Starting phenix.real_space_refine on Wed Mar 4 11:13:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nrv_0497/03_2026/6nrv_0497.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nrv_0497/03_2026/6nrv_0497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nrv_0497/03_2026/6nrv_0497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nrv_0497/03_2026/6nrv_0497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nrv_0497/03_2026/6nrv_0497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nrv_0497/03_2026/6nrv_0497.map" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.033 sd= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 8554 2.51 5 N 2236 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13637 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M Time building chain proxies: 1.21, per 1000 atoms: 0.09 Number of scatterers: 13637 At special positions: 0 Unit cell: (87.2, 88.29, 151.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 2808 8.00 N 2236 7.00 C 8554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 705.4 milliseconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 39 sheets defined 3.4% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 98 through 102 removed outlier: 4.004A pdb=" N GLY A 102 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 4.004A pdb=" N GLY B 102 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY C 102 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY D 102 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY E 102 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY F 102 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY G 102 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY H 102 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 102 removed outlier: 4.006A pdb=" N GLY I 102 " --> pdb=" O ALA I 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY J 102 " --> pdb=" O ALA J 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY K 102 " --> pdb=" O ALA K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY L 102 " --> pdb=" O ALA L 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY M 102 " --> pdb=" O ALA M 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 removed outlier: 7.774A pdb=" N LEU B 31 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR A 8 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 141 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL B 138 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN B 67 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP B 70 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 76 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.942A pdb=" N SER C 10 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 141 " --> pdb=" O LYS C 3 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 138 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN A 67 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 70 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 76 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 47 Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 96 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 10 removed outlier: 4.535A pdb=" N VAL D 138 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN D 67 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP D 70 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL D 76 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 47 Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 47 Processing sheet with id=AA9, first strand: chain 'C' and resid 94 through 96 Processing sheet with id=AB1, first strand: chain 'C' and resid 73 through 79 removed outlier: 6.342A pdb=" N VAL C 76 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP C 70 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN C 67 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL C 138 " --> pdb=" O GLN C 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 30 through 31 removed outlier: 7.939A pdb=" N LEU F 31 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR D 8 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL F 138 " --> pdb=" O GLN F 67 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN F 67 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP F 70 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL F 76 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 43 through 47 Processing sheet with id=AB4, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 31 removed outlier: 4.071A pdb=" N SER G 10 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL E 138 " --> pdb=" O GLN E 67 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN E 67 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP E 70 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL E 76 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 43 through 47 Processing sheet with id=AB7, first strand: chain 'E' and resid 94 through 96 Processing sheet with id=AB8, first strand: chain 'H' and resid 30 through 31 removed outlier: 8.033A pdb=" N LEU H 31 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR F 8 " --> pdb=" O LEU H 31 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU H 141 " --> pdb=" O LYS F 3 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL H 138 " --> pdb=" O GLN H 67 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN H 67 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP H 70 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL H 76 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 43 through 47 Processing sheet with id=AC1, first strand: chain 'F' and resid 94 through 96 Processing sheet with id=AC2, first strand: chain 'G' and resid 30 through 31 removed outlier: 3.915A pdb=" N SER I 10 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL G 138 " --> pdb=" O GLN G 67 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN G 67 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP G 70 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL G 76 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 43 through 47 Processing sheet with id=AC4, first strand: chain 'G' and resid 94 through 96 Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 10 removed outlier: 3.538A pdb=" N LEU J 141 " --> pdb=" O LYS H 3 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL J 138 " --> pdb=" O GLN J 67 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN J 67 " --> pdb=" O VAL J 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP J 70 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL J 76 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 43 through 47 Processing sheet with id=AC7, first strand: chain 'H' and resid 94 through 96 Processing sheet with id=AC8, first strand: chain 'I' and resid 43 through 47 Processing sheet with id=AC9, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AD1, first strand: chain 'I' and resid 73 through 79 removed outlier: 6.341A pdb=" N VAL I 76 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP I 70 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN I 67 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL I 138 " --> pdb=" O GLN I 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 3 through 10 removed outlier: 4.535A pdb=" N VAL L 138 " --> pdb=" O GLN L 67 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN L 67 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP L 70 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL L 76 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 43 through 47 Processing sheet with id=AD4, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AD5, first strand: chain 'K' and resid 30 through 31 removed outlier: 4.073A pdb=" N SER M 10 " --> pdb=" O LEU K 31 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU K 141 " --> pdb=" O LYS M 3 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL K 138 " --> pdb=" O GLN K 67 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN K 67 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP K 70 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL K 76 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 43 through 47 Processing sheet with id=AD7, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AD8, first strand: chain 'L' and resid 43 through 47 Processing sheet with id=AD9, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AE1, first strand: chain 'M' and resid 43 through 47 Processing sheet with id=AE2, first strand: chain 'M' and resid 94 through 96 Processing sheet with id=AE3, first strand: chain 'M' and resid 73 through 79 removed outlier: 6.341A pdb=" N VAL M 76 " --> pdb=" O ASP M 70 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP M 70 " --> pdb=" O VAL M 76 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4425 1.34 - 1.46: 2530 1.46 - 1.57: 6799 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 13832 Sorted by residual: bond pdb=" CA VAL A 29 " pdb=" CB VAL A 29 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.26e+00 bond pdb=" CA VAL M 29 " pdb=" CB VAL M 29 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.20e+00 bond pdb=" CA VAL E 29 " pdb=" CB VAL E 29 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.20e+00 bond pdb=" CA VAL I 29 " pdb=" CB VAL I 29 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.19e+00 bond pdb=" CA VAL J 29 " pdb=" CB VAL J 29 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.09e+00 ... (remaining 13827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 16181 1.22 - 2.43: 2158 2.43 - 3.65: 393 3.65 - 4.87: 133 4.87 - 6.08: 50 Bond angle restraints: 18915 Sorted by residual: angle pdb=" C ALA I 105 " pdb=" N SER I 106 " pdb=" CA SER I 106 " ideal model delta sigma weight residual 121.54 126.83 -5.29 1.91e+00 2.74e-01 7.68e+00 angle pdb=" C ALA D 105 " pdb=" N SER D 106 " pdb=" CA SER D 106 " ideal model delta sigma weight residual 121.54 126.83 -5.29 1.91e+00 2.74e-01 7.66e+00 angle pdb=" C ALA B 105 " pdb=" N SER B 106 " pdb=" CA SER B 106 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.64e+00 angle pdb=" C ALA J 105 " pdb=" N SER J 106 " pdb=" CA SER J 106 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.61e+00 angle pdb=" C ALA H 14 " pdb=" N ILE H 15 " pdb=" CA ILE H 15 " ideal model delta sigma weight residual 121.97 126.94 -4.97 1.80e+00 3.09e-01 7.61e+00 ... (remaining 18910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.39: 7384 8.39 - 16.78: 741 16.78 - 25.18: 182 25.18 - 33.57: 39 33.57 - 41.96: 39 Dihedral angle restraints: 8385 sinusoidal: 2912 harmonic: 5473 Sorted by residual: dihedral pdb=" CA ALA M 14 " pdb=" C ALA M 14 " pdb=" N ILE M 15 " pdb=" CA ILE M 15 " ideal model delta harmonic sigma weight residual 180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ALA K 14 " pdb=" C ALA K 14 " pdb=" N ILE K 15 " pdb=" CA ILE K 15 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ALA D 14 " pdb=" C ALA D 14 " pdb=" N ILE D 15 " pdb=" CA ILE D 15 " ideal model delta harmonic sigma weight residual 180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 8382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1312 0.030 - 0.061: 592 0.061 - 0.091: 230 0.091 - 0.121: 199 0.121 - 0.152: 85 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CA VAL J 45 " pdb=" N VAL J 45 " pdb=" C VAL J 45 " pdb=" CB VAL J 45 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA VAL K 45 " pdb=" N VAL K 45 " pdb=" C VAL K 45 " pdb=" CB VAL K 45 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA VAL C 45 " pdb=" N VAL C 45 " pdb=" C VAL C 45 " pdb=" CB VAL C 45 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 2415 not shown) Planarity restraints: 2392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 95 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.78e+00 pdb=" CD GLU I 95 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU I 95 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU I 95 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 95 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" CD GLU K 95 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU K 95 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU K 95 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 95 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" CD GLU E 95 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU E 95 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU E 95 " 0.008 2.00e-02 2.50e+03 ... (remaining 2389 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 141 2.56 - 3.14: 12164 3.14 - 3.73: 19943 3.73 - 4.31: 29518 4.31 - 4.90: 47167 Nonbonded interactions: 108933 Sorted by model distance: nonbonded pdb=" OE2 GLU H 2 " pdb=" OG SER J 140 " model vdw 1.971 3.040 nonbonded pdb=" OE2 GLU J 2 " pdb=" OG SER L 140 " model vdw 1.973 3.040 nonbonded pdb=" NZ LYS D 3 " pdb=" O LEU F 17 " model vdw 2.043 3.120 nonbonded pdb=" O LEU G 17 " pdb=" NZ LYS I 3 " model vdw 2.063 3.120 nonbonded pdb=" O LEU A 17 " pdb=" NZ LYS C 3 " model vdw 2.079 3.120 ... (remaining 108928 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.750 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 13832 Z= 0.319 Angle : 0.955 6.084 18915 Z= 0.506 Chirality : 0.051 0.152 2418 Planarity : 0.005 0.027 2392 Dihedral : 8.189 41.961 4849 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.59 (0.16), residues: 1872 helix: None (None), residues: 0 sheet: -3.10 (0.15), residues: 702 loop : -3.13 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.003 ARG A 44 TYR 0.008 0.002 TYR K 33 PHE 0.008 0.002 PHE K 40 TRP 0.015 0.005 TRP I 84 HIS 0.002 0.001 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00728 (13832) covalent geometry : angle 0.95530 (18915) hydrogen bonds : bond 0.26411 ( 394) hydrogen bonds : angle 14.29002 ( 873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.447 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7021 (p0) cc_final: 0.6197 (m-30) REVERT: B 16 ASP cc_start: 0.7535 (p0) cc_final: 0.6658 (p0) REVERT: B 17 LEU cc_start: 0.8482 (tp) cc_final: 0.8116 (pt) REVERT: C 16 ASP cc_start: 0.7771 (p0) cc_final: 0.7391 (m-30) REVERT: C 21 ASP cc_start: 0.8811 (p0) cc_final: 0.8504 (p0) REVERT: D 16 ASP cc_start: 0.7880 (p0) cc_final: 0.7313 (p0) REVERT: D 21 ASP cc_start: 0.8597 (p0) cc_final: 0.8283 (p0) REVERT: E 16 ASP cc_start: 0.7314 (p0) cc_final: 0.6598 (m-30) REVERT: E 17 LEU cc_start: 0.8585 (tp) cc_final: 0.8319 (pt) REVERT: F 16 ASP cc_start: 0.7629 (p0) cc_final: 0.7418 (m-30) REVERT: F 19 GLN cc_start: 0.7982 (tp40) cc_final: 0.7697 (mm-40) REVERT: F 21 ASP cc_start: 0.8680 (p0) cc_final: 0.8317 (p0) REVERT: F 23 ASN cc_start: 0.8489 (m-40) cc_final: 0.8276 (m-40) REVERT: G 16 ASP cc_start: 0.7568 (p0) cc_final: 0.6969 (m-30) REVERT: G 17 LEU cc_start: 0.8671 (tp) cc_final: 0.8437 (pt) REVERT: G 21 ASP cc_start: 0.8784 (p0) cc_final: 0.8548 (p0) REVERT: I 17 LEU cc_start: 0.8747 (tp) cc_final: 0.8531 (pt) REVERT: I 21 ASP cc_start: 0.8451 (p0) cc_final: 0.7678 (p0) REVERT: J 16 ASP cc_start: 0.7204 (p0) cc_final: 0.6554 (p0) REVERT: J 17 LEU cc_start: 0.8305 (tp) cc_final: 0.8099 (pt) REVERT: K 17 LEU cc_start: 0.8391 (tp) cc_final: 0.8108 (pt) REVERT: L 16 ASP cc_start: 0.7135 (p0) cc_final: 0.6258 (m-30) REVERT: M 16 ASP cc_start: 0.7471 (p0) cc_final: 0.6811 (m-30) REVERT: M 21 ASP cc_start: 0.8471 (p0) cc_final: 0.8208 (p0) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.1197 time to fit residues: 67.2727 Evaluate side-chains 181 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 40.0000 chunk 149 optimal weight: 6.9990 overall best weight: 12.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.049842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.045005 restraints weight = 97872.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.046059 restraints weight = 61013.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.046761 restraints weight = 41650.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.047281 restraints weight = 30450.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.047663 restraints weight = 23278.633| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13832 Z= 0.253 Angle : 0.796 7.903 18915 Z= 0.421 Chirality : 0.047 0.143 2418 Planarity : 0.005 0.033 2392 Dihedral : 6.863 26.794 1950 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 2.76 % Allowed : 5.72 % Favored : 91.52 % 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: -3.59 (0.17), residues: 1872 helix: None (None), residues: 0 sheet: -2.31 (0.16), residues: 806 loop : -2.45 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 44 TYR 0.026 0.003 TYR B 43 PHE 0.011 0.003 PHE H 96 TRP 0.013 0.002 TRP C 84 HIS 0.005 0.002 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00542 (13832) covalent geometry : angle 0.79560 (18915) hydrogen bonds : bond 0.05287 ( 394) hydrogen bonds : angle 8.18830 ( 873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.510 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7965 (p0) cc_final: 0.7369 (p0) REVERT: A 46 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7547 (mmp) REVERT: A 71 VAL cc_start: 0.8594 (m) cc_final: 0.8249 (m) REVERT: B 16 ASP cc_start: 0.7960 (p0) cc_final: 0.7147 (p0) REVERT: C 16 ASP cc_start: 0.8091 (p0) cc_final: 0.7456 (p0) REVERT: C 21 ASP cc_start: 0.8798 (p0) cc_final: 0.8485 (p0) REVERT: C 46 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7757 (mmm) REVERT: D 16 ASP cc_start: 0.8070 (p0) cc_final: 0.7585 (p0) REVERT: D 116 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.6129 (pm20) REVERT: E 16 ASP cc_start: 0.7946 (p0) cc_final: 0.7252 (p0) REVERT: F 16 ASP cc_start: 0.7871 (p0) cc_final: 0.7364 (p0) REVERT: G 19 GLN cc_start: 0.7978 (tp40) cc_final: 0.7775 (tp40) REVERT: G 21 ASP cc_start: 0.9034 (p0) cc_final: 0.8555 (p0) REVERT: G 23 ASN cc_start: 0.8725 (m-40) cc_final: 0.8266 (m110) REVERT: H 16 ASP cc_start: 0.8085 (p0) cc_final: 0.7768 (p0) REVERT: I 21 ASP cc_start: 0.8700 (p0) cc_final: 0.7734 (p0) REVERT: J 16 ASP cc_start: 0.7950 (p0) cc_final: 0.7341 (p0) REVERT: J 19 GLN cc_start: 0.7467 (tp40) cc_final: 0.7073 (tp40) REVERT: K 16 ASP cc_start: 0.7894 (p0) cc_final: 0.7476 (p0) REVERT: L 16 ASP cc_start: 0.8101 (p0) cc_final: 0.7480 (p0) REVERT: M 19 GLN cc_start: 0.7685 (tp40) cc_final: 0.7465 (tp40) outliers start: 42 outliers final: 23 residues processed: 210 average time/residue: 0.0859 time to fit residues: 29.1072 Evaluate side-chains 165 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain J residue 131 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain L residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 165 optimal weight: 20.0000 chunk 158 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 58 optimal weight: 50.0000 chunk 37 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 115 optimal weight: 2.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN D 87 GLN ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.049350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.044056 restraints weight = 96075.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.045201 restraints weight = 56261.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.046030 restraints weight = 37261.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046605 restraints weight = 26546.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.047032 restraints weight = 20107.682| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13832 Z= 0.154 Angle : 0.686 7.003 18915 Z= 0.362 Chirality : 0.044 0.138 2418 Planarity : 0.004 0.034 2392 Dihedral : 6.234 28.946 1950 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.97 % Allowed : 7.76 % Favored : 90.27 % 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: -2.83 (0.17), residues: 1872 helix: None (None), residues: 0 sheet: -1.45 (0.18), residues: 676 loop : -2.24 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 44 TYR 0.020 0.002 TYR G 43 PHE 0.010 0.002 PHE G 96 TRP 0.009 0.001 TRP C 84 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00338 (13832) covalent geometry : angle 0.68590 (18915) hydrogen bonds : bond 0.03823 ( 394) hydrogen bonds : angle 6.73689 ( 873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.507 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 16 ASP cc_start: 0.8067 (p0) cc_final: 0.7404 (p0) REVERT: A 143 MET cc_start: 0.8863 (tmm) cc_final: 0.8479 (tmm) REVERT: B 16 ASP cc_start: 0.8157 (p0) cc_final: 0.7371 (p0) REVERT: C 16 ASP cc_start: 0.8204 (p0) cc_final: 0.7601 (p0) REVERT: C 143 MET cc_start: 0.8783 (tmm) cc_final: 0.8558 (tmm) REVERT: D 16 ASP cc_start: 0.8391 (p0) cc_final: 0.8024 (p0) REVERT: E 16 ASP cc_start: 0.8105 (p0) cc_final: 0.7569 (p0) REVERT: F 16 ASP cc_start: 0.8052 (p0) cc_final: 0.7501 (p0) REVERT: F 103 TYR cc_start: 0.7408 (m-80) cc_final: 0.7197 (m-10) REVERT: G 23 ASN cc_start: 0.8942 (m-40) cc_final: 0.8580 (m110) REVERT: H 16 ASP cc_start: 0.8187 (p0) cc_final: 0.7562 (p0) REVERT: I 21 ASP cc_start: 0.8758 (p0) cc_final: 0.8335 (p0) REVERT: I 23 ASN cc_start: 0.8860 (m-40) cc_final: 0.8190 (m-40) REVERT: J 16 ASP cc_start: 0.8066 (p0) cc_final: 0.7511 (p0) REVERT: J 19 GLN cc_start: 0.7802 (tp40) cc_final: 0.7413 (tp40) REVERT: K 143 MET cc_start: 0.8606 (tmm) cc_final: 0.8247 (tmm) REVERT: L 16 ASP cc_start: 0.8410 (p0) cc_final: 0.7675 (p0) REVERT: L 23 ASN cc_start: 0.8440 (m-40) cc_final: 0.8018 (m110) REVERT: M 19 GLN cc_start: 0.7815 (tp40) cc_final: 0.7498 (tp40) outliers start: 30 outliers final: 20 residues processed: 183 average time/residue: 0.0875 time to fit residues: 25.5978 Evaluate side-chains 152 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 16 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 142 optimal weight: 0.4980 chunk 178 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 104 optimal weight: 20.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 19 GLN ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.049852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.044619 restraints weight = 96743.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.045710 restraints weight = 58390.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.046507 restraints weight = 39617.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.047087 restraints weight = 28525.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.047509 restraints weight = 21738.160| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13832 Z= 0.126 Angle : 0.655 7.323 18915 Z= 0.344 Chirality : 0.044 0.139 2418 Planarity : 0.004 0.037 2392 Dihedral : 5.789 28.123 1950 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 1.64 % Allowed : 9.20 % Favored : 89.15 % 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: -2.50 (0.17), residues: 1872 helix: None (None), residues: 0 sheet: -1.08 (0.19), residues: 663 loop : -2.10 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 44 TYR 0.027 0.002 TYR K 43 PHE 0.008 0.002 PHE H 96 TRP 0.007 0.001 TRP C 84 HIS 0.001 0.000 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00272 (13832) covalent geometry : angle 0.65503 (18915) hydrogen bonds : bond 0.03429 ( 394) hydrogen bonds : angle 6.20556 ( 873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7875 (p0) cc_final: 0.7274 (p0) REVERT: A 78 MET cc_start: 0.8971 (mmm) cc_final: 0.8382 (mmm) REVERT: B 16 ASP cc_start: 0.7929 (p0) cc_final: 0.7356 (p0) REVERT: C 16 ASP cc_start: 0.8089 (p0) cc_final: 0.7449 (p0) REVERT: C 43 TYR cc_start: 0.7566 (t80) cc_final: 0.7231 (t80) REVERT: C 103 TYR cc_start: 0.7059 (m-10) cc_final: 0.6835 (m-10) REVERT: C 143 MET cc_start: 0.8662 (tmm) cc_final: 0.8352 (tmm) REVERT: D 16 ASP cc_start: 0.8281 (p0) cc_final: 0.8029 (p0) REVERT: E 16 ASP cc_start: 0.7978 (p0) cc_final: 0.7421 (p0) REVERT: F 16 ASP cc_start: 0.7858 (p0) cc_final: 0.7522 (p0) REVERT: G 23 ASN cc_start: 0.8819 (m-40) cc_final: 0.8514 (m110) REVERT: G 143 MET cc_start: 0.8588 (tmm) cc_final: 0.8370 (tmm) REVERT: H 15 ILE cc_start: 0.2807 (OUTLIER) cc_final: 0.2567 (mt) REVERT: H 16 ASP cc_start: 0.8159 (p0) cc_final: 0.7678 (p0) REVERT: I 23 ASN cc_start: 0.8792 (m-40) cc_final: 0.8468 (m110) REVERT: I 143 MET cc_start: 0.8792 (tmm) cc_final: 0.8565 (tmm) REVERT: J 16 ASP cc_start: 0.7902 (p0) cc_final: 0.7627 (p0) REVERT: J 19 GLN cc_start: 0.7550 (tp40) cc_final: 0.7170 (tp40) REVERT: K 23 ASN cc_start: 0.8890 (m-40) cc_final: 0.8320 (m110) REVERT: K 78 MET cc_start: 0.8511 (mmm) cc_final: 0.8285 (mmm) REVERT: L 16 ASP cc_start: 0.8212 (p0) cc_final: 0.7631 (p0) REVERT: L 23 ASN cc_start: 0.8421 (m-40) cc_final: 0.8034 (m110) REVERT: M 19 GLN cc_start: 0.7661 (tp40) cc_final: 0.7410 (tp40) outliers start: 25 outliers final: 20 residues processed: 174 average time/residue: 0.0862 time to fit residues: 24.2926 Evaluate side-chains 147 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 109 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 78 optimal weight: 30.0000 chunk 168 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 61 optimal weight: 50.0000 chunk 159 optimal weight: 50.0000 chunk 102 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 91 optimal weight: 30.0000 chunk 88 optimal weight: 50.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041571 restraints weight = 102828.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.042658 restraints weight = 60592.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.043412 restraints weight = 40665.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.043973 restraints weight = 29870.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044378 restraints weight = 22952.838| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13832 Z= 0.282 Angle : 0.809 7.721 18915 Z= 0.420 Chirality : 0.045 0.144 2418 Planarity : 0.005 0.041 2392 Dihedral : 6.468 27.069 1950 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 3.42 % Allowed : 9.27 % Favored : 87.31 % 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: -2.49 (0.18), residues: 1872 helix: None (None), residues: 0 sheet: -1.01 (0.19), residues: 702 loop : -2.16 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 44 TYR 0.027 0.003 TYR E 43 PHE 0.023 0.003 PHE A 96 TRP 0.011 0.002 TRP C 84 HIS 0.005 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00605 (13832) covalent geometry : angle 0.80917 (18915) hydrogen bonds : bond 0.03789 ( 394) hydrogen bonds : angle 6.65828 ( 873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 VAL cc_start: 0.6113 (OUTLIER) cc_final: 0.5665 (m) REVERT: A 15 ILE cc_start: 0.4513 (OUTLIER) cc_final: 0.4128 (mt) REVERT: A 16 ASP cc_start: 0.8191 (p0) cc_final: 0.7685 (p0) REVERT: A 78 MET cc_start: 0.8949 (mmm) cc_final: 0.8312 (mmm) REVERT: A 143 MET cc_start: 0.8741 (tmm) cc_final: 0.8541 (tmm) REVERT: B 16 ASP cc_start: 0.8340 (p0) cc_final: 0.7517 (p0) REVERT: B 87 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: B 103 TYR cc_start: 0.7408 (m-10) cc_final: 0.7153 (m-10) REVERT: B 143 MET cc_start: 0.8589 (tmm) cc_final: 0.7916 (tmm) REVERT: C 1 VAL cc_start: 0.6047 (OUTLIER) cc_final: 0.5755 (m) REVERT: C 15 ILE cc_start: 0.4650 (OUTLIER) cc_final: 0.4145 (mt) REVERT: C 16 ASP cc_start: 0.8344 (p0) cc_final: 0.7741 (p0) REVERT: D 15 ILE cc_start: 0.4859 (OUTLIER) cc_final: 0.4515 (mt) REVERT: D 16 ASP cc_start: 0.8516 (p0) cc_final: 0.8074 (p0) REVERT: D 23 ASN cc_start: 0.8828 (m-40) cc_final: 0.8594 (m110) REVERT: E 1 VAL cc_start: 0.6722 (OUTLIER) cc_final: 0.5960 (m) REVERT: E 15 ILE cc_start: 0.4649 (OUTLIER) cc_final: 0.4296 (mt) REVERT: E 16 ASP cc_start: 0.8272 (p0) cc_final: 0.7974 (p0) REVERT: E 46 MET cc_start: 0.8093 (mmm) cc_final: 0.7798 (mmm) REVERT: F 15 ILE cc_start: 0.4770 (OUTLIER) cc_final: 0.4192 (mt) REVERT: F 16 ASP cc_start: 0.8213 (p0) cc_final: 0.7601 (p0) REVERT: F 23 ASN cc_start: 0.8961 (m-40) cc_final: 0.8619 (m-40) REVERT: G 15 ILE cc_start: 0.5250 (OUTLIER) cc_final: 0.4603 (mt) REVERT: G 78 MET cc_start: 0.8769 (mmm) cc_final: 0.8409 (mmm) REVERT: H 15 ILE cc_start: 0.4156 (OUTLIER) cc_final: 0.3956 (mt) REVERT: H 16 ASP cc_start: 0.8404 (p0) cc_final: 0.7951 (p0) REVERT: I 23 ASN cc_start: 0.8782 (m-40) cc_final: 0.8484 (m-40) REVERT: I 143 MET cc_start: 0.8919 (tmm) cc_final: 0.8135 (tmm) REVERT: J 15 ILE cc_start: 0.5163 (OUTLIER) cc_final: 0.4739 (mt) REVERT: J 16 ASP cc_start: 0.8135 (p0) cc_final: 0.7781 (p0) REVERT: K 1 VAL cc_start: 0.6991 (OUTLIER) cc_final: 0.6559 (m) REVERT: K 15 ILE cc_start: 0.4671 (OUTLIER) cc_final: 0.4282 (mt) REVERT: K 16 ASP cc_start: 0.8100 (p0) cc_final: 0.7724 (p0) REVERT: K 23 ASN cc_start: 0.8962 (m-40) cc_final: 0.8436 (m-40) REVERT: L 16 ASP cc_start: 0.8365 (p0) cc_final: 0.7846 (p0) REVERT: L 23 ASN cc_start: 0.8644 (m-40) cc_final: 0.8336 (m110) REVERT: M 15 ILE cc_start: 0.4988 (OUTLIER) cc_final: 0.4561 (mt) REVERT: M 19 GLN cc_start: 0.7967 (tp40) cc_final: 0.7473 (tp40) REVERT: M 23 ASN cc_start: 0.8971 (m-40) cc_final: 0.8540 (m-40) outliers start: 52 outliers final: 31 residues processed: 172 average time/residue: 0.0860 time to fit residues: 24.3100 Evaluate side-chains 162 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 116 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain K residue 1 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 109 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 74 optimal weight: 8.9990 chunk 121 optimal weight: 0.0770 chunk 82 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 154 optimal weight: 30.0000 chunk 159 optimal weight: 30.0000 chunk 109 optimal weight: 30.0000 chunk 150 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 overall best weight: 5.1346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 HIS ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.048314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042988 restraints weight = 98848.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.044133 restraints weight = 58589.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.044924 restraints weight = 39035.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.045510 restraints weight = 28294.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.045935 restraints weight = 21635.404| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13832 Z= 0.127 Angle : 0.664 10.237 18915 Z= 0.346 Chirality : 0.043 0.143 2418 Planarity : 0.005 0.043 2392 Dihedral : 5.818 27.574 1950 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.70 % Allowed : 10.12 % Favored : 87.18 % 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: -2.11 (0.18), residues: 1872 helix: None (None), residues: 0 sheet: -0.45 (0.20), residues: 676 loop : -2.10 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 44 TYR 0.025 0.002 TYR M 43 PHE 0.011 0.002 PHE L 96 TRP 0.010 0.002 TRP C 84 HIS 0.002 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00284 (13832) covalent geometry : angle 0.66401 (18915) hydrogen bonds : bond 0.03220 ( 394) hydrogen bonds : angle 6.06798 ( 873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 VAL cc_start: 0.6448 (OUTLIER) cc_final: 0.5898 (m) REVERT: A 15 ILE cc_start: 0.4443 (OUTLIER) cc_final: 0.3957 (mt) REVERT: A 16 ASP cc_start: 0.7961 (p0) cc_final: 0.7493 (p0) REVERT: A 78 MET cc_start: 0.9008 (mmm) cc_final: 0.8771 (mmm) REVERT: B 16 ASP cc_start: 0.8212 (p0) cc_final: 0.7528 (p0) REVERT: B 87 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: B 103 TYR cc_start: 0.7473 (m-10) cc_final: 0.7230 (m-10) REVERT: B 143 MET cc_start: 0.8613 (tmm) cc_final: 0.7820 (tmm) REVERT: C 16 ASP cc_start: 0.8186 (p0) cc_final: 0.7538 (p0) REVERT: D 15 ILE cc_start: 0.4383 (OUTLIER) cc_final: 0.4005 (mt) REVERT: D 16 ASP cc_start: 0.8353 (p0) cc_final: 0.8042 (p0) REVERT: D 103 TYR cc_start: 0.7336 (m-10) cc_final: 0.7088 (m-10) REVERT: E 15 ILE cc_start: 0.4484 (OUTLIER) cc_final: 0.4060 (mt) REVERT: F 15 ILE cc_start: 0.4360 (OUTLIER) cc_final: 0.3869 (mt) REVERT: F 16 ASP cc_start: 0.8001 (p0) cc_final: 0.7534 (p0) REVERT: F 23 ASN cc_start: 0.8929 (m-40) cc_final: 0.8640 (m-40) REVERT: G 78 MET cc_start: 0.8771 (mmm) cc_final: 0.8418 (mmm) REVERT: H 15 ILE cc_start: 0.3903 (OUTLIER) cc_final: 0.3613 (mt) REVERT: H 16 ASP cc_start: 0.8230 (p0) cc_final: 0.7756 (p0) REVERT: I 23 ASN cc_start: 0.8759 (m-40) cc_final: 0.8469 (m110) REVERT: I 78 MET cc_start: 0.8613 (mmm) cc_final: 0.8115 (mmm) REVERT: I 143 MET cc_start: 0.8790 (tmm) cc_final: 0.8258 (tmm) REVERT: J 16 ASP cc_start: 0.7909 (p0) cc_final: 0.7565 (p0) REVERT: J 43 TYR cc_start: 0.8025 (t80) cc_final: 0.7627 (t80) REVERT: J 78 MET cc_start: 0.9050 (mmm) cc_final: 0.8730 (mmm) REVERT: K 1 VAL cc_start: 0.6849 (OUTLIER) cc_final: 0.6528 (m) REVERT: K 16 ASP cc_start: 0.8005 (p0) cc_final: 0.7689 (p0) REVERT: K 23 ASN cc_start: 0.8931 (m-40) cc_final: 0.8416 (m-40) REVERT: L 16 ASP cc_start: 0.8319 (p0) cc_final: 0.7777 (p0) REVERT: L 23 ASN cc_start: 0.8669 (m-40) cc_final: 0.8342 (m110) REVERT: L 78 MET cc_start: 0.8389 (tpp) cc_final: 0.7995 (tmm) REVERT: M 19 GLN cc_start: 0.7893 (tp40) cc_final: 0.7404 (tp40) outliers start: 41 outliers final: 29 residues processed: 174 average time/residue: 0.0928 time to fit residues: 25.1846 Evaluate side-chains 154 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain K residue 1 VAL Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 104 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 chunk 115 optimal weight: 9.9990 chunk 129 optimal weight: 30.0000 chunk 13 optimal weight: 40.0000 chunk 141 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 40.0000 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 30.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.048876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.043497 restraints weight = 96608.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.044655 restraints weight = 56744.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.045449 restraints weight = 37998.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.046041 restraints weight = 27648.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046473 restraints weight = 21216.494| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13832 Z= 0.113 Angle : 0.645 7.974 18915 Z= 0.336 Chirality : 0.043 0.143 2418 Planarity : 0.004 0.044 2392 Dihedral : 5.454 27.190 1950 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.89 % Allowed : 11.24 % Favored : 85.86 % 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: -1.94 (0.18), residues: 1872 helix: None (None), residues: 0 sheet: -0.30 (0.21), residues: 663 loop : -1.99 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 44 TYR 0.031 0.002 TYR A 43 PHE 0.006 0.001 PHE J 96 TRP 0.007 0.001 TRP L 84 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00252 (13832) covalent geometry : angle 0.64451 (18915) hydrogen bonds : bond 0.03041 ( 394) hydrogen bonds : angle 5.73633 ( 873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 VAL cc_start: 0.6527 (OUTLIER) cc_final: 0.5890 (m) REVERT: A 15 ILE cc_start: 0.3988 (OUTLIER) cc_final: 0.3554 (mt) REVERT: A 16 ASP cc_start: 0.7923 (p0) cc_final: 0.7470 (p0) REVERT: A 23 ASN cc_start: 0.8810 (m-40) cc_final: 0.8535 (m110) REVERT: A 78 MET cc_start: 0.8969 (mmm) cc_final: 0.8620 (mmm) REVERT: B 15 ILE cc_start: 0.4392 (OUTLIER) cc_final: 0.3589 (mt) REVERT: B 16 ASP cc_start: 0.8123 (p0) cc_final: 0.7617 (p0) REVERT: B 87 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: B 103 TYR cc_start: 0.7368 (m-10) cc_final: 0.7115 (m-10) REVERT: B 143 MET cc_start: 0.8614 (tmm) cc_final: 0.7828 (tmm) REVERT: C 16 ASP cc_start: 0.8271 (p0) cc_final: 0.7649 (p0) REVERT: C 78 MET cc_start: 0.9086 (mmm) cc_final: 0.8486 (mmm) REVERT: C 103 TYR cc_start: 0.7499 (m-80) cc_final: 0.7210 (m-10) REVERT: D 15 ILE cc_start: 0.4402 (OUTLIER) cc_final: 0.4023 (mt) REVERT: D 16 ASP cc_start: 0.8328 (p0) cc_final: 0.8000 (p0) REVERT: D 21 ASP cc_start: 0.9172 (p0) cc_final: 0.8800 (p0) REVERT: D 23 ASN cc_start: 0.8852 (m-40) cc_final: 0.8519 (m-40) REVERT: E 15 ILE cc_start: 0.4686 (OUTLIER) cc_final: 0.4287 (mt) REVERT: F 15 ILE cc_start: 0.4247 (OUTLIER) cc_final: 0.3797 (mt) REVERT: F 16 ASP cc_start: 0.7938 (p0) cc_final: 0.7478 (p0) REVERT: F 23 ASN cc_start: 0.8913 (m-40) cc_final: 0.8631 (m-40) REVERT: G 78 MET cc_start: 0.8743 (mmm) cc_final: 0.8349 (mmm) REVERT: H 15 ILE cc_start: 0.3837 (OUTLIER) cc_final: 0.3495 (mt) REVERT: H 16 ASP cc_start: 0.8209 (p0) cc_final: 0.7742 (p0) REVERT: I 23 ASN cc_start: 0.8861 (m-40) cc_final: 0.8565 (m-40) REVERT: I 78 MET cc_start: 0.8643 (mmm) cc_final: 0.8224 (mmm) REVERT: I 143 MET cc_start: 0.8726 (tmm) cc_final: 0.8322 (tmm) REVERT: J 15 ILE cc_start: 0.4940 (OUTLIER) cc_final: 0.4263 (mt) REVERT: J 43 TYR cc_start: 0.8074 (t80) cc_final: 0.7828 (t80) REVERT: J 78 MET cc_start: 0.8982 (mmm) cc_final: 0.8746 (mmm) REVERT: K 1 VAL cc_start: 0.6771 (OUTLIER) cc_final: 0.6124 (m) REVERT: K 15 ILE cc_start: 0.4616 (OUTLIER) cc_final: 0.4239 (mt) REVERT: K 23 ASN cc_start: 0.8930 (m-40) cc_final: 0.8399 (m-40) REVERT: L 16 ASP cc_start: 0.8287 (p0) cc_final: 0.7748 (p0) REVERT: L 23 ASN cc_start: 0.8653 (m-40) cc_final: 0.8201 (m110) REVERT: L 78 MET cc_start: 0.8340 (tpp) cc_final: 0.8085 (mmm) REVERT: M 19 GLN cc_start: 0.7814 (tp40) cc_final: 0.7303 (tp40) outliers start: 44 outliers final: 28 residues processed: 173 average time/residue: 0.0946 time to fit residues: 25.9824 Evaluate side-chains 159 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain K residue 1 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 170 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 169 optimal weight: 0.0970 chunk 94 optimal weight: 30.0000 chunk 99 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 11 optimal weight: 40.0000 chunk 55 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 GLN ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.048760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.043403 restraints weight = 96486.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.044543 restraints weight = 56991.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.045364 restraints weight = 38115.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.045887 restraints weight = 27525.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.046360 restraints weight = 21631.676| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13832 Z= 0.119 Angle : 0.642 7.468 18915 Z= 0.334 Chirality : 0.043 0.139 2418 Planarity : 0.004 0.042 2392 Dihedral : 5.381 27.956 1950 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.96 % Allowed : 11.31 % Favored : 85.73 % 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: -1.83 (0.19), residues: 1872 helix: None (None), residues: 0 sheet: 0.06 (0.21), residues: 689 loop : -2.15 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 44 TYR 0.033 0.002 TYR F 43 PHE 0.006 0.001 PHE F 96 TRP 0.007 0.001 TRP L 84 HIS 0.001 0.000 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00267 (13832) covalent geometry : angle 0.64165 (18915) hydrogen bonds : bond 0.02985 ( 394) hydrogen bonds : angle 5.58019 ( 873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 VAL cc_start: 0.6535 (OUTLIER) cc_final: 0.5970 (m) REVERT: A 15 ILE cc_start: 0.4366 (OUTLIER) cc_final: 0.3871 (mt) REVERT: A 16 ASP cc_start: 0.7922 (p0) cc_final: 0.7499 (p0) REVERT: A 23 ASN cc_start: 0.8779 (m-40) cc_final: 0.8504 (m110) REVERT: A 78 MET cc_start: 0.8961 (mmm) cc_final: 0.8606 (mmm) REVERT: B 15 ILE cc_start: 0.4307 (OUTLIER) cc_final: 0.3520 (mt) REVERT: B 16 ASP cc_start: 0.8172 (p0) cc_final: 0.7674 (p0) REVERT: B 87 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: B 103 TYR cc_start: 0.7382 (m-10) cc_final: 0.7125 (m-10) REVERT: B 143 MET cc_start: 0.8605 (tmm) cc_final: 0.8098 (tmm) REVERT: C 15 ILE cc_start: 0.4374 (OUTLIER) cc_final: 0.3967 (mt) REVERT: C 16 ASP cc_start: 0.8273 (p0) cc_final: 0.7765 (p0) REVERT: C 78 MET cc_start: 0.9038 (mmm) cc_final: 0.8387 (mmm) REVERT: C 103 TYR cc_start: 0.7491 (m-80) cc_final: 0.7210 (m-10) REVERT: D 15 ILE cc_start: 0.4358 (OUTLIER) cc_final: 0.3989 (mt) REVERT: D 23 ASN cc_start: 0.8825 (m-40) cc_final: 0.8588 (m-40) REVERT: D 103 TYR cc_start: 0.7231 (m-10) cc_final: 0.6998 (m-10) REVERT: E 15 ILE cc_start: 0.4678 (OUTLIER) cc_final: 0.4257 (mt) REVERT: F 15 ILE cc_start: 0.4151 (OUTLIER) cc_final: 0.3729 (mt) REVERT: F 16 ASP cc_start: 0.7976 (p0) cc_final: 0.7518 (p0) REVERT: F 23 ASN cc_start: 0.8903 (m-40) cc_final: 0.8610 (m-40) REVERT: G 78 MET cc_start: 0.8714 (mmm) cc_final: 0.8304 (mmm) REVERT: H 15 ILE cc_start: 0.3865 (OUTLIER) cc_final: 0.3538 (mt) REVERT: H 16 ASP cc_start: 0.8215 (p0) cc_final: 0.7748 (p0) REVERT: I 23 ASN cc_start: 0.8924 (m-40) cc_final: 0.8679 (m-40) REVERT: I 78 MET cc_start: 0.8620 (mmm) cc_final: 0.8217 (mmm) REVERT: J 15 ILE cc_start: 0.4997 (OUTLIER) cc_final: 0.4286 (mt) REVERT: J 23 ASN cc_start: 0.8986 (m-40) cc_final: 0.8302 (m110) REVERT: J 43 TYR cc_start: 0.8182 (t80) cc_final: 0.7897 (t80) REVERT: J 78 MET cc_start: 0.8977 (mmm) cc_final: 0.8744 (mmm) REVERT: K 1 VAL cc_start: 0.6947 (OUTLIER) cc_final: 0.6568 (m) REVERT: K 15 ILE cc_start: 0.4628 (OUTLIER) cc_final: 0.4231 (mt) REVERT: K 23 ASN cc_start: 0.8927 (m-40) cc_final: 0.8382 (m-40) REVERT: L 16 ASP cc_start: 0.8302 (p0) cc_final: 0.7766 (p0) REVERT: M 19 GLN cc_start: 0.7790 (tp40) cc_final: 0.7270 (tp40) outliers start: 45 outliers final: 33 residues processed: 173 average time/residue: 0.0903 time to fit residues: 25.1054 Evaluate side-chains 164 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain K residue 1 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 87 GLN Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 103 optimal weight: 20.0000 chunk 110 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 58 optimal weight: 0.4980 chunk 31 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 40.0000 chunk 140 optimal weight: 40.0000 overall best weight: 7.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.048094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.042762 restraints weight = 97873.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043886 restraints weight = 57688.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.044701 restraints weight = 38553.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.045299 restraints weight = 27951.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.045737 restraints weight = 21268.853| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13832 Z= 0.150 Angle : 0.680 8.211 18915 Z= 0.350 Chirality : 0.043 0.141 2418 Planarity : 0.004 0.042 2392 Dihedral : 5.492 28.406 1950 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 3.29 % Allowed : 10.91 % Favored : 85.80 % 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: -1.82 (0.19), residues: 1872 helix: None (None), residues: 0 sheet: 0.03 (0.21), residues: 676 loop : -2.09 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 44 TYR 0.032 0.002 TYR F 43 PHE 0.008 0.002 PHE G 96 TRP 0.007 0.001 TRP L 84 HIS 0.001 0.000 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00329 (13832) covalent geometry : angle 0.68033 (18915) hydrogen bonds : bond 0.03104 ( 394) hydrogen bonds : angle 5.64724 ( 873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 120 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 VAL cc_start: 0.6639 (OUTLIER) cc_final: 0.6038 (m) REVERT: A 15 ILE cc_start: 0.4313 (OUTLIER) cc_final: 0.3921 (mt) REVERT: A 16 ASP cc_start: 0.8013 (p0) cc_final: 0.7616 (p0) REVERT: A 23 ASN cc_start: 0.8762 (m-40) cc_final: 0.8504 (m110) REVERT: A 78 MET cc_start: 0.8980 (mmm) cc_final: 0.8607 (mmm) REVERT: B 15 ILE cc_start: 0.4138 (OUTLIER) cc_final: 0.3323 (mt) REVERT: B 16 ASP cc_start: 0.8157 (p0) cc_final: 0.7678 (p0) REVERT: B 87 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: B 103 TYR cc_start: 0.7366 (m-10) cc_final: 0.7113 (m-10) REVERT: B 143 MET cc_start: 0.8625 (tmm) cc_final: 0.8150 (tmm) REVERT: C 15 ILE cc_start: 0.4464 (OUTLIER) cc_final: 0.4060 (mt) REVERT: C 16 ASP cc_start: 0.8308 (p0) cc_final: 0.7814 (p0) REVERT: C 103 TYR cc_start: 0.7596 (m-80) cc_final: 0.7325 (m-10) REVERT: D 15 ILE cc_start: 0.4502 (OUTLIER) cc_final: 0.4054 (mt) REVERT: D 23 ASN cc_start: 0.8802 (m-40) cc_final: 0.8557 (m-40) REVERT: D 103 TYR cc_start: 0.7242 (m-10) cc_final: 0.7005 (m-10) REVERT: E 15 ILE cc_start: 0.4634 (OUTLIER) cc_final: 0.4209 (mt) REVERT: F 15 ILE cc_start: 0.4197 (OUTLIER) cc_final: 0.3835 (mt) REVERT: F 16 ASP cc_start: 0.8149 (p0) cc_final: 0.7571 (p0) REVERT: F 23 ASN cc_start: 0.8925 (m-40) cc_final: 0.8607 (m110) REVERT: G 78 MET cc_start: 0.8704 (mmm) cc_final: 0.8276 (mmm) REVERT: H 15 ILE cc_start: 0.4183 (OUTLIER) cc_final: 0.3847 (mt) REVERT: H 16 ASP cc_start: 0.8228 (p0) cc_final: 0.7761 (p0) REVERT: H 124 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7161 (ptpp) REVERT: I 23 ASN cc_start: 0.8919 (m-40) cc_final: 0.8425 (m110) REVERT: I 78 MET cc_start: 0.8643 (mmm) cc_final: 0.8222 (mmm) REVERT: J 15 ILE cc_start: 0.5080 (OUTLIER) cc_final: 0.4351 (mt) REVERT: J 23 ASN cc_start: 0.8978 (m-40) cc_final: 0.8311 (m110) REVERT: J 43 TYR cc_start: 0.8248 (t80) cc_final: 0.7910 (t80) REVERT: J 78 MET cc_start: 0.8944 (mmm) cc_final: 0.8688 (mmm) REVERT: K 15 ILE cc_start: 0.4621 (OUTLIER) cc_final: 0.4200 (mt) REVERT: K 23 ASN cc_start: 0.8965 (m-40) cc_final: 0.8433 (m-40) REVERT: K 87 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7398 (pm20) REVERT: L 16 ASP cc_start: 0.8274 (p0) cc_final: 0.7863 (p0) REVERT: M 15 ILE cc_start: 0.5032 (OUTLIER) cc_final: 0.4664 (mt) REVERT: M 19 GLN cc_start: 0.7840 (tp40) cc_final: 0.7317 (tp40) outliers start: 50 outliers final: 33 residues processed: 165 average time/residue: 0.0853 time to fit residues: 23.0693 Evaluate side-chains 165 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 87 GLN Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 15 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 50.0000 chunk 114 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 chunk 16 optimal weight: 0.0070 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 GLN K 87 GLN ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.048860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.043534 restraints weight = 95907.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.044689 restraints weight = 56436.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.045508 restraints weight = 37405.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.046097 restraints weight = 27005.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046535 restraints weight = 20650.922| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13832 Z= 0.110 Angle : 0.660 9.239 18915 Z= 0.340 Chirality : 0.043 0.141 2418 Planarity : 0.004 0.042 2392 Dihedral : 5.304 29.347 1950 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.89 % Allowed : 11.37 % Favored : 85.73 % 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: -1.73 (0.19), residues: 1872 helix: None (None), residues: 0 sheet: 0.12 (0.21), residues: 689 loop : -2.07 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 44 TYR 0.028 0.002 TYR E 43 PHE 0.006 0.001 PHE G 40 TRP 0.007 0.001 TRP L 84 HIS 0.001 0.000 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00249 (13832) covalent geometry : angle 0.66039 (18915) hydrogen bonds : bond 0.02928 ( 394) hydrogen bonds : angle 5.47324 ( 873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 VAL cc_start: 0.6667 (OUTLIER) cc_final: 0.6094 (m) REVERT: A 15 ILE cc_start: 0.4410 (OUTLIER) cc_final: 0.4015 (mt) REVERT: A 16 ASP cc_start: 0.8044 (p0) cc_final: 0.7656 (p0) REVERT: A 23 ASN cc_start: 0.8739 (m-40) cc_final: 0.8417 (m110) REVERT: B 15 ILE cc_start: 0.4465 (OUTLIER) cc_final: 0.3683 (mt) REVERT: B 16 ASP cc_start: 0.8107 (p0) cc_final: 0.7629 (p0) REVERT: B 87 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: B 103 TYR cc_start: 0.7428 (m-10) cc_final: 0.7169 (m-10) REVERT: B 143 MET cc_start: 0.8610 (tmm) cc_final: 0.8121 (tmm) REVERT: C 15 ILE cc_start: 0.4328 (OUTLIER) cc_final: 0.3946 (mt) REVERT: C 16 ASP cc_start: 0.8293 (p0) cc_final: 0.7830 (p0) REVERT: C 103 TYR cc_start: 0.7568 (m-80) cc_final: 0.7347 (m-10) REVERT: D 23 ASN cc_start: 0.8722 (m-40) cc_final: 0.8485 (m-40) REVERT: E 15 ILE cc_start: 0.4694 (OUTLIER) cc_final: 0.4306 (mt) REVERT: F 15 ILE cc_start: 0.4103 (OUTLIER) cc_final: 0.3482 (mt) REVERT: F 16 ASP cc_start: 0.8048 (p0) cc_final: 0.7520 (p0) REVERT: F 23 ASN cc_start: 0.8925 (m-40) cc_final: 0.8607 (m-40) REVERT: G 78 MET cc_start: 0.8655 (mmm) cc_final: 0.8207 (tmm) REVERT: H 15 ILE cc_start: 0.4113 (OUTLIER) cc_final: 0.3742 (mt) REVERT: H 16 ASP cc_start: 0.8120 (p0) cc_final: 0.7654 (p0) REVERT: I 23 ASN cc_start: 0.8904 (m-40) cc_final: 0.8622 (m-40) REVERT: I 78 MET cc_start: 0.8543 (mmm) cc_final: 0.8180 (mmm) REVERT: J 23 ASN cc_start: 0.8952 (m-40) cc_final: 0.8401 (m110) REVERT: J 43 TYR cc_start: 0.8234 (t80) cc_final: 0.7962 (t80) REVERT: J 78 MET cc_start: 0.8996 (mmm) cc_final: 0.8780 (mmm) REVERT: K 15 ILE cc_start: 0.4631 (OUTLIER) cc_final: 0.4083 (mt) REVERT: K 23 ASN cc_start: 0.8948 (m-40) cc_final: 0.8363 (m-40) REVERT: L 16 ASP cc_start: 0.8278 (p0) cc_final: 0.7842 (p0) REVERT: M 15 ILE cc_start: 0.4845 (OUTLIER) cc_final: 0.4471 (mt) REVERT: M 19 GLN cc_start: 0.7796 (tp40) cc_final: 0.7270 (tp40) outliers start: 44 outliers final: 32 residues processed: 169 average time/residue: 0.0863 time to fit residues: 23.7061 Evaluate side-chains 160 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 87 GLN Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 15 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 125 optimal weight: 40.0000 chunk 35 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 121 optimal weight: 40.0000 chunk 12 optimal weight: 0.9980 chunk 130 optimal weight: 30.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** H 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 GLN ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.049122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.043880 restraints weight = 97390.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.044982 restraints weight = 57990.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.045794 restraints weight = 39296.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.046389 restraints weight = 28448.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046825 restraints weight = 21667.875| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13832 Z= 0.110 Angle : 0.662 9.325 18915 Z= 0.339 Chirality : 0.043 0.140 2418 Planarity : 0.004 0.043 2392 Dihedral : 5.238 29.081 1950 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.96 % Allowed : 11.70 % Favored : 85.34 % 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: -1.70 (0.19), residues: 1872 helix: None (None), residues: 0 sheet: -0.11 (0.21), residues: 650 loop : -1.81 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 44 TYR 0.033 0.002 TYR G 43 PHE 0.007 0.001 PHE C 96 TRP 0.011 0.001 TRP K 84 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00249 (13832) covalent geometry : angle 0.66180 (18915) hydrogen bonds : bond 0.02880 ( 394) hydrogen bonds : angle 5.45292 ( 873) =============================================================================== Job complete usr+sys time: 1657.47 seconds wall clock time: 29 minutes 56.20 seconds (1796.20 seconds total)