 0.8764 (tp30) REVERT: C 110 ASN cc_start: 0.9155 (t0) cc_final: 0.8916 (t0) REVERT: C 118 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8301 (ptpt) REVERT: E 59 GLU cc_start: 0.8464 (pm20) cc_final: 0.8162 (pm20) REVERT: L 325 TRP cc_start: 0.7752 (t-100) cc_final: 0.7495 (t-100) outliers start: 13 outliers final: 10 residues processed: 127 average time/residue: 0.1248 time to fit residues: 22.4346 Evaluate side-chains 126 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 34 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 90 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 98 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 30.0000 chunk 116 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS L 34 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.093809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.055058 restraints weight = 71449.530| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.01 r_work: 0.2770 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15522 Z= 0.137 Angle : 0.558 6.824 22198 Z= 0.332 Chirality : 0.040 0.252 2507 Planarity : 0.004 0.049 1802 Dihedral : 29.301 146.890 4406 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.91 % Favored : 97.00 % Rotamer: Outliers : 0.76 % Allowed : 9.78 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.37 (0.26), residues: 1067 helix: 2.37 (0.19), residues: 728 sheet: 1.33 (0.81), residues: 29 loop : -0.36 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.029 0.002 TYR H 83 PHE 0.007 0.001 PHE A 67 TRP 0.003 0.001 TRP L 325 HIS 0.006 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (15522) covalent geometry : angle 0.55816 / 0.33 (22198) hydrogen bonds : bond 0.03893 / 2.60 ( 892) hydrogen bonds : angle 3.06225 / 2.20 ( 2283) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8722 (mt-10) REVERT: A 120 MET cc_start: 0.8670 (mtm) cc_final: 0.8308 (mtp) REVERT: C 36 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8878 (ttmt) REVERT: C 61 GLU cc_start: 0.8866 (tp30) cc_final: 0.8592 (tp30) REVERT: C 118 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8336 (ptpt) REVERT: E 59 GLU cc_start: 0.8356 (pm20) cc_final: 0.7997 (pm20) REVERT: L 236 MET cc_start: 0.9093 (mpp) cc_final: 0.8877 (mmp) REVERT: L 325 TRP cc_start: 0.7847 (t-100) cc_final: 0.7575 (t-100) outliers start: 7 outliers final: 5 residues processed: 123 average time/residue: 0.1315 time to fit residues: 22.7612 Evaluate side-chains 120 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 34 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 99 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.093281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.054897 restraints weight = 71213.343| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.89 r_work: 0.2774 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15522 Z= 0.143 Angle : 0.562 7.898 22198 Z= 0.332 Chirality : 0.040 0.250 2507 Planarity : 0.003 0.049 1802 Dihedral : 29.317 147.405 4406 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 1.41 % Allowed : 10.22 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.43 (0.26), residues: 1067 helix: 2.41 (0.19), residues: 728 sheet: 1.44 (0.79), residues: 29 loop : -0.34 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.027 0.002 TYR H 83 PHE 0.009 0.001 PHE A 67 TRP 0.003 0.001 TRP L 325 HIS 0.006 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (15522) covalent geometry : angle 0.56217 / 0.33 (22198) hydrogen bonds : bond 0.03874 / 2.60 ( 892) hydrogen bonds : angle 3.01162 / 2.16 ( 2283) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8709 (mt-10) REVERT: A 120 MET cc_start: 0.8656 (mtm) cc_final: 0.8441 (mtp) REVERT: C 36 LYS cc_start: 0.9135 (mtpt) cc_final: 0.8871 (ttmt) REVERT: C 61 GLU cc_start: 0.8853 (tp30) cc_final: 0.8568 (tp30) REVERT: G 35 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7796 (mtp85) REVERT: L 236 MET cc_start: 0.9074 (mpp) cc_final: 0.8858 (mmp) REVERT: L 325 TRP cc_start: 0.7834 (t-100) cc_final: 0.7570 (t-100) outliers start: 13 outliers final: 9 residues processed: 126 average time/residue: 0.1336 time to fit residues: 23.3308 Evaluate side-chains 126 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 34 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 50.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.092916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.054217 restraints weight = 67818.631| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.82 r_work: 0.2763 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15522 Z= 0.165 Angle : 0.572 7.786 22198 Z= 0.335 Chirality : 0.040 0.251 2507 Planarity : 0.004 0.048 1802 Dihedral : 29.354 148.037 4406 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 1.20 % Allowed : 11.09 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.45 (0.26), residues: 1067 helix: 2.43 (0.19), residues: 728 sheet: 1.55 (0.79), residues: 29 loop : -0.35 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.025 0.002 TYR D 83 PHE 0.008 0.001 PHE A 67 TRP 0.003 0.001 TRP L 325 HIS 0.006 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (15522) covalent geometry : angle 0.57238 / 0.34 (22198) hydrogen bonds : bond 0.03909 / 2.64 ( 892) hydrogen bonds : angle 3.01248 / 2.16 ( 2283) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.468 Fit side-chains REVERT: A 50 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8707 (mt-10) REVERT: A 120 MET cc_start: 0.8659 (mtm) cc_final: 0.8441 (mtp) REVERT: C 36 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8880 (ttmt) REVERT: C 61 GLU cc_start: 0.8883 (tp30) cc_final: 0.8618 (tp30) REVERT: E 59 GLU cc_start: 0.8299 (pm20) cc_final: 0.8063 (pm20) REVERT: F 84 MET cc_start: 0.8821 (mmm) cc_final: 0.8488 (mmm) REVERT: G 35 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7813 (mtp85) REVERT: L 236 MET cc_start: 0.9085 (mpp) cc_final: 0.8877 (mmp) REVERT: L 325 TRP cc_start: 0.7840 (t-100) cc_final: 0.7585 (t-100) outliers start: 11 outliers final: 9 residues processed: 125 average time/residue: 0.1578 time to fit residues: 27.5269 Evaluate side-chains 126 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 67 optimal weight: 0.7980 chunk 122 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 64 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 116 optimal weight: 40.0000 chunk 27 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.093758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054340 restraints weight = 88788.249| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.33 r_work: 0.2748 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15522 Z= 0.138 Angle : 0.560 7.800 22198 Z= 0.331 Chirality : 0.040 0.254 2507 Planarity : 0.004 0.048 1802 Dihedral : 29.351 149.040 4406 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 1.52 % Allowed : 10.98 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.53 (0.26), residues: 1067 helix: 2.48 (0.19), residues: 728 sheet: 1.60 (0.76), residues: 29 loop : -0.31 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.022 0.001 TYR D 83 PHE 0.008 0.001 PHE A 67 TRP 0.003 0.001 TRP L 325 HIS 0.006 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (15522) covalent geometry : angle 0.56016 / 0.33 (22198) hydrogen bonds : bond 0.03733 / 2.52 ( 892) hydrogen bonds : angle 2.94036 / 2.11 ( 2283) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.455 Fit side-chains REVERT: A 50 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8739 (mt-10) REVERT: A 120 MET cc_start: 0.8668 (mtm) cc_final: 0.8457 (mtp) REVERT: C 36 LYS cc_start: 0.9147 (mtpt) cc_final: 0.8884 (ttmt) REVERT: C 61 GLU cc_start: 0.8914 (tp30) cc_final: 0.8650 (tp30) REVERT: E 59 GLU cc_start: 0.8273 (pm20) cc_final: 0.7873 (pm20) REVERT: L 325 TRP cc_start: 0.7865 (t-100) cc_final: 0.7624 (t-100) outliers start: 14 outliers final: 10 residues processed: 126 average time/residue: 0.1503 time to fit residues: 26.6439 Evaluate side-chains 124 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 34 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 128 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.093732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.054939 restraints weight = 79938.868| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.09 r_work: 0.2775 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15522 Z= 0.131 Angle : 0.559 8.670 22198 Z= 0.330 Chirality : 0.040 0.253 2507 Planarity : 0.004 0.049 1802 Dihedral : 29.343 149.851 4406 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 1.20 % Allowed : 11.30 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.61 (0.27), residues: 1067 helix: 2.59 (0.20), residues: 720 sheet: 1.40 (0.79), residues: 29 loop : -0.30 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 35 TYR 0.020 0.001 TYR H 83 PHE 0.009 0.001 PHE A 67 TRP 0.003 0.001 TRP L 325 HIS 0.006 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.13 (15522) covalent geometry : angle 0.55866 / 0.33 (22198) hydrogen bonds : bond 0.03647 / 2.46 ( 892) hydrogen bonds : angle 2.89769 / 2.07 ( 2283) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.482 Fit side-chains REVERT: A 50 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8714 (mt-10) REVERT: A 120 MET cc_start: 0.8638 (mtm) cc_final: 0.8402 (mtp) REVERT: C 36 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8875 (ttmt) REVERT: C 61 GLU cc_start: 0.8889 (tp30) cc_final: 0.8635 (tp30) REVERT: E 59 GLU cc_start: 0.8222 (pm20) cc_final: 0.7774 (pm20) REVERT: L 325 TRP cc_start: 0.7860 (t-100) cc_final: 0.7566 (t-100) outliers start: 11 outliers final: 8 residues processed: 126 average time/residue: 0.1511 time to fit residues: 26.5967 Evaluate side-chains 124 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 34 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.0060 chunk 83 optimal weight: 40.0000 chunk 28 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 22 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS ** L 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.094426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.055864 restraints weight = 75611.307| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.09 r_work: 0.2790 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15522 Z= 0.125 Angle : 0.562 8.604 22198 Z= 0.331 Chirality : 0.040 0.254 2507 Planarity : 0.004 0.050 1802 Dihedral : 29.336 150.330 4406 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 1.20 % Allowed : 12.17 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.64 (0.27), residues: 1067 helix: 2.61 (0.20), residues: 720 sheet: 1.27 (0.78), residues: 29 loop : -0.28 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.024 0.001 TYR D 83 PHE 0.008 0.001 PHE A 67 TRP 0.003 0.001 TRP L 325 HIS 0.006 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.13 (15522) covalent geometry : angle 0.56176 / 0.33 (22198) hydrogen bonds : bond 0.03595 / 2.44 ( 892) hydrogen bonds : angle 2.86783 / 2.05 ( 2283) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.484 Fit side-chains REVERT: A 50 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8721 (mt-10) REVERT: A 60 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7898 (mt) REVERT: A 120 MET cc_start: 0.8615 (mtm) cc_final: 0.8374 (mtp) REVERT: C 36 LYS cc_start: 0.9125 (mtpt) cc_final: 0.8863 (ttmt) REVERT: C 61 GLU cc_start: 0.8851 (tp30) cc_final: 0.8595 (tp30) REVERT: E 59 GLU cc_start: 0.8251 (pm20) cc_final: 0.7832 (pm20) REVERT: L 325 TRP cc_start: 0.7837 (t-100) cc_final: 0.7476 (t-100) outliers start: 11 outliers final: 8 residues processed: 125 average time/residue: 0.1470 time to fit residues: 25.6876 Evaluate side-chains 125 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 34 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 0.9980 chunk 97 optimal weight: 30.0000 chunk 39 optimal weight: 0.2980 chunk 87 optimal weight: 50.0000 chunk 113 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS ** L 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.094458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.055490 restraints weight = 80200.192| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.16 r_work: 0.2786 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15522 Z= 0.132 Angle : 0.572 8.871 22198 Z= 0.335 Chirality : 0.039 0.254 2507 Planarity : 0.004 0.049 1802 Dihedral : 29.356 150.847 4406 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 1.09 % Allowed : 12.61 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.64 (0.27), residues: 1067 helix: 2.61 (0.20), residues: 720 sheet: 1.34 (0.81), residues: 29 loop : -0.26 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 35 TYR 0.024 0.001 TYR D 83 PHE 0.008 0.001 PHE A 67 TRP 0.003 0.001 TRP L 325 HIS 0.007 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (15522) covalent geometry : angle 0.57168 / 0.33 (22198) hydrogen bonds : bond 0.03628 / 2.48 ( 892) hydrogen bonds : angle 2.86841 / 2.05 ( 2283) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.490 Fit side-chains REVERT: A 50 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8700 (mt-10) REVERT: A 120 MET cc_start: 0.8614 (mtm) cc_final: 0.8353 (mtp) REVERT: C 36 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8878 (ttmt) REVERT: C 61 GLU cc_start: 0.8872 (tp30) cc_final: 0.8604 (tp30) REVERT: E 59 GLU cc_start: 0.8245 (pm20) cc_final: 0.7789 (pm20) REVERT: G 36 LYS cc_start: 0.9131 (tppt) cc_final: 0.8526 (tttt) REVERT: L 325 TRP cc_start: 0.7853 (t-100) cc_final: 0.7500 (t-100) outliers start: 10 outliers final: 10 residues processed: 123 average time/residue: 0.1481 time to fit residues: 25.4873 Evaluate side-chains 125 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 34 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS L 135 HIS ** L 212 HIS ** 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 = 0.3904 r_free = 0.3904 target = 0.094371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055307 restraints weight = 79293.099| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.15 r_work: 0.2782 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15522 Z= 0.141 Angle : 0.579 9.120 22198 Z= 0.337 Chirality : 0.039 0.253 2507 Planarity : 0.004 0.049 1802 Dihedral : 29.368 151.001 4406 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 1.30 % Allowed : 12.39 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 2.66 (0.27), residues: 1067 helix: 2.62 (0.20), residues: 721 sheet: 1.28 (0.80), residues: 29 loop : -0.24 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 35 TYR 0.026 0.001 TYR D 83 PHE 0.007 0.001 PHE A 67 TRP 0.002 0.001 TRP L 325 HIS 0.008 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (15522) covalent geometry : angle 0.57928 / 0.34 (22198) hydrogen bonds : bond 0.03644 / 2.49 ( 892) hydrogen bonds : angle 2.87792 / 2.06 ( 2283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6472.40 seconds wall clock time: 110 minutes 38.74 seconds (6638.74 seconds total)