Starting phenix.real_space_refine on Thu Aug 6 19:58:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h1t_34431/08_2026/8h1t_34431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1t_34431/08_2026/8h1t_34431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h1t_34431/08_2026/8h1t_34431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1t_34431/08_2026/8h1t_34431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h1t_34431/08_2026/8h1t_34431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1t_34431/08_2026/8h1t_34431.map" } resolution = 3.0 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= -0.013 sd= 1.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 334 5.49 5 S 28 5.16 5 C 9881 2.51 5 N 3214 2.21 5 O 3908 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: 17365 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3398 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "J" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3449 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "K" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 520 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2433 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 15, 'TRANS': 285} Chain breaks: 2 Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "N" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 903 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Time building chain proxies: 3.68, per 1000 atoms: 0.21 Number of scatterers: 17365 At special positions: 0 Unit cell: (121, 118, 159, 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 28 16.00 P 334 15.00 O 3908 8.00 N 3214 7.00 C 9881 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 508.6 milliseconds 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 61.6% alpha, 5.7% beta 166 base pairs and 273 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.982A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 48 through 76 removed outlier: 4.078A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.538A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.471A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 58 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.925A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.516A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.651A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.512A 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 27 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.347A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.526A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 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 removed outlier: 3.559A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.658A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 49 removed outlier: 4.154A pdb=" N LEU K 42 " --> pdb=" O PRO K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 69 Processing helix chain 'K' and resid 75 through 85 Processing helix chain 'L' and resid 11 through 23 Processing helix chain 'L' and resid 54 through 60 Processing helix chain 'L' and resid 74 through 80 Processing helix chain 'L' and resid 90 through 102 Processing helix chain 'L' and resid 109 through 120 Processing helix chain 'L' and resid 123 through 133 Processing helix chain 'L' and resid 134 through 144 removed outlier: 3.616A pdb=" N HIS L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 152 Processing helix chain 'L' and resid 202 through 218 Processing helix chain 'L' and resid 236 through 243 removed outlier: 3.990A pdb=" N LYS L 240 " --> pdb=" O ASP L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 648 through 668 removed outlier: 3.545A pdb=" N THR L 668 " --> pdb=" O ASP L 664 " (cutoff:3.500A) Processing helix chain 'L' and resid 671 through 686 Processing helix chain 'L' and resid 687 through 695 removed outlier: 3.625A pdb=" N LEU L 691 " --> pdb=" O MET L 687 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU L 693 " --> pdb=" O ALA L 689 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 removed outlier: 3.548A pdb=" N VAL M 26 " --> pdb=" O THR M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 55 through 59 Processing helix chain 'N' and resid 263 through 268 Processing helix chain 'N' and resid 269 through 275 Processing helix chain 'N' and resid 277 through 286 removed outlier: 3.732A pdb=" N PHE N 286 " --> pdb=" O GLN N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 327 Processing helix chain 'N' and resid 330 through 352 removed outlier: 4.396A pdb=" N ARG N 336 " --> pdb=" O GLU N 332 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU N 344 " --> pdb=" O GLU N 340 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS N 345 " --> pdb=" O MET N 341 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS N 346 " --> pdb=" O GLU N 342 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL N 347 " --> pdb=" O LYS N 343 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN N 349 " --> pdb=" O LYS N 345 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP N 350 " --> pdb=" O LYS N 346 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS N 351 " --> pdb=" O VAL N 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.038A 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 'B' and resid 96 through 98 removed outlier: 6.450A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.464A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.577A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.026A 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 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.223A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 56 through 57 Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 9 removed outlier: 3.770A pdb=" N LEU L 8 " --> pdb=" O GLY M 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 28 through 30 removed outlier: 4.375A pdb=" N ALA L 167 " --> pdb=" O TRP L 52 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE L 191 " --> pdb=" O GLU L 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 15 Processing sheet with id=AB5, first strand: chain 'N' and resid 293 through 295 598 hydrogen bonds defined for protein. 1749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 858 hydrogen bond angles 0 basepair planarities 166 basepair parallelities 273 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3600 1.33 - 1.45: 5397 1.45 - 1.57: 8649 1.57 - 1.69: 666 1.69 - 1.81: 48 Bond restraints: 18360 Sorted by residual: bond pdb=" C3' DC J 119 " pdb=" C2' DC J 119 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DG J 27 " pdb=" C2' DG J 27 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DG I 42 " pdb=" C2' DG I 42 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DC I 10 " pdb=" C2' DC I 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.77e+00 bond pdb=" C3' DG I 43 " pdb=" C2' DG I 43 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.58e+00 ... (remaining 18355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 25750 2.32 - 4.63: 451 4.63 - 6.95: 7 6.95 - 9.26: 0 9.26 - 11.58: 1 Bond angle restraints: 26209 Sorted by residual: angle pdb=" C GLY M 75 " pdb=" N GLY M 76 " pdb=" CA GLY M 76 " ideal model delta sigma weight residual 121.70 133.28 -11.58 1.80e+00 3.09e-01 4.14e+01 angle pdb=" N3 DT J 62 " pdb=" C4 DT J 62 " pdb=" O4 DT J 62 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT J 99 " pdb=" C4 DT J 99 " pdb=" O4 DT J 99 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" O5' DC J 165 " pdb=" C5' DC J 165 " pdb=" C4' DC J 165 " ideal model delta sigma weight residual 109.40 112.92 -3.52 8.00e-01 1.56e+00 1.93e+01 angle pdb=" N3 DT J 120 " pdb=" C4 DT J 120 " pdb=" O4 DT J 120 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 ... (remaining 26204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 8216 27.39 - 54.78: 1664 54.78 - 82.17: 308 82.17 - 109.56: 4 109.56 - 136.96: 2 Dihedral angle restraints: 10194 sinusoidal: 6377 harmonic: 3817 Sorted by residual: dihedral pdb=" C4' DC J 119 " pdb=" C3' DC J 119 " pdb=" O3' DC J 119 " pdb=" P DT J 120 " ideal model delta sinusoidal sigma weight residual 220.00 83.04 136.96 1 3.50e+01 8.16e-04 1.36e+01 dihedral pdb=" C4' DG J 27 " pdb=" C3' DG J 27 " pdb=" O3' DG J 27 " pdb=" P DT J 28 " ideal model delta sinusoidal sigma weight residual 220.00 87.80 132.20 1 3.50e+01 8.16e-04 1.31e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 10191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2241 0.047 - 0.094: 586 0.094 - 0.141: 130 0.141 - 0.187: 1 0.187 - 0.234: 2 Chirality restraints: 2960 Sorted by residual: chirality pdb=" C3' DC J 7 " pdb=" C4' DC J 7 " pdb=" O3' DC J 7 " pdb=" C2' DC J 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C3' DG I 161 " pdb=" C4' DG I 161 " pdb=" O3' DG I 161 " pdb=" C2' DG I 161 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA GLU L 148 " pdb=" N GLU L 148 " pdb=" C GLU L 148 " pdb=" CB GLU L 148 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 2957 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 659 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C LYS L 659 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS L 659 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE L 660 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 234 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO L 235 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO L 235 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 235 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 165 " 0.013 2.00e-02 2.50e+03 9.02e-03 1.83e+00 pdb=" N1 DC I 165 " -0.020 2.00e-02 2.50e+03 pdb=" C2 DC I 165 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DC I 165 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC I 165 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC I 165 " 0.002 2.00e-02 2.50e+03 pdb=" N4 DC I 165 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DC I 165 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 165 " -0.001 2.00e-02 2.50e+03 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 769 2.71 - 3.26: 16082 3.26 - 3.81: 32948 3.81 - 4.35: 39282 4.35 - 4.90: 57777 Nonbonded interactions: 146858 Sorted by model distance: nonbonded pdb=" CD1 LEU M 73 " pdb=" O ARG M 74 " model vdw 2.164 3.460 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.290 3.040 nonbonded pdb=" NE2 GLN E 55 " pdb=" O ARG F 40 " model vdw 2.294 3.120 ... (remaining 146853 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 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 118) selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.410 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 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 0.094 18361 Z= 0.455 Angle : 0.673 11.575 26209 Z= 0.607 Chirality : 0.043 0.234 2960 Planarity : 0.003 0.041 2176 Dihedral : 24.612 136.956 7726 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.24), residues: 1295 helix: 2.55 (0.19), residues: 759 sheet: -0.00 (0.61), residues: 70 loop : -0.02 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.006 0.001 TYR C 50 PHE 0.005 0.001 PHE C 25 TRP 0.006 0.001 TRP N 320 HIS 0.003 0.000 HIS L 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.45 (18360) covalent geometry : angle 0.67332 / 0.61 (26209) hydrogen bonds : bond 0.10243 / 6.87 ( 1027) hydrogen bonds : angle 3.98155 / 2.87 ( 2607) Misc. bond : bond 0.09441 / 6.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7555 (pm20) cc_final: 0.7220 (pm20) REVERT: B 84 MET cc_start: 0.8037 (tpt) cc_final: 0.7803 (tpt) REVERT: C 23 LEU cc_start: 0.8181 (tp) cc_final: 0.7873 (mt) REVERT: C 24 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8353 (mm-40) REVERT: C 90 ASP cc_start: 0.8592 (t0) cc_final: 0.8151 (t70) REVERT: C 92 GLU cc_start: 0.7722 (pm20) cc_final: 0.7348 (pm20) REVERT: D 34 LYS cc_start: 0.8060 (mppt) cc_final: 0.7779 (mppt) REVERT: D 115 THR cc_start: 0.8675 (m) cc_final: 0.8464 (m) REVERT: D 120 LYS cc_start: 0.8026 (tttp) cc_final: 0.7718 (tttp) REVERT: E 64 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8193 (mtmm) REVERT: F 77 LYS cc_start: 0.8364 (mmtm) cc_final: 0.8049 (mmmm) REVERT: F 84 MET cc_start: 0.8561 (tpt) cc_final: 0.8285 (mmm) REVERT: G 73 ASN cc_start: 0.8682 (t0) cc_final: 0.8263 (t0) REVERT: H 34 LYS cc_start: 0.7711 (tptm) cc_final: 0.7332 (mmtm) REVERT: H 47 GLN cc_start: 0.8660 (tt0) cc_final: 0.8339 (tt0) REVERT: K 74 LYS cc_start: 0.8516 (mmtp) cc_final: 0.8185 (tppt) REVERT: L 204 ASP cc_start: 0.8030 (t0) cc_final: 0.7760 (t0) REVERT: L 654 VAL cc_start: 0.9040 (p) cc_final: 0.8660 (m) REVERT: L 655 GLU cc_start: 0.8653 (pt0) cc_final: 0.8427 (tp30) REVERT: L 658 LYS cc_start: 0.9193 (mttt) cc_final: 0.8980 (tppt) REVERT: L 695 ASN cc_start: 0.8667 (m-40) cc_final: 0.8461 (m110) REVERT: M 38 PRO cc_start: 0.8112 (Cg_exo) cc_final: 0.7826 (Cg_endo) REVERT: N 286 PHE cc_start: 0.7411 (m-80) cc_final: 0.6780 (m-80) REVERT: N 305 SER cc_start: 0.8360 (m) cc_final: 0.8046 (t) REVERT: N 333 MET cc_start: 0.8773 (ttt) cc_final: 0.8364 (tmt) REVERT: N 334 GLN cc_start: 0.8836 (tp40) cc_final: 0.8561 (tp40) REVERT: N 337 ILE cc_start: 0.8294 (mt) cc_final: 0.6833 (mt) outliers start: 0 outliers final: 1 residues processed: 351 average time/residue: 0.6202 time to fit residues: 239.3716 Evaluate side-chains 231 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.2328 > 50:) chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN B 27 GLN B 75 HIS B 93 GLN C 38 ASN D 47 GLN D 95 GLN E 39 HIS E 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 HIS L 151 HIS ** L 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.131997 restraints weight = 43831.651| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.47 r_work: 0.3603 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 495 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 568 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 18361 Z= 0.405 Angle : 0.874 20.768 26209 Z= 0.470 Chirality : 0.051 0.252 2960 Planarity : 0.007 0.061 2176 Dihedral : 29.697 133.661 5084 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.54 % Allowed : 15.05 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.23), residues: 1295 helix: 1.53 (0.18), residues: 796 sheet: 0.01 (0.66), residues: 71 loop : -0.75 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 74 TYR 0.031 0.003 TYR E 54 PHE 0.031 0.004 PHE L 181 TRP 0.030 0.004 TRP L 5 HIS 0.008 0.002 HIS L 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00871 / 0.40 (18360) covalent geometry : angle 0.87376 / 0.47 (26209) hydrogen bonds : bond 0.05530 / 3.72 ( 1027) hydrogen bonds : angle 3.89187 / 2.87 ( 2607) Misc. bond : bond 0.01796 / 1.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8780 (mtt) cc_final: 0.8383 (mtt) REVERT: A 123 ASP cc_start: 0.9042 (m-30) cc_final: 0.8761 (m-30) REVERT: B 35 ARG cc_start: 0.8616 (mtp85) cc_final: 0.8174 (mtp85) REVERT: C 89 ASN cc_start: 0.8942 (m-40) cc_final: 0.8716 (m110) REVERT: C 90 ASP cc_start: 0.8553 (t0) cc_final: 0.8065 (t70) REVERT: C 104 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7896 (mm110) REVERT: D 57 LYS cc_start: 0.8391 (tppp) cc_final: 0.8001 (tptp) REVERT: D 68 ASP cc_start: 0.8952 (t70) cc_final: 0.8744 (t0) REVERT: E 42 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7423 (mmt180) REVERT: F 44 LYS cc_start: 0.8863 (ptpp) cc_final: 0.8642 (ptmm) REVERT: F 53 GLU cc_start: 0.8586 (tp30) cc_final: 0.8340 (tp30) REVERT: F 77 LYS cc_start: 0.8741 (mmtm) cc_final: 0.8379 (mmmm) REVERT: H 34 LYS cc_start: 0.8032 (tptm) cc_final: 0.7650 (mmtm) REVERT: H 47 GLN cc_start: 0.8824 (tt0) cc_final: 0.8505 (tt0) REVERT: H 95 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8715 (tt0) REVERT: L 652 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6720 (pt0) REVERT: M 1 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.6251 (tpt) REVERT: N 337 ILE cc_start: 0.8138 (mt) cc_final: 0.7218 (mt) outliers start: 51 outliers final: 24 residues processed: 265 average time/residue: 0.5827 time to fit residues: 171.8089 Evaluate side-chains 235 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain L residue 675 ILE Chi-restraints excluded: chain L residue 698 VAL Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 286 PHE Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 324 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 27 GLN C 94 ASN D 47 GLN D 109 HIS E 39 HIS E 76 GLN E 125 GLN F 75 HIS H 84 ASN L 84 HIS L 193 HIS L 665 GLN L 695 ASN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.158554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.134375 restraints weight = 43440.085| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.53 r_work: 0.3640 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 568 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 577 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18361 Z= 0.158 Angle : 0.663 12.835 26209 Z= 0.369 Chirality : 0.043 0.245 2960 Planarity : 0.005 0.085 2176 Dihedral : 29.759 134.333 5082 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.27 % Allowed : 19.59 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.23), residues: 1295 helix: 1.97 (0.18), residues: 783 sheet: -0.12 (0.65), residues: 71 loop : -0.56 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 129 TYR 0.012 0.002 TYR L 173 PHE 0.025 0.002 PHE N 286 TRP 0.016 0.002 TRP L 196 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (18360) covalent geometry : angle 0.66280 / 0.37 (26209) hydrogen bonds : bond 0.04065 / 2.72 ( 1027) hydrogen bonds : angle 3.43044 / 2.54 ( 2607) Misc. bond : bond 0.00370 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 0.498 Fit side-chains REVERT: A 79 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.6937 (tttt) REVERT: A 120 MET cc_start: 0.8620 (mtt) cc_final: 0.8104 (mtt) REVERT: A 123 ASP cc_start: 0.9069 (m-30) cc_final: 0.8756 (m-30) REVERT: A 125 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8175 (mp10) REVERT: C 89 ASN cc_start: 0.8894 (m-40) cc_final: 0.8657 (m110) REVERT: C 90 ASP cc_start: 0.8579 (t0) cc_final: 0.7684 (t70) REVERT: C 92 GLU cc_start: 0.8156 (pm20) cc_final: 0.7887 (pm20) REVERT: D 34 LYS cc_start: 0.8038 (mppt) cc_final: 0.7807 (mppt) REVERT: D 57 LYS cc_start: 0.8273 (tppp) cc_final: 0.7595 (tppt) REVERT: D 68 ASP cc_start: 0.8883 (t70) cc_final: 0.8638 (t0) REVERT: E 42 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7284 (mtt180) REVERT: E 59 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7292 (pm20) REVERT: E 73 GLU cc_start: 0.8504 (tt0) cc_final: 0.8188 (tt0) REVERT: E 125 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: F 44 LYS cc_start: 0.8796 (ptpp) cc_final: 0.8541 (ptpp) REVERT: F 77 LYS cc_start: 0.8581 (mmtm) cc_final: 0.8302 (mmmm) REVERT: G 92 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7970 (mt-10) REVERT: H 34 LYS cc_start: 0.7848 (tptm) cc_final: 0.7380 (mmtm) REVERT: H 47 GLN cc_start: 0.8754 (tt0) cc_final: 0.8433 (tt0) REVERT: H 95 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: L 652 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6706 (pt0) REVERT: L 694 GLN cc_start: 0.8195 (mt0) cc_final: 0.7901 (mt0) REVERT: L 710 HIS cc_start: 0.6614 (OUTLIER) cc_final: 0.6320 (m-70) REVERT: N 333 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7871 (tmm) REVERT: N 337 ILE cc_start: 0.7977 (mt) cc_final: 0.7605 (mt) outliers start: 48 outliers final: 18 residues processed: 260 average time/residue: 0.6270 time to fit residues: 180.8386 Evaluate side-chains 236 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 333 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 94 ASN D 63 ASN D 84 ASN D 95 GLN L 84 HIS ** L 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.155544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130691 restraints weight = 43224.654| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.48 r_work: 0.3614 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 577 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 590 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18361 Z= 0.240 Angle : 0.694 13.405 26209 Z= 0.383 Chirality : 0.045 0.381 2960 Planarity : 0.005 0.074 2176 Dihedral : 29.832 133.887 5082 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.34 % Allowed : 20.21 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.23), residues: 1295 helix: 1.75 (0.18), residues: 793 sheet: -0.44 (0.59), residues: 81 loop : -0.70 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 86 TYR 0.013 0.002 TYR D 83 PHE 0.021 0.002 PHE N 313 TRP 0.014 0.002 TRP L 5 HIS 0.007 0.001 HIS L 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.24 (18360) covalent geometry : angle 0.69383 / 0.38 (26209) hydrogen bonds : bond 0.04352 / 2.93 ( 1027) hydrogen bonds : angle 3.54523 / 2.62 ( 2607) Misc. bond : bond 0.00025 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 220 time to evaluate : 0.356 Fit side-chains REVERT: A 79 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.6904 (tttt) REVERT: A 120 MET cc_start: 0.8715 (mtt) cc_final: 0.8277 (mtt) REVERT: A 123 ASP cc_start: 0.9003 (m-30) cc_final: 0.8774 (m-30) REVERT: C 24 GLN cc_start: 0.8347 (mm110) cc_final: 0.8132 (mm-40) REVERT: C 89 ASN cc_start: 0.8928 (m-40) cc_final: 0.8650 (m110) REVERT: C 90 ASP cc_start: 0.8505 (t0) cc_final: 0.7936 (t70) REVERT: C 92 GLU cc_start: 0.8077 (pm20) cc_final: 0.7748 (pm20) REVERT: C 104 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7900 (mm110) REVERT: D 57 LYS cc_start: 0.8446 (tppp) cc_final: 0.8008 (tptp) REVERT: D 68 ASP cc_start: 0.8997 (t70) cc_final: 0.8768 (t0) REVERT: E 42 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7306 (mtt180) REVERT: E 59 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: E 73 GLU cc_start: 0.8506 (tt0) cc_final: 0.7983 (tt0) REVERT: F 44 LYS cc_start: 0.8829 (ptpp) cc_final: 0.8578 (ptpp) REVERT: F 77 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8312 (mmmm) REVERT: G 92 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: H 34 LYS cc_start: 0.7975 (tptm) cc_final: 0.7504 (mmtm) REVERT: H 47 GLN cc_start: 0.8770 (tt0) cc_final: 0.8464 (tt0) REVERT: H 95 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: L 652 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6839 (pt0) REVERT: L 672 ASP cc_start: 0.7897 (p0) cc_final: 0.7693 (OUTLIER) REVERT: L 710 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.6481 (m-70) REVERT: N 337 ILE cc_start: 0.8031 (mt) cc_final: 0.7645 (mt) outliers start: 60 outliers final: 34 residues processed: 256 average time/residue: 0.5358 time to fit residues: 153.6533 Evaluate side-chains 244 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain L residue 679 ILE Chi-restraints excluded: chain L residue 698 VAL Chi-restraints excluded: chain L residue 710 HIS Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 286 PHE Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 324 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 157 optimal weight: 0.6980 chunk 115 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 94 ASN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN D 95 GLN E 68 GLN E 125 GLN L 133 ASN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.157980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133575 restraints weight = 42894.475| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.48 r_work: 0.3634 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 590 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 602 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18361 Z= 0.144 Angle : 0.646 11.679 26209 Z= 0.357 Chirality : 0.042 0.243 2960 Planarity : 0.004 0.063 2176 Dihedral : 29.811 134.308 5082 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.99 % Allowed : 20.39 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.23), residues: 1295 helix: 1.96 (0.18), residues: 794 sheet: -0.65 (0.58), residues: 81 loop : -0.54 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 74 TYR 0.015 0.002 TYR D 83 PHE 0.021 0.001 PHE L 118 TRP 0.015 0.002 TRP L 202 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (18360) covalent geometry : angle 0.64637 / 0.36 (26209) hydrogen bonds : bond 0.03779 / 2.52 ( 1027) hydrogen bonds : angle 3.36867 / 2.49 ( 2607) Misc. bond : bond 0.00139 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.333 Fit side-chains REVERT: A 79 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.6845 (tttt) REVERT: A 120 MET cc_start: 0.8606 (mtt) cc_final: 0.8048 (mtt) REVERT: A 123 ASP cc_start: 0.9030 (m-30) cc_final: 0.8776 (m-30) REVERT: A 125 GLN cc_start: 0.8702 (mt0) cc_final: 0.8479 (mt0) REVERT: C 89 ASN cc_start: 0.8934 (m-40) cc_final: 0.8660 (m110) REVERT: C 90 ASP cc_start: 0.8500 (t0) cc_final: 0.7393 (t70) REVERT: C 92 GLU cc_start: 0.8141 (pm20) cc_final: 0.7640 (pm20) REVERT: D 57 LYS cc_start: 0.8347 (tppp) cc_final: 0.7916 (tptp) REVERT: D 68 ASP cc_start: 0.8977 (t70) cc_final: 0.8769 (t0) REVERT: E 42 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7311 (mmt180) REVERT: E 59 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: E 73 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: F 35 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.8031 (mtp85) REVERT: F 44 LYS cc_start: 0.8754 (ptpp) cc_final: 0.8496 (ptpp) REVERT: F 77 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8321 (mmmm) REVERT: F 80 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8658 (p) REVERT: G 92 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7898 (mt-10) REVERT: H 34 LYS cc_start: 0.7961 (tptm) cc_final: 0.7495 (mmtm) REVERT: H 47 GLN cc_start: 0.8779 (tt0) cc_final: 0.8464 (tt0) REVERT: H 95 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: L 652 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6937 (pt0) REVERT: N 292 ASP cc_start: 0.6519 (p0) cc_final: 0.6202 (p0) REVERT: N 337 ILE cc_start: 0.8068 (mt) cc_final: 0.7735 (mt) outliers start: 56 outliers final: 29 residues processed: 250 average time/residue: 0.5206 time to fit residues: 145.7430 Evaluate side-chains 243 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain L residue 672 ASP Chi-restraints excluded: chain L residue 698 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 286 PHE Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 347 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 76 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 131 optimal weight: 0.1980 chunk 133 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 94 ASN D 49 HIS D 84 ASN E 125 GLN L 133 ASN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.157546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134105 restraints weight = 42822.061| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.52 r_work: 0.3626 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 602 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 599 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18361 Z= 0.150 Angle : 0.641 10.308 26209 Z= 0.354 Chirality : 0.042 0.243 2960 Planarity : 0.004 0.055 2176 Dihedral : 29.787 134.520 5082 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.90 % Allowed : 21.28 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.23), residues: 1295 helix: 2.01 (0.19), residues: 794 sheet: -0.65 (0.58), residues: 81 loop : -0.49 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 74 TYR 0.017 0.002 TYR D 83 PHE 0.018 0.001 PHE N 313 TRP 0.014 0.001 TRP L 202 HIS 0.008 0.001 HIS L 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (18360) covalent geometry : angle 0.64111 / 0.35 (26209) hydrogen bonds : bond 0.03791 / 2.53 ( 1027) hydrogen bonds : angle 3.32025 / 2.44 ( 2607) Misc. bond : bond 0.00081 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 217 time to evaluate : 0.418 Fit side-chains REVERT: A 79 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.6820 (tttt) REVERT: A 120 MET cc_start: 0.8617 (mtt) cc_final: 0.8101 (mtt) REVERT: A 123 ASP cc_start: 0.9021 (m-30) cc_final: 0.8774 (m-30) REVERT: A 125 GLN cc_start: 0.8731 (mt0) cc_final: 0.8241 (mp10) REVERT: C 24 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7240 (mm-40) REVERT: C 89 ASN cc_start: 0.8947 (m-40) cc_final: 0.8682 (m110) REVERT: C 90 ASP cc_start: 0.8514 (t0) cc_final: 0.7464 (t70) REVERT: C 92 GLU cc_start: 0.8159 (pm20) cc_final: 0.7790 (pm20) REVERT: D 57 LYS cc_start: 0.8371 (tppp) cc_final: 0.7935 (tptp) REVERT: D 113 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7681 (mm-30) REVERT: E 42 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7311 (mtt180) REVERT: E 59 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: E 73 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: F 35 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.7957 (ttp80) REVERT: F 44 LYS cc_start: 0.8767 (ptpp) cc_final: 0.8517 (ptpp) REVERT: F 77 LYS cc_start: 0.8636 (mmtm) cc_final: 0.8353 (mmmm) REVERT: F 92 ARG cc_start: 0.8840 (ptm-80) cc_final: 0.8540 (ptm160) REVERT: G 92 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: H 34 LYS cc_start: 0.7954 (tptm) cc_final: 0.7502 (mmtm) REVERT: H 47 GLN cc_start: 0.8774 (tt0) cc_final: 0.8453 (tt0) REVERT: H 95 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: L 652 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6977 (pt0) REVERT: N 292 ASP cc_start: 0.6383 (p0) cc_final: 0.6118 (p0) outliers start: 55 outliers final: 31 residues processed: 246 average time/residue: 0.4565 time to fit residues: 126.0129 Evaluate side-chains 246 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain L residue 672 ASP Chi-restraints excluded: chain L residue 698 VAL Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 286 PHE Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 347 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 37 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 68 GLN E 125 GLN L 133 ASN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.156671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132829 restraints weight = 42582.888| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.53 r_work: 0.3603 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 599 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 605 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18361 Z= 0.175 Angle : 0.659 13.114 26209 Z= 0.360 Chirality : 0.042 0.244 2960 Planarity : 0.004 0.055 2176 Dihedral : 29.801 134.165 5082 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.99 % Allowed : 21.46 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.23), residues: 1295 helix: 1.95 (0.18), residues: 794 sheet: -0.66 (0.58), residues: 81 loop : -0.53 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 74 TYR 0.018 0.002 TYR D 83 PHE 0.019 0.001 PHE N 313 TRP 0.013 0.002 TRP L 202 HIS 0.008 0.001 HIS L 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (18360) covalent geometry : angle 0.65884 / 0.36 (26209) hydrogen bonds : bond 0.03869 / 2.58 ( 1027) hydrogen bonds : angle 3.35018 / 2.46 ( 2607) Misc. bond : bond 0.00080 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 0.424 Fit side-chains REVERT: A 59 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: A 79 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.6796 (tttt) REVERT: A 120 MET cc_start: 0.8642 (mtt) cc_final: 0.8153 (mtt) REVERT: A 123 ASP cc_start: 0.9042 (m-30) cc_final: 0.8815 (m-30) REVERT: A 125 GLN cc_start: 0.8701 (mt0) cc_final: 0.8205 (mp10) REVERT: A 129 ARG cc_start: 0.8473 (tpt90) cc_final: 0.8078 (tpp80) REVERT: C 24 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7276 (mm-40) REVERT: C 89 ASN cc_start: 0.8978 (m-40) cc_final: 0.8694 (m110) REVERT: C 90 ASP cc_start: 0.8542 (t0) cc_final: 0.7953 (t70) REVERT: C 92 GLU cc_start: 0.8143 (pm20) cc_final: 0.7807 (pm20) REVERT: D 57 LYS cc_start: 0.8431 (tppp) cc_final: 0.7977 (tptp) REVERT: D 113 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7647 (mm-30) REVERT: E 42 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7308 (mtt180) REVERT: E 59 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: E 73 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: F 35 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.7972 (ttp80) REVERT: F 44 LYS cc_start: 0.8765 (ptpp) cc_final: 0.8546 (ptpp) REVERT: F 77 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8395 (mmmm) REVERT: F 92 ARG cc_start: 0.8867 (ptm-80) cc_final: 0.8600 (ptm160) REVERT: G 19 SER cc_start: 0.8585 (t) cc_final: 0.8211 (p) REVERT: G 92 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: H 34 LYS cc_start: 0.7985 (tptm) cc_final: 0.7514 (mmtm) REVERT: H 47 GLN cc_start: 0.8781 (tt0) cc_final: 0.8449 (tt0) REVERT: H 95 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8593 (tt0) REVERT: L 652 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7041 (pt0) REVERT: N 292 ASP cc_start: 0.6440 (p0) cc_final: 0.6164 (p0) outliers start: 56 outliers final: 33 residues processed: 249 average time/residue: 0.5312 time to fit residues: 147.5117 Evaluate side-chains 254 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain L residue 672 ASP Chi-restraints excluded: chain L residue 679 ILE Chi-restraints excluded: chain L residue 698 VAL Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 286 PHE Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 312 PHE Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 347 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 120 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 68 GLN E 125 GLN L 133 ASN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.156529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131962 restraints weight = 42839.389| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.47 r_work: 0.3630 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 605 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 609 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18361 Z= 0.174 Angle : 0.662 14.083 26209 Z= 0.361 Chirality : 0.043 0.244 2960 Planarity : 0.004 0.053 2176 Dihedral : 29.810 134.054 5082 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.45 % Allowed : 22.44 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.23), residues: 1295 helix: 1.92 (0.18), residues: 794 sheet: -0.69 (0.58), residues: 81 loop : -0.53 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 74 TYR 0.019 0.002 TYR D 83 PHE 0.018 0.001 PHE N 313 TRP 0.014 0.002 TRP L 202 HIS 0.007 0.001 HIS L 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (18360) covalent geometry : angle 0.66245 / 0.36 (26209) hydrogen bonds : bond 0.03838 / 2.56 ( 1027) hydrogen bonds : angle 3.37079 / 2.48 ( 2607) Misc. bond : bond 0.00095 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.386 Fit side-chains REVERT: A 79 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.6760 (tttt) REVERT: A 120 MET cc_start: 0.8650 (mtt) cc_final: 0.8175 (mtt) REVERT: A 123 ASP cc_start: 0.9029 (m-30) cc_final: 0.8784 (m-30) REVERT: A 125 GLN cc_start: 0.8663 (mt0) cc_final: 0.8162 (mp10) REVERT: A 129 ARG cc_start: 0.8504 (tpt90) cc_final: 0.8091 (tpp80) REVERT: C 18 SER cc_start: 0.8588 (m) cc_final: 0.8203 (m) REVERT: C 36 LYS cc_start: 0.8582 (mmpt) cc_final: 0.7952 (mmmm) REVERT: C 89 ASN cc_start: 0.8976 (m-40) cc_final: 0.8694 (m110) REVERT: C 90 ASP cc_start: 0.8516 (t0) cc_final: 0.7907 (t70) REVERT: C 92 GLU cc_start: 0.8148 (pm20) cc_final: 0.7891 (pm20) REVERT: D 57 LYS cc_start: 0.8404 (tppp) cc_final: 0.7958 (tptp) REVERT: E 42 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7306 (mtt180) REVERT: E 59 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: E 73 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: F 35 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.7900 (ttp80) REVERT: F 44 LYS cc_start: 0.8764 (ptpp) cc_final: 0.8538 (ptpp) REVERT: F 77 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8354 (mmmm) REVERT: F 92 ARG cc_start: 0.8849 (ptm-80) cc_final: 0.8620 (ptm160) REVERT: G 19 SER cc_start: 0.8641 (t) cc_final: 0.8260 (p) REVERT: G 62 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8369 (tt) REVERT: G 73 ASN cc_start: 0.8419 (t0) cc_final: 0.7924 (t0) REVERT: G 92 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: H 34 LYS cc_start: 0.7921 (tptm) cc_final: 0.7456 (mmtm) REVERT: H 95 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: L 652 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7065 (pt0) REVERT: N 292 ASP cc_start: 0.6587 (p0) cc_final: 0.6325 (p0) outliers start: 50 outliers final: 30 residues processed: 250 average time/residue: 0.4739 time to fit residues: 132.5593 Evaluate side-chains 251 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain L residue 679 ILE Chi-restraints excluded: chain L residue 698 VAL Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 286 PHE Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 312 PHE Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain N residue 347 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 73 optimal weight: 50.0000 chunk 151 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 68 GLN E 125 GLN L 133 ASN ** N 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.157250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132819 restraints weight = 42864.935| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.47 r_work: 0.3624 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 609 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 609 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18361 Z= 0.149 Angle : 0.664 14.663 26209 Z= 0.361 Chirality : 0.042 0.300 2960 Planarity : 0.004 0.058 2176 Dihedral : 29.762 134.304 5082 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.19 % Allowed : 23.24 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.23), residues: 1295 helix: 1.96 (0.18), residues: 788 sheet: -0.73 (0.64), residues: 67 loop : -0.39 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 74 TYR 0.022 0.002 TYR D 83 PHE 0.018 0.001 PHE N 313 TRP 0.014 0.001 TRP L 202 HIS 0.007 0.001 HIS L 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (18360) covalent geometry : angle 0.66445 / 0.36 (26209) hydrogen bonds : bond 0.03691 / 2.44 ( 1027) hydrogen bonds : angle 3.36488 / 2.47 ( 2607) Misc. bond : bond 0.00059 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.485 Fit side-chains REVERT: A 59 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: A 79 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.6707 (tttt) REVERT: A 120 MET cc_start: 0.8618 (mtt) cc_final: 0.8090 (mtt) REVERT: A 123 ASP cc_start: 0.9019 (m-30) cc_final: 0.8800 (m-30) REVERT: A 125 GLN cc_start: 0.8667 (mt0) cc_final: 0.8176 (mp10) REVERT: A 129 ARG cc_start: 0.8497 (tpt90) cc_final: 0.8095 (tpp80) REVERT: C 18 SER cc_start: 0.8505 (m) cc_final: 0.8125 (m) REVERT: C 89 ASN cc_start: 0.8976 (m-40) cc_final: 0.8699 (m110) REVERT: C 90 ASP cc_start: 0.8519 (t0) cc_final: 0.7906 (t70) REVERT: C 92 GLU cc_start: 0.8151 (pm20) cc_final: 0.7837 (pm20) REVERT: C 104 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7913 (mm-40) REVERT: D 57 LYS cc_start: 0.8427 (tppp) cc_final: 0.7965 (tptp) REVERT: E 42 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7292 (mtt180) REVERT: E 59 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: E 73 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: F 35 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.7903 (ttp80) REVERT: F 44 LYS cc_start: 0.8770 (ptpp) cc_final: 0.8532 (ptpp) REVERT: F 77 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8353 (mmmm) REVERT: F 92 ARG cc_start: 0.8905 (ptm-80) cc_final: 0.8515 (ptm160) REVERT: G 19 SER cc_start: 0.8633 (t) cc_final: 0.8259 (p) REVERT: G 62 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8416 (tt) REVERT: G 73 ASN cc_start: 0.8429 (t0) cc_final: 0.7925 (t0) REVERT: G 92 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: H 34 LYS cc_start: 0.7940 (tptm) cc_final: 0.7475 (mmtm) REVERT: H 95 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: L 652 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7135 (pt0) REVERT: N 292 ASP cc_start: 0.6575 (p0) cc_final: 0.6344 (p0) outliers start: 47 outliers final: 29 residues processed: 247 average time/residue: 0.5010 time to fit residues: 138.8848 Evaluate side-chains 256 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain L residue 679 ILE Chi-restraints excluded: chain L residue 698 VAL Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 312 PHE Chi-restraints excluded: chain N residue 347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 chunk 141 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 68 GLN E 125 GLN L 133 ASN ** N 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 294 GLN ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.157649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.133141 restraints weight = 42502.033| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.45 r_work: 0.3634 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 609 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 613 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18361 Z= 0.149 Angle : 0.662 12.949 26209 Z= 0.361 Chirality : 0.043 0.265 2960 Planarity : 0.004 0.050 2176 Dihedral : 29.722 134.252 5082 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.92 % Allowed : 24.04 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.23), residues: 1295 helix: 1.97 (0.18), residues: 787 sheet: -0.76 (0.61), residues: 73 loop : -0.34 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 86 TYR 0.026 0.002 TYR D 83 PHE 0.019 0.001 PHE N 313 TRP 0.014 0.001 TRP L 202 HIS 0.006 0.001 HIS L 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (18360) covalent geometry : angle 0.66199 / 0.36 (26209) hydrogen bonds : bond 0.03696 / 2.44 ( 1027) hydrogen bonds : angle 3.36335 / 2.47 ( 2607) Misc. bond : bond 0.00063 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.347 Fit side-chains REVERT: A 79 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.6725 (tttt) REVERT: A 120 MET cc_start: 0.8594 (mtt) cc_final: 0.8071 (mtt) REVERT: A 123 ASP cc_start: 0.8990 (m-30) cc_final: 0.8757 (m-30) REVERT: A 125 GLN cc_start: 0.8669 (mt0) cc_final: 0.8121 (mp10) REVERT: A 129 ARG cc_start: 0.8498 (tpt90) cc_final: 0.8111 (tpp80) REVERT: B 88 TYR cc_start: 0.8419 (m-10) cc_final: 0.8146 (m-10) REVERT: C 41 GLU cc_start: 0.8569 (tt0) cc_final: 0.8170 (tt0) REVERT: C 89 ASN cc_start: 0.8983 (m-40) cc_final: 0.8743 (m110) REVERT: C 90 ASP cc_start: 0.8506 (t0) cc_final: 0.7888 (t70) REVERT: C 92 GLU cc_start: 0.8133 (pm20) cc_final: 0.7816 (pm20) REVERT: C 104 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7915 (mm-40) REVERT: D 57 LYS cc_start: 0.8440 (tppp) cc_final: 0.7973 (tptp) REVERT: E 42 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7308 (mtt180) REVERT: E 59 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: E 73 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: F 35 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.7883 (ttp80) REVERT: F 44 LYS cc_start: 0.8770 (ptpp) cc_final: 0.8555 (ptmm) REVERT: F 77 LYS cc_start: 0.8619 (mmtm) cc_final: 0.8404 (mmmm) REVERT: F 92 ARG cc_start: 0.8892 (ptm-80) cc_final: 0.8611 (ptm160) REVERT: G 19 SER cc_start: 0.8599 (t) cc_final: 0.8227 (p) REVERT: G 62 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8410 (tt) REVERT: G 73 ASN cc_start: 0.8421 (t0) cc_final: 0.7908 (t0) REVERT: G 92 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: H 34 LYS cc_start: 0.7915 (tptm) cc_final: 0.7487 (mmtm) REVERT: H 95 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: K 78 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7539 (mtm180) REVERT: L 652 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7225 (pt0) REVERT: L 690 ASN cc_start: 0.8129 (t0) cc_final: 0.7727 (t0) REVERT: N 292 ASP cc_start: 0.6500 (p0) cc_final: 0.6151 (p0) outliers start: 44 outliers final: 31 residues processed: 246 average time/residue: 0.5266 time to fit residues: 144.5277 Evaluate side-chains 251 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 202 TRP Chi-restraints excluded: chain L residue 652 GLU Chi-restraints excluded: chain L residue 679 ILE Chi-restraints excluded: chain L residue 698 VAL Chi-restraints excluded: chain M residue 4 PHE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 305 SER Chi-restraints excluded: chain N residue 312 PHE Chi-restraints excluded: chain N residue 347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 111 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 73 optimal weight: 50.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 68 GLN E 125 GLN G 110 ASN L 133 ASN ** N 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.156253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131604 restraints weight = 42876.523| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.45 r_work: 0.3613 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 613 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 621 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18361 Z= 0.182 Angle : 0.668 12.517 26209 Z= 0.367 Chirality : 0.043 0.269 2960 Planarity : 0.005 0.051 2176 Dihedral : 29.753 133.741 5082 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.10 % Allowed : 23.78 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.23), residues: 1295 helix: 1.81 (0.18), residues: 795 sheet: -0.77 (0.61), residues: 73 loop : -0.49 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 86 TYR 0.031 0.002 TYR D 83 PHE 0.020 0.002 PHE N 313 TRP 0.013 0.002 TRP L 202 HIS 0.007 0.001 HIS L 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (18360) covalent geometry : angle 0.66806 / 0.37 (26209) hydrogen bonds : bond 0.03829 / 2.54 ( 1027) hydrogen bonds : angle 3.42066 / 2.51 ( 2607) Misc. bond : bond 0.00090 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5216.36 seconds wall clock time: 89 minutes 22.16 seconds (5362.16 seconds total)