Starting phenix.real_space_refine on Sat Jul 4 02:25:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwi_47249/07_2026/9dwi_47249.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwi_47249/07_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_47249/07_2026/9dwi_47249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwi_47249/07_2026/9dwi_47249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwi_47249/07_2026/9dwi_47249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwi_47249/07_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-dev-6108/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: 3.26, per 1000 atoms: 0.22 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: 1.21 Conformation dependent library (CDL) restraints added in 488.2 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: 2.02 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: 2.78 Time building geometry restraints manager: 1.64 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: 22126 3.39 - 6.78: 61 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.970 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.680 Find NCS groups from input model: 0.100 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.600 ------------------------------------------------------------------------------- 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 : 0.769 16.954 22198 Z= 0.639 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 0.76948 / 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 : 0.398 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: 0.1467 time to fit residues: 31.7833 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 : 0.537 ------------------------------------------------------------------------------- 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: 10.0000 chunk 122 optimal weight: 0.0370 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.0970 overall best weight: 1.4262 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.095098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.056884 restraints weight = 63477.743| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.70 r_work: 0.2793 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 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 = 0.2785 r_free = 0.2785 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: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15522 Z= 0.153 Angle : 0.577 8.110 22198 Z= 0.348 Chirality : 0.041 0.206 2507 Planarity : 0.004 0.053 1802 Dihedral : 29.070 144.844 4410 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.35 % Favored : 97.56 % Rotamer: Outliers : 0.65 % Allowed : 6.63 % Favored : 92.72 % 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: 2.12 (0.26), residues: 1067 helix: 2.17 (0.19), residues: 720 sheet: 1.15 (0.87), residues: 29 loop : -0.33 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 40 TYR 0.034 0.002 TYR H 83 PHE 0.008 0.001 PHE L 181 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 0.00276 / 0.15 (15522) covalent geometry : angle 0.57692 / 0.35 (22198) hydrogen bonds : bond 0.04467 / 2.98 ( 892) hydrogen bonds : angle 3.33857 / 2.38 ( 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 : 0.538 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8675 (mt-10) REVERT: A 120 MET cc_start: 0.8684 (mtm) cc_final: 0.8402 (mtp) REVERT: C 36 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8866 (ttmt) REVERT: C 61 GLU cc_start: 0.8866 (tp30) cc_final: 0.8530 (tp30) REVERT: G 110 ASN cc_start: 0.8986 (t0) cc_final: 0.8645 (t0) REVERT: H 83 TYR cc_start: 0.8505 (m-80) cc_final: 0.8283 (m-80) REVERT: L 72 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8450 (mptt) REVERT: L 282 MET cc_start: -0.1102 (mmp) cc_final: -0.1350 (mmp) REVERT: L 325 TRP cc_start: 0.7800 (t-100) cc_final: 0.7502 (t-100) outliers start: 6 outliers final: 3 residues processed: 133 average time/residue: 0.1493 time to fit residues: 27.7001 Evaluate side-chains 124 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 43 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 87 optimal weight: 50.0000 chunk 85 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 116 optimal weight: 30.0000 chunk 83 optimal weight: 50.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN D 67 ASN E 39 HIS ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.091786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.052719 restraints weight = 85065.302| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.07 r_work: 0.2668 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 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 = 0.2659 r_free = 0.2659 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: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15522 Z= 0.277 Angle : 0.674 6.829 22198 Z= 0.382 Chirality : 0.044 0.232 2507 Planarity : 0.004 0.046 1802 Dihedral : 29.533 147.209 4410 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.15 % Rotamer: Outliers : 1.52 % Allowed : 8.37 % Favored : 90.11 % 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: 1.91 (0.26), residues: 1067 helix: 2.05 (0.19), residues: 724 sheet: 1.04 (0.84), residues: 29 loop : -0.56 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 83 TYR 0.041 0.003 TYR F 88 PHE 0.038 0.002 PHE L 181 TRP 0.002 0.001 TRP L 325 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.28 (15522) covalent geometry : angle 0.67429 / 0.38 (22198) hydrogen bonds : bond 0.05344 / 3.66 ( 892) hydrogen bonds : angle 3.39661 / 2.43 ( 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 134 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8762 (mt-10) REVERT: A 120 MET cc_start: 0.8753 (mtm) cc_final: 0.8552 (mtp) REVERT: C 36 LYS cc_start: 0.9183 (mtpt) cc_final: 0.8913 (ttmt) REVERT: C 61 GLU cc_start: 0.9008 (tp30) cc_final: 0.8801 (tp30) REVERT: C 110 ASN cc_start: 0.9169 (t0) cc_final: 0.8930 (t0) REVERT: C 118 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8361 (ptpt) REVERT: E 59 GLU cc_start: 0.8448 (pm20) cc_final: 0.8196 (pm20) REVERT: G 36 LYS cc_start: 0.9193 (tppt) cc_final: 0.8689 (tttt) REVERT: L 325 TRP cc_start: 0.7788 (t-100) cc_final: 0.7537 (t-100) outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 0.1457 time to fit residues: 26.4347 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 : 0.462 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 30.0000 chunk 116 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS ** L 34 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 = 0.3890 r_free = 0.3890 target = 0.092988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.054109 restraints weight = 72067.732| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.93 r_work: 0.2756 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 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 = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15522 Z= 0.146 Angle : 0.556 6.868 22198 Z= 0.332 Chirality : 0.040 0.236 2507 Planarity : 0.004 0.049 1802 Dihedral : 29.409 148.314 4406 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.00 % Favored : 96.90 % 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: 2.29 (0.26), residues: 1067 helix: 2.33 (0.19), residues: 726 sheet: 1.32 (0.81), residues: 29 loop : -0.44 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.024 0.001 TYR D 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 0.00269 / 0.15 (15522) covalent geometry : angle 0.55617 / 0.33 (22198) hydrogen bonds : bond 0.03922 / 2.63 ( 892) hydrogen bonds : angle 3.08099 / 2.21 ( 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 137 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8711 (mt-10) REVERT: A 120 MET cc_start: 0.8680 (mtm) cc_final: 0.8474 (mtp) REVERT: C 36 LYS cc_start: 0.9144 (mtpt) cc_final: 0.8878 (ttmt) REVERT: C 61 GLU cc_start: 0.8874 (tp30) cc_final: 0.8566 (tp30) REVERT: E 59 GLU cc_start: 0.8308 (pm20) cc_final: 0.8026 (pm20) REVERT: G 36 LYS cc_start: 0.9154 (tppt) cc_final: 0.8666 (tmmt) REVERT: L 191 MET cc_start: 0.5331 (pmm) cc_final: 0.4813 (pmm) REVERT: L 236 MET cc_start: 0.9094 (mpp) cc_final: 0.8813 (mmp) REVERT: L 325 TRP cc_start: 0.7840 (t-100) cc_final: 0.7574 (t-100) outliers start: 13 outliers final: 11 residues processed: 131 average time/residue: 0.1437 time to fit residues: 26.1866 Evaluate side-chains 129 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 F residue 22 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 255 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 99 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS ** L 34 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 = 0.3892 r_free = 0.3892 target = 0.093601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.054433 restraints weight = 71072.050| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.96 r_work: 0.2762 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 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 = 0.2751 r_free = 0.2751 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: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15522 Z= 0.138 Angle : 0.550 6.790 22198 Z= 0.329 Chirality : 0.040 0.234 2507 Planarity : 0.003 0.049 1802 Dihedral : 29.402 148.951 4406 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 1.63 % Allowed : 10.76 % Favored : 87.61 % 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: 2.39 (0.26), residues: 1067 helix: 2.40 (0.19), residues: 728 sheet: 1.48 (0.80), residues: 29 loop : -0.42 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.028 0.001 TYR D 83 PHE 0.009 0.001 PHE A 67 TRP 0.003 0.001 TRP L 325 HIS 0.005 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (15522) covalent geometry : angle 0.54995 / 0.33 (22198) hydrogen bonds : bond 0.03828 / 2.57 ( 892) hydrogen bonds : angle 2.98871 / 2.14 ( 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 137 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8695 (mt-10) REVERT: A 120 MET cc_start: 0.8667 (mtm) cc_final: 0.8445 (mtp) REVERT: C 36 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8883 (ttmt) REVERT: C 61 GLU cc_start: 0.8874 (tp30) cc_final: 0.8603 (tp30) REVERT: E 58 THR cc_start: 0.9067 (p) cc_final: 0.8761 (p) REVERT: E 59 GLU cc_start: 0.8306 (pm20) cc_final: 0.7869 (pm20) REVERT: G 35 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7796 (mtp85) REVERT: G 36 LYS cc_start: 0.9142 (tppt) cc_final: 0.8648 (tmmt) REVERT: L 191 MET cc_start: 0.5464 (pmm) cc_final: 0.5026 (pmm) REVERT: L 236 MET cc_start: 0.9103 (mpp) cc_final: 0.8835 (mmp) REVERT: L 325 TRP cc_start: 0.7844 (t-100) cc_final: 0.7588 (t-100) outliers start: 15 outliers final: 10 residues processed: 129 average time/residue: 0.1435 time to fit residues: 25.6440 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 : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR 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 84 MET 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 Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 255 ILE 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: 7.9990 chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 39 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 87 optimal weight: 50.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS ** L 34 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 = 0.3898 r_free = 0.3898 target = 0.093472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.055251 restraints weight = 67581.875| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.81 r_work: 0.2785 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 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 = 0.2774 r_free = 0.2774 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: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15522 Z= 0.130 Angle : 0.539 7.046 22198 Z= 0.324 Chirality : 0.039 0.235 2507 Planarity : 0.003 0.049 1802 Dihedral : 29.390 149.794 4406 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 1.30 % Allowed : 11.63 % Favored : 87.07 % 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: 2.48 (0.26), residues: 1067 helix: 2.47 (0.20), residues: 726 sheet: 1.53 (0.78), residues: 29 loop : -0.37 (0.36), residues: 312 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 0.009 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 0.00219 / 0.13 (15522) covalent geometry : angle 0.53948 / 0.32 (22198) hydrogen bonds : bond 0.03670 / 2.46 ( 892) hydrogen bonds : angle 2.92808 / 2.10 ( 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 134 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8687 (mt-10) REVERT: A 120 MET cc_start: 0.8632 (mtm) cc_final: 0.8424 (mtp) REVERT: C 36 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8869 (ttmt) REVERT: C 61 GLU cc_start: 0.8866 (tp30) cc_final: 0.8607 (tp30) REVERT: E 58 THR cc_start: 0.9074 (p) cc_final: 0.8750 (p) REVERT: E 59 GLU cc_start: 0.8278 (pm20) cc_final: 0.7806 (pm20) REVERT: G 36 LYS cc_start: 0.9142 (tppt) cc_final: 0.8657 (tmmt) REVERT: L 191 MET cc_start: 0.5482 (pmm) cc_final: 0.5075 (pmm) REVERT: L 325 TRP cc_start: 0.7856 (t-100) cc_final: 0.7598 (t-100) outliers start: 12 outliers final: 11 residues processed: 128 average time/residue: 0.1372 time to fit residues: 24.4273 Evaluate side-chains 126 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 44 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 255 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 67 optimal weight: 1.9990 chunk 122 optimal weight: 40.0000 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 45 optimal weight: 0.0670 chunk 64 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 116 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 84 optimal weight: 40.0000 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS ** L 34 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 = 0.3891 r_free = 0.3891 target = 0.093052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053852 restraints weight = 89197.229| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.26 r_work: 0.2744 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 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 = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15522 Z= 0.159 Angle : 0.564 6.676 22198 Z= 0.333 Chirality : 0.040 0.237 2507 Planarity : 0.004 0.048 1802 Dihedral : 29.453 150.616 4406 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 1.41 % Allowed : 12.17 % Favored : 86.41 % 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: 2.46 (0.26), residues: 1067 helix: 2.47 (0.20), residues: 721 sheet: 1.32 (0.80), residues: 29 loop : -0.35 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 35 TYR 0.042 0.002 TYR H 83 PHE 0.008 0.001 PHE A 67 TRP 0.002 0.001 TRP L 325 HIS 0.005 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (15522) covalent geometry : angle 0.56354 / 0.33 (22198) hydrogen bonds : bond 0.03866 / 2.62 ( 892) hydrogen bonds : angle 2.96753 / 2.12 ( 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 133 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8761 (mt-10) REVERT: A 120 MET cc_start: 0.8684 (mtm) cc_final: 0.8457 (mtp) REVERT: C 36 LYS cc_start: 0.9150 (mtpt) cc_final: 0.8889 (ttmt) REVERT: C 61 GLU cc_start: 0.8910 (tp30) cc_final: 0.8648 (tp30) REVERT: E 58 THR cc_start: 0.9073 (p) cc_final: 0.8730 (p) REVERT: E 59 GLU cc_start: 0.8356 (pm20) cc_final: 0.7863 (pm20) REVERT: L 191 MET cc_start: 0.5567 (pmm) cc_final: 0.5294 (pmm) REVERT: L 325 TRP cc_start: 0.7865 (t-100) cc_final: 0.7509 (t-100) outliers start: 13 outliers final: 9 residues processed: 129 average time/residue: 0.1273 time to fit residues: 22.9169 Evaluate side-chains 128 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 L residue 158 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 6.9990 chunk 127 optimal weight: 40.0000 chunk 128 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** 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 = 0.3894 r_free = 0.3894 target = 0.093270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054800 restraints weight = 79371.012| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.05 r_work: 0.2769 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 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 = 0.2753 r_free = 0.2753 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: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15522 Z= 0.140 Angle : 0.558 7.937 22198 Z= 0.331 Chirality : 0.040 0.240 2507 Planarity : 0.004 0.048 1802 Dihedral : 29.444 151.424 4406 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 1.30 % Allowed : 12.17 % Favored : 86.52 % 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: 2.46 (0.26), residues: 1067 helix: 2.48 (0.20), residues: 720 sheet: 1.21 (0.79), residues: 29 loop : -0.34 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 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 0.006 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (15522) covalent geometry : angle 0.55775 / 0.33 (22198) hydrogen bonds : bond 0.03715 / 2.51 ( 892) hydrogen bonds : angle 2.92296 / 2.09 ( 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 133 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8730 (mt-10) REVERT: A 120 MET cc_start: 0.8655 (mtm) cc_final: 0.8434 (mtp) REVERT: C 36 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8880 (ttmt) REVERT: C 61 GLU cc_start: 0.8885 (tp30) cc_final: 0.8630 (tp30) REVERT: E 58 THR cc_start: 0.9071 (p) cc_final: 0.8719 (p) REVERT: E 59 GLU cc_start: 0.8329 (pm20) cc_final: 0.7826 (pm20) REVERT: L 191 MET cc_start: 0.5736 (pmm) cc_final: 0.5377 (pmm) REVERT: L 325 TRP cc_start: 0.7864 (t-100) cc_final: 0.7498 (t-100) outliers start: 12 outliers final: 11 residues processed: 129 average time/residue: 0.1427 time to fit residues: 25.7487 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 : 0.475 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 255 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 83 optimal weight: 40.0000 chunk 28 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 22 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** 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 = 0.3905 r_free = 0.3905 target = 0.093893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055684 restraints weight = 75676.510| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.99 r_work: 0.2795 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15522 Z= 0.129 Angle : 0.553 7.990 22198 Z= 0.329 Chirality : 0.039 0.238 2507 Planarity : 0.004 0.050 1802 Dihedral : 29.416 151.984 4406 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 1.30 % Allowed : 12.72 % Favored : 85.98 % 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: 2.48 (0.27), residues: 1067 helix: 2.48 (0.20), residues: 720 sheet: 1.05 (0.82), residues: 29 loop : -0.29 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 35 TYR 0.023 0.001 TYR F 88 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 0.00219 / 0.13 (15522) covalent geometry : angle 0.55347 / 0.33 (22198) hydrogen bonds : bond 0.03629 / 2.46 ( 892) hydrogen bonds : angle 2.89871 / 2.07 ( 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 134 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8731 (mt-10) REVERT: A 120 MET cc_start: 0.8612 (mtm) cc_final: 0.8371 (mtp) REVERT: C 36 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8873 (ttmt) REVERT: C 61 GLU cc_start: 0.8861 (tp30) cc_final: 0.8600 (tp30) REVERT: E 58 THR cc_start: 0.9044 (p) cc_final: 0.8694 (p) REVERT: E 59 GLU cc_start: 0.8295 (pm20) cc_final: 0.7783 (pm20) REVERT: L 191 MET cc_start: 0.5740 (pmm) cc_final: 0.5438 (pmm) REVERT: L 325 TRP cc_start: 0.7864 (t-100) cc_final: 0.7447 (t-100) outliers start: 12 outliers final: 11 residues processed: 129 average time/residue: 0.1453 time to fit residues: 26.1925 Evaluate side-chains 129 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 255 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 87 optimal weight: 50.0000 chunk 113 optimal weight: 0.5980 chunk 92 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 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 = 0.3908 r_free = 0.3908 target = 0.094118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.055320 restraints weight = 80744.630| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.11 r_work: 0.2786 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 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: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15522 Z= 0.131 Angle : 0.560 8.858 22198 Z= 0.332 Chirality : 0.039 0.237 2507 Planarity : 0.004 0.050 1802 Dihedral : 29.428 152.362 4406 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 1.30 % Allowed : 13.26 % Favored : 85.43 % 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: 2.44 (0.27), residues: 1067 helix: 2.45 (0.20), residues: 719 sheet: 0.99 (0.83), residues: 29 loop : -0.28 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 35 TYR 0.019 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 0.00226 / 0.13 (15522) covalent geometry : angle 0.55999 / 0.33 (22198) hydrogen bonds : bond 0.03684 / 2.52 ( 892) hydrogen bonds : angle 2.89103 / 2.06 ( 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 130 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8736 (mt-10) REVERT: A 120 MET cc_start: 0.8612 (mtm) cc_final: 0.8363 (mtp) REVERT: C 36 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8875 (ttmt) REVERT: C 61 GLU cc_start: 0.8872 (tp30) cc_final: 0.8607 (tp30) REVERT: E 58 THR cc_start: 0.9042 (p) cc_final: 0.8699 (p) REVERT: E 59 GLU cc_start: 0.8335 (pm20) cc_final: 0.7833 (pm20) REVERT: L 191 MET cc_start: 0.5772 (pmm) cc_final: 0.5523 (pmm) REVERT: L 325 TRP cc_start: 0.7846 (t-100) cc_final: 0.7499 (t-100) outliers start: 12 outliers final: 11 residues processed: 125 average time/residue: 0.1490 time to fit residues: 26.0940 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 : 0.463 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 255 ILE 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: 4.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 212 HIS ** 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 = 0.3906 r_free = 0.3906 target = 0.093984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.055273 restraints weight = 79795.859| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.08 r_work: 0.2787 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 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 = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15522 Z= 0.138 Angle : 0.563 8.867 22198 Z= 0.333 Chirality : 0.039 0.237 2507 Planarity : 0.004 0.049 1802 Dihedral : 29.436 152.483 4406 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 1.30 % Allowed : 13.26 % Favored : 85.43 % 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 (0.27), residues: 1067 helix: 2.45 (0.20), residues: 719 sheet: 1.00 (0.82), residues: 29 loop : -0.27 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 35 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 G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (15522) covalent geometry : angle 0.56264 / 0.33 (22198) hydrogen bonds : bond 0.03690 / 2.53 ( 892) hydrogen bonds : angle 2.89293 / 2.07 ( 2283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6657.62 seconds wall clock time: 113 minutes 38.88 seconds (6818.88 seconds total)