Starting phenix.real_space_refine on Sun Oct 12 03:54:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2z_38023/10_2025/8x2z_38023.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2z_38023/10_2025/8x2z_38023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2z_38023/10_2025/8x2z_38023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2z_38023/10_2025/8x2z_38023.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2z_38023/10_2025/8x2z_38023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2z_38023/10_2025/8x2z_38023.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.020 sd= 0.471 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5013 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 22 5.16 5 C 9831 2.51 5 N 3053 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16972 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 699 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2364 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain: "L" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 353 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain breaks: 1 Chain: "M" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1734 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain breaks: 1 Chain: "N" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain breaks: 1 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Time building chain proxies: 3.77, per 1000 atoms: 0.22 Number of scatterers: 16972 At special positions: 0 Unit cell: (133.12, 140.4, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 290 15.00 O 3776 8.00 N 3053 7.00 C 9831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 419.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 7 sheets defined 49.4% alpha, 2.0% beta 141 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.604A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 4.014A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.621A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.900A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.710A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.866A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.752A pdb=" N ARG C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 49 through 62 removed outlier: 3.539A pdb=" N LEU C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA C 55 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 56 " --> pdb=" O TYR C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 5.031A pdb=" N GLU C 66 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 80 through 87 removed outlier: 3.560A pdb=" N LEU C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 87 " --> pdb=" O HIS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 4.144A pdb=" N ASP C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 60 through 87 Processing helix chain 'D' and resid 93 through 104 removed outlier: 4.222A pdb=" N ILE D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 127 removed outlier: 4.260A pdb=" N SER D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.526A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.868A pdb=" N ILE E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 41 removed outlier: 5.637A pdb=" N ARG F 39 " --> pdb=" O ARG F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 76 removed outlier: 4.351A pdb=" N ASP F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 27 through 39 Processing helix chain 'G' and resid 49 through 72 removed outlier: 4.171A pdb=" N LEU G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU G 63 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN G 70 " --> pdb=" O GLU G 66 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 81 through 89 removed outlier: 4.325A pdb=" N LEU G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 52 removed outlier: 3.595A pdb=" N ILE H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 4.077A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU H 105 " --> pdb=" O VAL H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 removed outlier: 3.618A pdb=" N SER H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 190 removed outlier: 3.666A pdb=" N LEU K 189 " --> pdb=" O PRO K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 217 Processing helix chain 'K' and resid 246 through 254 removed outlier: 3.659A pdb=" N LEU K 251 " --> pdb=" O TRP K 247 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS K 252 " --> pdb=" O CYS K 248 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU K 253 " --> pdb=" O ARG K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 347 through 359 removed outlier: 4.753A pdb=" N LEU K 357 " --> pdb=" O TRP K 353 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE K 358 " --> pdb=" O SER K 354 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR K 359 " --> pdb=" O ASP K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 377 removed outlier: 4.198A pdb=" N SER K 374 " --> pdb=" O ILE K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 391 removed outlier: 3.660A pdb=" N LEU K 391 " --> pdb=" O THR K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 416 Processing helix chain 'L' and resid 23 through 28 removed outlier: 3.950A pdb=" N ASP L 27 " --> pdb=" O ARG L 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR L 28 " --> pdb=" O GLU L 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 23 through 28' Processing helix chain 'L' and resid 29 through 30 No H-bonds generated for 'chain 'L' and resid 29 through 30' Processing helix chain 'L' and resid 31 through 39 removed outlier: 4.056A pdb=" N GLU L 35 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE L 36 " --> pdb=" O GLN L 33 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR L 37 " --> pdb=" O GLN L 34 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP L 38 " --> pdb=" O GLU L 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 158 Processing helix chain 'M' and resid 194 through 196 No H-bonds generated for 'chain 'M' and resid 194 through 196' Processing helix chain 'M' and resid 197 through 204 removed outlier: 3.911A pdb=" N HIS M 201 " --> pdb=" O GLU M 197 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU M 202 " --> pdb=" O HIS M 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN M 204 " --> pdb=" O ILE M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 226 removed outlier: 4.066A pdb=" N ILE M 225 " --> pdb=" O LYS M 221 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS M 226 " --> pdb=" O PRO M 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 221 through 226' Processing helix chain 'M' and resid 267 through 272 Processing helix chain 'M' and resid 275 through 283 removed outlier: 3.506A pdb=" N LYS M 283 " --> pdb=" O TRP M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 286 No H-bonds generated for 'chain 'M' and resid 284 through 286' Processing helix chain 'M' and resid 354 through 359 removed outlier: 3.624A pdb=" N LEU M 359 " --> pdb=" O GLU M 355 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 11 removed outlier: 4.471A pdb=" N THR N 10 " --> pdb=" O LEU N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 24 removed outlier: 3.797A pdb=" N LEU N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 32 Processing helix chain 'N' and resid 33 through 35 No H-bonds generated for 'chain 'N' and resid 33 through 35' Processing helix chain 'N' and resid 82 through 84 No H-bonds generated for 'chain 'N' and resid 82 through 84' Processing helix chain 'N' and resid 85 through 91 removed outlier: 3.641A pdb=" N LEU N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 107 removed outlier: 3.582A pdb=" N LYS N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 111 Processing sheet with id=AA1, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA2, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.453A pdb=" N THR G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'K' and resid 170 through 172 removed outlier: 3.809A pdb=" N ILE K 170 " --> pdb=" O ILE K 177 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR K 175 " --> pdb=" O MET K 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 234 through 239 Processing sheet with id=AA7, first strand: chain 'K' and resid 288 through 289 395 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3343 1.33 - 1.45: 5443 1.45 - 1.57: 8478 1.57 - 1.69: 583 1.69 - 1.81: 34 Bond restraints: 17881 Sorted by residual: bond pdb=" C THR G 81 " pdb=" N PRO G 82 " ideal model delta sigma weight residual 1.335 1.382 -0.046 1.36e-02 5.41e+03 1.16e+01 bond pdb=" CA ASP H 54 " pdb=" CB ASP H 54 " ideal model delta sigma weight residual 1.523 1.482 0.042 1.27e-02 6.20e+03 1.07e+01 bond pdb=" CA PRO N 18 " pdb=" C PRO N 18 " ideal model delta sigma weight residual 1.524 1.499 0.024 1.06e-02 8.90e+03 5.31e+00 bond pdb=" CG1 ILE K 239 " pdb=" CD1 ILE K 239 " ideal model delta sigma weight residual 1.513 1.427 0.086 3.90e-02 6.57e+02 4.88e+00 bond pdb=" CB LYS H 49 " pdb=" CG LYS H 49 " ideal model delta sigma weight residual 1.520 1.581 -0.061 3.00e-02 1.11e+03 4.19e+00 ... (remaining 17876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 24484 3.02 - 6.04: 771 6.04 - 9.06: 96 9.06 - 12.07: 22 12.07 - 15.09: 9 Bond angle restraints: 25382 Sorted by residual: angle pdb=" N VAL N 14 " pdb=" CA VAL N 14 " pdb=" C VAL N 14 " ideal model delta sigma weight residual 113.10 105.41 7.69 9.70e-01 1.06e+00 6.28e+01 angle pdb=" N ILE M 191 " pdb=" CA ILE M 191 " pdb=" C ILE M 191 " ideal model delta sigma weight residual 111.81 106.32 5.49 8.60e-01 1.35e+00 4.08e+01 angle pdb=" C ARG K 395 " pdb=" N TYR K 396 " pdb=" CA TYR K 396 " ideal model delta sigma weight residual 122.35 131.53 -9.18 1.46e+00 4.69e-01 3.95e+01 angle pdb=" N VAL M 351 " pdb=" CA VAL M 351 " pdb=" C VAL M 351 " ideal model delta sigma weight residual 113.20 107.33 5.87 9.60e-01 1.09e+00 3.74e+01 angle pdb=" N VAL N 6 " pdb=" CA VAL N 6 " pdb=" C VAL N 6 " ideal model delta sigma weight residual 111.91 106.66 5.25 8.90e-01 1.26e+00 3.48e+01 ... (remaining 25377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.59: 8412 34.59 - 69.18: 1676 69.18 - 103.77: 29 103.77 - 138.36: 1 138.36 - 172.95: 1 Dihedral angle restraints: 10119 sinusoidal: 6137 harmonic: 3982 Sorted by residual: dihedral pdb=" CA LYS K 339 " pdb=" C LYS K 339 " pdb=" N PRO K 340 " pdb=" CA PRO K 340 " ideal model delta harmonic sigma weight residual -180.00 -121.21 -58.79 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA LEU N 17 " pdb=" C LEU N 17 " pdb=" N PRO N 18 " pdb=" CA PRO N 18 " ideal model delta harmonic sigma weight residual 180.00 133.60 46.40 0 5.00e+00 4.00e-02 8.61e+01 dihedral pdb=" CA THR E 80 " pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta harmonic sigma weight residual -180.00 -139.18 -40.82 0 5.00e+00 4.00e-02 6.67e+01 ... (remaining 10116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2155 0.071 - 0.143: 584 0.143 - 0.214: 102 0.214 - 0.286: 21 0.286 - 0.357: 2 Chirality restraints: 2864 Sorted by residual: chirality pdb=" CB ILE F 26 " pdb=" CA ILE F 26 " pdb=" CG1 ILE F 26 " pdb=" CG2 ILE F 26 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA THR C 81 " pdb=" N THR C 81 " pdb=" C THR C 81 " pdb=" CB THR C 81 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL K 268 " pdb=" CA VAL K 268 " pdb=" CG1 VAL K 268 " pdb=" CG2 VAL K 268 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2861 not shown) Planarity restraints: 2198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " -0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO F 32 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 339 " 0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO K 340 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO K 340 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO K 340 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 17 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO N 18 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO N 18 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 18 " -0.041 5.00e-02 4.00e+02 ... (remaining 2195 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2273 2.75 - 3.28: 15414 3.28 - 3.82: 33655 3.82 - 4.36: 37398 4.36 - 4.90: 52263 Nonbonded interactions: 141003 Sorted by model distance: nonbonded pdb=" O THR M 223 " pdb=" OG SER M 227 " model vdw 2.207 3.040 nonbonded pdb=" O PHE L 95 " pdb=" NH1 ARG N 22 " model vdw 2.279 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" O THR B 80 " model vdw 2.295 3.040 nonbonded pdb=" O ALA K 351 " pdb=" OG SER K 354 " model vdw 2.297 3.040 nonbonded pdb=" O ASP M 210 " pdb=" OG SER M 213 " model vdw 2.301 3.040 ... (remaining 140998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 112) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 128) } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.580 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 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 0.086 17881 Z= 0.333 Angle : 1.284 15.093 25382 Z= 0.714 Chirality : 0.067 0.357 2864 Planarity : 0.008 0.082 2198 Dihedral : 26.278 172.953 7535 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.88 % Favored : 88.89 % Rotamer: Outliers : 4.25 % Allowed : 15.01 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 1.84 % 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 aren not related in a simple way. whole: -5.58 (0.16), residues: 1323 helix: -3.83 (0.13), residues: 628 sheet: -2.83 (0.80), residues: 33 loop : -3.65 (0.19), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 90 TYR 0.048 0.005 TYR N 23 PHE 0.044 0.004 PHE M 171 TRP 0.014 0.003 TRP K 353 HIS 0.013 0.003 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00709 (17881) covalent geometry : angle 1.28371 (25382) hydrogen bonds : bond 0.15719 ( 735) hydrogen bonds : angle 6.57463 ( 1811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 538 time to evaluate : 0.436 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: A 51 ILE cc_start: 0.5781 (pp) cc_final: 0.5155 (pt) REVERT: A 106 ASP cc_start: 0.7028 (p0) cc_final: 0.6783 (p0) REVERT: B 85 ASP cc_start: 0.8226 (p0) cc_final: 0.8022 (p0) REVERT: C 67 LEU cc_start: 0.6408 (tp) cc_final: 0.6114 (tp) REVERT: D 74 GLU cc_start: 0.6997 (tp30) cc_final: 0.6681 (tp30) REVERT: D 83 LEU cc_start: 0.7602 (tm) cc_final: 0.7175 (mt) REVERT: E 50 GLU cc_start: 0.7104 (tp30) cc_final: 0.6684 (tp30) REVERT: F 87 VAL cc_start: 0.7766 (m) cc_final: 0.7481 (p) REVERT: G 67 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7661 (mm) REVERT: G 87 LEU cc_start: 0.8064 (pt) cc_final: 0.7715 (pt) REVERT: H 51 THR cc_start: 0.6711 (m) cc_final: 0.6192 (p) REVERT: H 74 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7384 (tp30) REVERT: H 93 SER cc_start: 0.8660 (t) cc_final: 0.8327 (t) REVERT: H 118 THR cc_start: 0.8147 (m) cc_final: 0.7853 (p) REVERT: H 119 ARG cc_start: 0.7674 (ptm-80) cc_final: 0.7174 (ttp80) REVERT: H 122 THR cc_start: 0.8059 (m) cc_final: 0.7226 (m) REVERT: H 123 LYS cc_start: 0.8249 (mppt) cc_final: 0.7991 (mppt) REVERT: K 274 TYR cc_start: 0.7178 (m-80) cc_final: 0.6886 (m-80) REVERT: K 289 TYR cc_start: 0.5299 (p90) cc_final: 0.4900 (p90) REVERT: K 321 ILE cc_start: 0.8731 (pp) cc_final: 0.8421 (tt) REVERT: K 329 LYS cc_start: 0.7794 (ptpp) cc_final: 0.7506 (mttm) REVERT: K 333 LYS cc_start: 0.8637 (tmtm) cc_final: 0.8143 (tmtm) REVERT: K 393 ILE cc_start: 0.6019 (OUTLIER) cc_final: 0.5798 (pp) REVERT: K 406 ASN cc_start: 0.6260 (m110) cc_final: 0.5586 (m-40) REVERT: L 34 GLN cc_start: 0.8393 (mm110) cc_final: 0.8177 (mp10) REVERT: M 169 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7324 (mt-10) REVERT: M 209 MET cc_start: 0.6033 (pp-130) cc_final: 0.5629 (pp-130) REVERT: M 232 PHE cc_start: 0.6551 (p90) cc_final: 0.6243 (p90) REVERT: M 238 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7601 (tm) REVERT: M 279 TRP cc_start: 0.7699 (t-100) cc_final: 0.7084 (t-100) REVERT: N 13 ASP cc_start: 0.6089 (p0) cc_final: 0.5692 (p0) REVERT: N 85 GLU cc_start: 0.8513 (pp20) cc_final: 0.8251 (pp20) outliers start: 51 outliers final: 6 residues processed: 560 average time/residue: 0.1728 time to fit residues: 132.9305 Evaluate side-chains 449 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 440 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 393 ILE Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 262 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN B 75 HIS ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS D 59 GLN F 27 GLN G 84 HIS H 52 HIS H 66 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 210 GLN K 301 ASN ** K 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 427 ASN K 440 GLN ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 236 ASN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 363 ASN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.110895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093929 restraints weight = 53296.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.096167 restraints weight = 28721.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.097652 restraints weight = 18571.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.098591 restraints weight = 13773.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.099224 restraints weight = 11339.879| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 : 0.005 0.072 17881 Z= 0.238 Angle : 0.943 18.651 25382 Z= 0.512 Chirality : 0.049 0.241 2864 Planarity : 0.008 0.148 2198 Dihedral : 29.339 168.090 4790 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 7.67 % Allowed : 23.69 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.31 % 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 aren not related in a simple way. whole: -4.25 (0.19), residues: 1323 helix: -2.39 (0.16), residues: 629 sheet: -2.18 (0.94), residues: 27 loop : -3.36 (0.20), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 83 TYR 0.035 0.003 TYR D 86 PHE 0.037 0.003 PHE N 21 TRP 0.011 0.002 TRP M 130 HIS 0.008 0.002 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00531 (17881) covalent geometry : angle 0.94297 (25382) hydrogen bonds : bond 0.06316 ( 735) hydrogen bonds : angle 4.60082 ( 1811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 494 time to evaluate : 0.462 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: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8037 (pp20) cc_final: 0.7667 (pp20) REVERT: A 68 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: A 97 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 105 GLU cc_start: 0.8038 (pp20) cc_final: 0.7568 (pp20) REVERT: B 31 LYS cc_start: 0.8522 (ttpp) cc_final: 0.8231 (ttpp) REVERT: C 21 ARG cc_start: 0.6632 (OUTLIER) cc_final: 0.6119 (ppp-140) REVERT: C 32 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8117 (ttmm) REVERT: C 76 LYS cc_start: 0.7979 (tttt) cc_final: 0.7637 (tttt) REVERT: D 74 GLU cc_start: 0.7132 (tp30) cc_final: 0.6665 (tp30) REVERT: D 82 LYS cc_start: 0.8397 (mtpp) cc_final: 0.8051 (tptp) REVERT: D 101 VAL cc_start: 0.8541 (m) cc_final: 0.8305 (p) REVERT: E 50 GLU cc_start: 0.7159 (tp30) cc_final: 0.6691 (tp30) REVERT: E 60 LEU cc_start: 0.9013 (tp) cc_final: 0.8492 (tp) REVERT: E 62 ILE cc_start: 0.8559 (tp) cc_final: 0.8000 (tt) REVERT: E 82 LEU cc_start: 0.7779 (mp) cc_final: 0.7191 (mp) REVERT: E 121 LYS cc_start: 0.8441 (mttp) cc_final: 0.8196 (mttt) REVERT: F 60 SER cc_start: 0.8206 (m) cc_final: 0.7446 (t) REVERT: F 72 TYR cc_start: 0.8540 (m-80) cc_final: 0.8234 (m-80) REVERT: F 79 LYS cc_start: 0.7744 (ptmm) cc_final: 0.7466 (tppt) REVERT: F 87 VAL cc_start: 0.8308 (m) cc_final: 0.8096 (p) REVERT: G 57 LEU cc_start: 0.8663 (tt) cc_final: 0.8388 (tp) REVERT: G 59 TYR cc_start: 0.6484 (p90) cc_final: 0.6155 (p90) REVERT: G 67 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7704 (mm) REVERT: H 51 THR cc_start: 0.7140 (m) cc_final: 0.6720 (p) REVERT: H 74 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7489 (tm-30) REVERT: H 118 THR cc_start: 0.7864 (m) cc_final: 0.7554 (t) REVERT: H 119 ARG cc_start: 0.8195 (ptm-80) cc_final: 0.7475 (ttt-90) REVERT: K 301 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7256 (p0) REVERT: K 333 LYS cc_start: 0.8702 (tmtm) cc_final: 0.8368 (tmtm) REVERT: K 350 ARG cc_start: 0.7401 (mmm-85) cc_final: 0.6985 (mmm-85) REVERT: L 34 GLN cc_start: 0.8470 (mm110) cc_final: 0.8230 (mm-40) REVERT: M 133 TYR cc_start: 0.5462 (m-80) cc_final: 0.5048 (m-10) REVERT: M 168 ASP cc_start: 0.6968 (p0) cc_final: 0.6575 (p0) REVERT: M 209 MET cc_start: 0.5513 (pp-130) cc_final: 0.5227 (pp-130) REVERT: M 232 PHE cc_start: 0.6605 (p90) cc_final: 0.6270 (p90) REVERT: N 31 ASN cc_start: 0.6411 (p0) cc_final: 0.5700 (p0) REVERT: N 32 ASP cc_start: 0.7911 (m-30) cc_final: 0.7597 (m-30) outliers start: 92 outliers final: 37 residues processed: 541 average time/residue: 0.1841 time to fit residues: 136.0890 Evaluate side-chains 479 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 438 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain K residue 181 TYR Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 301 ASN Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 432 LYS Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 363 ASN Chi-restraints excluded: chain N residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 147 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 113 HIS G 84 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 210 GLN ** K 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN M 363 ASN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.111017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093740 restraints weight = 54665.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.095980 restraints weight = 29688.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.097485 restraints weight = 19315.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.098440 restraints weight = 14385.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.099055 restraints weight = 11869.241| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17881 Z= 0.206 Angle : 0.863 15.561 25382 Z= 0.468 Chirality : 0.047 0.227 2864 Planarity : 0.006 0.080 2198 Dihedral : 29.157 170.120 4779 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 7.26 % Allowed : 25.60 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -3.71 (0.20), residues: 1323 helix: -1.76 (0.18), residues: 643 sheet: -2.20 (0.94), residues: 22 loop : -3.28 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 52 TYR 0.027 0.002 TYR N 23 PHE 0.036 0.002 PHE M 217 TRP 0.022 0.002 TRP M 130 HIS 0.027 0.002 HIS G 84 Details of bonding type rmsd covalent geometry : bond 0.00459 (17881) covalent geometry : angle 0.86322 (25382) hydrogen bonds : bond 0.05436 ( 735) hydrogen bonds : angle 4.29192 ( 1811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 455 time to evaluate : 0.340 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: symmetry clash REVERT: A 49 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8214 (mtp-110) REVERT: A 64 LYS cc_start: 0.8921 (mmmm) cc_final: 0.8588 (mmmm) REVERT: A 67 PHE cc_start: 0.8723 (t80) cc_final: 0.8411 (t80) REVERT: A 68 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: A 79 LYS cc_start: 0.7891 (pttm) cc_final: 0.7591 (pttm) REVERT: A 105 GLU cc_start: 0.7868 (pp20) cc_final: 0.7617 (pp20) REVERT: C 21 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6607 (ppp-140) REVERT: C 105 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.8918 (p) REVERT: D 39 THR cc_start: 0.8768 (t) cc_final: 0.8501 (m) REVERT: D 73 PHE cc_start: 0.8770 (t80) cc_final: 0.8570 (t80) REVERT: D 74 GLU cc_start: 0.7352 (tp30) cc_final: 0.6812 (tp30) REVERT: D 79 GLU cc_start: 0.7536 (pp20) cc_final: 0.7264 (pp20) REVERT: D 82 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8249 (mmmt) REVERT: E 50 GLU cc_start: 0.7381 (tp30) cc_final: 0.7109 (tp30) REVERT: E 53 ARG cc_start: 0.7813 (ptm-80) cc_final: 0.7602 (ptm-80) REVERT: F 53 GLU cc_start: 0.7385 (pm20) cc_final: 0.6955 (pm20) REVERT: F 60 SER cc_start: 0.8109 (m) cc_final: 0.7553 (t) REVERT: F 91 LYS cc_start: 0.8424 (ttpp) cc_final: 0.8183 (ttpt) REVERT: G 21 ARG cc_start: 0.8278 (ppt170) cc_final: 0.7646 (ppt170) REVERT: G 54 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7216 (p) REVERT: H 51 THR cc_start: 0.7227 (m) cc_final: 0.6761 (p) REVERT: H 79 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8165 (tp30) REVERT: H 96 GLU cc_start: 0.8122 (pm20) cc_final: 0.7568 (pm20) REVERT: H 119 ARG cc_start: 0.8010 (ptm-80) cc_final: 0.7737 (ttp80) REVERT: K 252 CYS cc_start: 0.8231 (p) cc_final: 0.7480 (t) REVERT: K 304 CYS cc_start: 0.7726 (p) cc_final: 0.7453 (p) REVERT: K 322 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6482 (pm20) REVERT: K 328 SER cc_start: 0.7336 (m) cc_final: 0.7088 (p) REVERT: K 329 LYS cc_start: 0.7752 (mmtp) cc_final: 0.7511 (mtpp) REVERT: K 333 LYS cc_start: 0.8695 (tmtm) cc_final: 0.8475 (tppt) REVERT: K 347 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7473 (tt) REVERT: L 33 GLN cc_start: 0.8204 (pm20) cc_final: 0.7943 (mp10) REVERT: M 155 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7815 (mm-30) REVERT: M 209 MET cc_start: 0.5408 (pp-130) cc_final: 0.5109 (pp-130) REVERT: M 215 LEU cc_start: 0.8418 (pp) cc_final: 0.8215 (pp) REVERT: M 232 PHE cc_start: 0.6972 (p90) cc_final: 0.6689 (p90) REVERT: M 242 ILE cc_start: 0.6294 (mm) cc_final: 0.6034 (mm) REVERT: M 259 MET cc_start: 0.5752 (mmt) cc_final: 0.5217 (mmt) REVERT: N 17 LEU cc_start: 0.7168 (tp) cc_final: 0.6907 (mt) REVERT: N 22 ARG cc_start: 0.7885 (mmm160) cc_final: 0.7664 (mmm160) REVERT: N 86 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7618 (mmmt) REVERT: N 94 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7826 (mt) outliers start: 87 outliers final: 43 residues processed: 498 average time/residue: 0.1871 time to fit residues: 126.3509 Evaluate side-chains 477 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 427 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 262 ARG Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain N residue 110 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 91 optimal weight: 0.0970 chunk 54 optimal weight: 0.0170 chunk 95 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN B 25 ASN D 59 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS H 66 ASN H 98 GLN ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.113356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095765 restraints weight = 54809.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.098046 restraints weight = 29777.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.099572 restraints weight = 19395.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.100531 restraints weight = 14429.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.101171 restraints weight = 11903.362| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17881 Z= 0.171 Angle : 0.821 13.618 25382 Z= 0.438 Chirality : 0.044 0.223 2864 Planarity : 0.005 0.073 2198 Dihedral : 28.902 171.704 4771 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 7.09 % Allowed : 28.19 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -3.29 (0.21), residues: 1323 helix: -1.43 (0.19), residues: 639 sheet: -2.04 (1.02), residues: 22 loop : -3.03 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 55 TYR 0.024 0.002 TYR D 86 PHE 0.033 0.002 PHE M 217 TRP 0.011 0.002 TRP M 130 HIS 0.003 0.001 HIS N 100 Details of bonding type rmsd covalent geometry : bond 0.00375 (17881) covalent geometry : angle 0.82051 (25382) hydrogen bonds : bond 0.04894 ( 735) hydrogen bonds : angle 4.17667 ( 1811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 450 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: A 49 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8136 (mtp-110) REVERT: A 76 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: A 93 GLN cc_start: 0.7640 (tt0) cc_final: 0.7302 (tt0) REVERT: A 105 GLU cc_start: 0.7899 (pp20) cc_final: 0.7658 (pp20) REVERT: A 115 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8508 (tppp) REVERT: A 131 ARG cc_start: 0.8781 (mtp85) cc_final: 0.8464 (mtp85) REVERT: B 31 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8256 (ttpp) REVERT: C 21 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6394 (ppp-140) REVERT: C 105 SER cc_start: 0.9303 (OUTLIER) cc_final: 0.9011 (p) REVERT: D 50 GLN cc_start: 0.8364 (pt0) cc_final: 0.8132 (pt0) REVERT: D 79 GLU cc_start: 0.7517 (pp20) cc_final: 0.7301 (pp20) REVERT: D 102 ARG cc_start: 0.8747 (mtp-110) cc_final: 0.8293 (ttp80) REVERT: E 50 GLU cc_start: 0.7372 (tp30) cc_final: 0.7065 (tp30) REVERT: E 53 ARG cc_start: 0.7795 (ptm-80) cc_final: 0.7574 (ptm-80) REVERT: F 35 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7878 (mtm-85) REVERT: F 36 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7167 (mtt90) REVERT: F 50 ILE cc_start: 0.8290 (pt) cc_final: 0.8040 (mm) REVERT: F 51 TYR cc_start: 0.8318 (m-80) cc_final: 0.7710 (m-80) REVERT: F 60 SER cc_start: 0.8067 (m) cc_final: 0.7719 (t) REVERT: F 91 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8274 (ttpt) REVERT: G 21 ARG cc_start: 0.8087 (ppt170) cc_final: 0.7807 (ppt170) REVERT: G 37 ARG cc_start: 0.7303 (ttm110) cc_final: 0.7019 (ttm110) REVERT: H 49 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7340 (tmmt) REVERT: H 51 THR cc_start: 0.7307 (m) cc_final: 0.6870 (p) REVERT: H 82 LYS cc_start: 0.8424 (tmtt) cc_final: 0.8202 (tmtt) REVERT: H 96 GLU cc_start: 0.8068 (pm20) cc_final: 0.7478 (pm20) REVERT: H 119 ARG cc_start: 0.8126 (ptm-80) cc_final: 0.7615 (tmm160) REVERT: K 252 CYS cc_start: 0.8217 (p) cc_final: 0.7425 (t) REVERT: K 322 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6448 (pm20) REVERT: K 328 SER cc_start: 0.7075 (m) cc_final: 0.6811 (p) REVERT: K 333 LYS cc_start: 0.8657 (tmtm) cc_final: 0.8318 (tmtm) REVERT: K 386 HIS cc_start: 0.7457 (t-90) cc_final: 0.7257 (t70) REVERT: M 209 MET cc_start: 0.5297 (pp-130) cc_final: 0.5027 (pp-130) REVERT: M 215 LEU cc_start: 0.8493 (pp) cc_final: 0.8233 (pp) REVERT: M 259 MET cc_start: 0.5746 (mmt) cc_final: 0.5080 (mmt) REVERT: N 22 ARG cc_start: 0.7751 (mmm160) cc_final: 0.6916 (mmm160) REVERT: N 94 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7726 (mm) outliers start: 85 outliers final: 37 residues processed: 490 average time/residue: 0.1851 time to fit residues: 123.3550 Evaluate side-chains 481 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 437 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 363 ASN Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 81 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 122 optimal weight: 0.0570 chunk 7 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS ** K 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN K 401 HIS M 243 ASN ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.112894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.095214 restraints weight = 54494.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.097438 restraints weight = 30027.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.098950 restraints weight = 19634.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.099926 restraints weight = 14640.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100564 restraints weight = 12057.640| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.7225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17881 Z= 0.181 Angle : 0.838 13.248 25382 Z= 0.444 Chirality : 0.045 0.230 2864 Planarity : 0.006 0.140 2198 Dihedral : 28.792 175.510 4767 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 7.34 % Allowed : 29.02 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -3.09 (0.21), residues: 1323 helix: -1.21 (0.19), residues: 636 sheet: -1.77 (1.12), residues: 22 loop : -2.99 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 335 TYR 0.022 0.002 TYR C 52 PHE 0.037 0.002 PHE M 217 TRP 0.011 0.002 TRP K 353 HIS 0.004 0.001 HIS N 100 Details of bonding type rmsd covalent geometry : bond 0.00403 (17881) covalent geometry : angle 0.83754 (25382) hydrogen bonds : bond 0.04950 ( 735) hydrogen bonds : angle 4.10756 ( 1811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 459 time to evaluate : 0.581 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: A 49 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8200 (mtp-110) REVERT: A 76 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8631 (pm20) REVERT: A 115 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8590 (tppp) REVERT: A 131 ARG cc_start: 0.8879 (mtp85) cc_final: 0.8550 (mmm160) REVERT: B 92 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8053 (tmt170) REVERT: C 21 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6376 (ppp-140) REVERT: C 76 LYS cc_start: 0.8241 (tttt) cc_final: 0.7765 (tttt) REVERT: C 105 SER cc_start: 0.9386 (OUTLIER) cc_final: 0.9180 (p) REVERT: D 79 GLU cc_start: 0.7452 (pp20) cc_final: 0.7200 (pp20) REVERT: D 95 ARG cc_start: 0.7544 (ptm160) cc_final: 0.7340 (ptm160) REVERT: D 102 ARG cc_start: 0.8785 (mtp-110) cc_final: 0.8434 (ttp80) REVERT: E 50 GLU cc_start: 0.7400 (tp30) cc_final: 0.7055 (tp30) REVERT: E 53 ARG cc_start: 0.7896 (ptm-80) cc_final: 0.7691 (ptm-80) REVERT: E 121 LYS cc_start: 0.8391 (mmtp) cc_final: 0.8167 (mmtm) REVERT: F 51 TYR cc_start: 0.8257 (m-80) cc_final: 0.7983 (m-10) REVERT: F 53 GLU cc_start: 0.7109 (pm20) cc_final: 0.6184 (pm20) REVERT: F 91 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8333 (ttpt) REVERT: G 21 ARG cc_start: 0.8184 (ppt170) cc_final: 0.7878 (ppt170) REVERT: G 37 ARG cc_start: 0.7402 (ttm110) cc_final: 0.7177 (ttm110) REVERT: G 54 THR cc_start: 0.7750 (p) cc_final: 0.7506 (p) REVERT: H 51 THR cc_start: 0.7279 (m) cc_final: 0.6985 (p) REVERT: H 96 GLU cc_start: 0.8004 (pm20) cc_final: 0.7413 (pm20) REVERT: H 116 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7305 (tm-30) REVERT: K 233 TYR cc_start: 0.5332 (OUTLIER) cc_final: 0.3423 (p90) REVERT: K 291 SER cc_start: 0.8348 (m) cc_final: 0.8112 (t) REVERT: K 402 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8615 (pt) REVERT: M 149 LYS cc_start: 0.6463 (ptmt) cc_final: 0.6203 (pttp) REVERT: M 209 MET cc_start: 0.5415 (pp-130) cc_final: 0.5133 (pp-130) REVERT: M 215 LEU cc_start: 0.8428 (pp) cc_final: 0.8134 (pp) REVERT: M 232 PHE cc_start: 0.6661 (p90) cc_final: 0.5549 (p90) REVERT: M 342 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7670 (tmtm) REVERT: N 9 GLN cc_start: 0.8304 (pm20) cc_final: 0.8058 (pm20) outliers start: 88 outliers final: 47 residues processed: 496 average time/residue: 0.1982 time to fit residues: 132.3607 Evaluate side-chains 491 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 437 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 402 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 243 ASN Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 87 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 131 optimal weight: 2.9990 chunk 126 optimal weight: 0.3980 chunk 140 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** K 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN N 100 HIS ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.113189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095463 restraints weight = 54609.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.097712 restraints weight = 30384.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.099208 restraints weight = 20036.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.100154 restraints weight = 15033.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.100816 restraints weight = 12459.012| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.7768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17881 Z= 0.181 Angle : 0.847 14.073 25382 Z= 0.445 Chirality : 0.044 0.220 2864 Planarity : 0.006 0.074 2198 Dihedral : 28.664 177.428 4767 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 6.76 % Allowed : 31.61 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -2.99 (0.21), residues: 1323 helix: -1.22 (0.19), residues: 640 sheet: -1.60 (1.17), residues: 22 loop : -2.85 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 79 TYR 0.020 0.002 TYR G 52 PHE 0.037 0.002 PHE E 67 TRP 0.012 0.002 TRP K 353 HIS 0.005 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00405 (17881) covalent geometry : angle 0.84691 (25382) hydrogen bonds : bond 0.04877 ( 735) hydrogen bonds : angle 4.16763 ( 1811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 451 time to evaluate : 0.519 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: A 49 ARG cc_start: 0.8367 (mtp85) cc_final: 0.8161 (mtp-110) REVERT: A 73 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7016 (tp30) REVERT: A 76 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: A 105 GLU cc_start: 0.7768 (pp20) cc_final: 0.7501 (pp20) REVERT: A 115 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8626 (tppp) REVERT: B 36 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8171 (ttm110) REVERT: B 92 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8119 (tmt170) REVERT: C 21 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6184 (ppp-140) REVERT: C 76 LYS cc_start: 0.8227 (tttt) cc_final: 0.7713 (tttt) REVERT: C 105 SER cc_start: 0.9418 (m) cc_final: 0.9160 (p) REVERT: D 46 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8116 (pptt) REVERT: D 79 GLU cc_start: 0.7418 (pp20) cc_final: 0.7134 (pp20) REVERT: D 102 ARG cc_start: 0.8827 (mtp-110) cc_final: 0.8475 (ttp80) REVERT: E 50 GLU cc_start: 0.7462 (tp30) cc_final: 0.7019 (tp30) REVERT: F 44 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8540 (mtpp) REVERT: F 51 TYR cc_start: 0.7940 (m-80) cc_final: 0.7684 (m-10) REVERT: F 91 LYS cc_start: 0.8692 (ttpp) cc_final: 0.8417 (ttpt) REVERT: F 92 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8497 (tmt-80) REVERT: G 21 ARG cc_start: 0.8168 (ppt170) cc_final: 0.7629 (ppt170) REVERT: G 44 ARG cc_start: 0.7324 (tmm160) cc_final: 0.6907 (ttp80) REVERT: H 48 LEU cc_start: 0.8009 (pp) cc_final: 0.7770 (pp) REVERT: H 51 THR cc_start: 0.7184 (m) cc_final: 0.6866 (p) REVERT: H 96 GLU cc_start: 0.7940 (pm20) cc_final: 0.7393 (pm20) REVERT: H 123 LYS cc_start: 0.8203 (mppt) cc_final: 0.7913 (mppt) REVERT: K 233 TYR cc_start: 0.5597 (OUTLIER) cc_final: 0.3758 (p90) REVERT: K 291 SER cc_start: 0.8346 (m) cc_final: 0.8128 (t) REVERT: K 333 LYS cc_start: 0.8757 (tppt) cc_final: 0.8457 (tppt) REVERT: K 402 ILE cc_start: 0.8836 (pt) cc_final: 0.8553 (pt) REVERT: K 412 ARG cc_start: 0.7082 (mpp-170) cc_final: 0.6485 (mpp80) REVERT: K 436 PHE cc_start: 0.6417 (p90) cc_final: 0.6190 (p90) REVERT: M 149 LYS cc_start: 0.6418 (ptmt) cc_final: 0.6119 (pttp) REVERT: M 209 MET cc_start: 0.5411 (pp-130) cc_final: 0.5133 (pp-130) REVERT: M 215 LEU cc_start: 0.8440 (pp) cc_final: 0.8227 (pp) REVERT: M 217 PHE cc_start: 0.6075 (p90) cc_final: 0.5749 (p90) REVERT: M 342 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7566 (tmtm) outliers start: 81 outliers final: 47 residues processed: 491 average time/residue: 0.1923 time to fit residues: 127.4953 Evaluate side-chains 486 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 431 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 326 GLU Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain M residue 145 THR Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 363 ASN Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 108 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 118 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN ** M 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.113215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095487 restraints weight = 54442.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.097685 restraints weight = 30408.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.099145 restraints weight = 20087.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.100128 restraints weight = 15142.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.100681 restraints weight = 12523.484| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.8184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 17881 Z= 0.182 Angle : 0.863 15.036 25382 Z= 0.451 Chirality : 0.045 0.240 2864 Planarity : 0.006 0.072 2198 Dihedral : 28.593 178.741 4767 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 6.42 % Allowed : 34.20 % Favored : 59.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -2.91 (0.22), residues: 1323 helix: -1.24 (0.19), residues: 648 sheet: -1.42 (1.24), residues: 22 loop : -2.72 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG M 235 TYR 0.021 0.002 TYR G 52 PHE 0.034 0.002 PHE M 217 TRP 0.010 0.002 TRP K 353 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00416 (17881) covalent geometry : angle 0.86335 (25382) hydrogen bonds : bond 0.04910 ( 735) hydrogen bonds : angle 4.12407 ( 1811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 444 time to evaluate : 0.513 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: A 73 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7016 (tp30) REVERT: A 76 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7998 (pp30) REVERT: A 105 GLU cc_start: 0.7657 (pp20) cc_final: 0.7457 (pp20) REVERT: A 106 ASP cc_start: 0.7610 (p0) cc_final: 0.7262 (p0) REVERT: A 115 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8654 (tppp) REVERT: B 49 LEU cc_start: 0.9088 (mm) cc_final: 0.8883 (mp) REVERT: B 59 LYS cc_start: 0.8725 (ptmm) cc_final: 0.8419 (ttpp) REVERT: B 92 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8147 (tmt170) REVERT: C 21 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6768 (ppp-140) REVERT: C 52 TYR cc_start: 0.7710 (t80) cc_final: 0.7504 (t80) REVERT: C 64 VAL cc_start: 0.7230 (m) cc_final: 0.6924 (m) REVERT: C 76 LYS cc_start: 0.8291 (tttt) cc_final: 0.7702 (tttt) REVERT: C 99 ILE cc_start: 0.7579 (mp) cc_final: 0.7372 (mp) REVERT: C 105 SER cc_start: 0.9434 (m) cc_final: 0.9177 (p) REVERT: D 46 LYS cc_start: 0.8318 (pttp) cc_final: 0.8108 (pptt) REVERT: D 79 GLU cc_start: 0.7317 (pp20) cc_final: 0.7012 (pp20) REVERT: D 89 LYS cc_start: 0.8597 (mmmm) cc_final: 0.8302 (mmmm) REVERT: D 95 ARG cc_start: 0.7500 (ptm160) cc_final: 0.7086 (ptm160) REVERT: D 102 ARG cc_start: 0.8848 (mtp-110) cc_final: 0.8528 (ttp80) REVERT: E 50 GLU cc_start: 0.7421 (tp30) cc_final: 0.7014 (tp30) REVERT: F 51 TYR cc_start: 0.7871 (m-80) cc_final: 0.7546 (m-10) REVERT: F 53 GLU cc_start: 0.7132 (pm20) cc_final: 0.6557 (pm20) REVERT: F 58 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8839 (tp) REVERT: F 91 LYS cc_start: 0.8760 (ttpp) cc_final: 0.8526 (ttpt) REVERT: G 21 ARG cc_start: 0.8095 (ppt170) cc_final: 0.7601 (ppt170) REVERT: G 44 ARG cc_start: 0.7394 (tmm160) cc_final: 0.7171 (ttp80) REVERT: H 51 THR cc_start: 0.7136 (m) cc_final: 0.6840 (p) REVERT: H 93 SER cc_start: 0.8762 (t) cc_final: 0.8487 (p) REVERT: H 96 GLU cc_start: 0.7815 (pm20) cc_final: 0.6989 (pm20) REVERT: H 123 LYS cc_start: 0.8213 (mppt) cc_final: 0.7842 (mppt) REVERT: K 233 TYR cc_start: 0.5575 (OUTLIER) cc_final: 0.3709 (p90) REVERT: K 333 LYS cc_start: 0.8782 (tppt) cc_final: 0.8357 (tppt) REVERT: K 357 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7957 (pp) REVERT: K 402 ILE cc_start: 0.8797 (pt) cc_final: 0.8472 (mm) REVERT: K 436 PHE cc_start: 0.6358 (p90) cc_final: 0.6146 (p90) REVERT: M 209 MET cc_start: 0.5422 (pp-130) cc_final: 0.5116 (pp-130) REVERT: M 232 PHE cc_start: 0.6841 (p90) cc_final: 0.6540 (p90) REVERT: M 342 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7555 (tmtm) REVERT: N 25 LEU cc_start: 0.6070 (mp) cc_final: 0.5808 (mt) REVERT: N 85 GLU cc_start: 0.8960 (pp20) cc_final: 0.8626 (pp20) outliers start: 77 outliers final: 47 residues processed: 481 average time/residue: 0.1999 time to fit residues: 129.3233 Evaluate side-chains 484 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 429 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 271 PHE Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 398 LYS Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 243 ASN Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 363 ASN Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 108 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 62 optimal weight: 0.0060 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 HIS ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** M 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.113019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.095129 restraints weight = 54726.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.097411 restraints weight = 30532.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.098909 restraints weight = 20157.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099868 restraints weight = 15187.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.100495 restraints weight = 12592.338| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.8555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17881 Z= 0.188 Angle : 0.890 14.607 25382 Z= 0.463 Chirality : 0.046 0.256 2864 Planarity : 0.006 0.074 2198 Dihedral : 28.571 179.733 4767 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 6.01 % Allowed : 34.95 % Favored : 59.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -3.00 (0.22), residues: 1323 helix: -1.30 (0.19), residues: 656 sheet: -2.34 (0.98), residues: 28 loop : -2.75 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 44 TYR 0.051 0.002 TYR N 23 PHE 0.041 0.002 PHE K 323 TRP 0.010 0.002 TRP K 353 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00428 (17881) covalent geometry : angle 0.88980 (25382) hydrogen bonds : bond 0.04994 ( 735) hydrogen bonds : angle 4.14778 ( 1811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 445 time to evaluate : 0.521 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: A 73 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: A 76 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7994 (pp30) REVERT: A 106 ASP cc_start: 0.7679 (p0) cc_final: 0.7444 (p0) REVERT: A 115 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8682 (tppp) REVERT: B 92 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8146 (tmt170) REVERT: C 21 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6862 (ppp-140) REVERT: C 64 VAL cc_start: 0.7292 (m) cc_final: 0.7083 (m) REVERT: C 76 LYS cc_start: 0.8343 (tttt) cc_final: 0.7749 (tttt) REVERT: C 105 SER cc_start: 0.9527 (OUTLIER) cc_final: 0.9270 (p) REVERT: D 79 GLU cc_start: 0.7280 (pp20) cc_final: 0.6984 (pp20) REVERT: D 102 ARG cc_start: 0.8867 (mtp-110) cc_final: 0.8519 (ttp80) REVERT: E 50 GLU cc_start: 0.7465 (tp30) cc_final: 0.6995 (tp30) REVERT: F 51 TYR cc_start: 0.7757 (m-80) cc_final: 0.7537 (m-10) REVERT: F 91 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8595 (ttpt) REVERT: G 21 ARG cc_start: 0.8118 (ppt170) cc_final: 0.7646 (ppt170) REVERT: G 93 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8199 (t0) REVERT: H 51 THR cc_start: 0.7039 (m) cc_final: 0.6717 (p) REVERT: H 93 SER cc_start: 0.8781 (t) cc_final: 0.8454 (p) REVERT: H 96 GLU cc_start: 0.7879 (pm20) cc_final: 0.7062 (pm20) REVERT: H 104 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8560 (tp) REVERT: H 123 LYS cc_start: 0.8228 (mppt) cc_final: 0.7868 (mppt) REVERT: K 210 GLN cc_start: 0.6798 (pp30) cc_final: 0.6382 (tt0) REVERT: K 233 TYR cc_start: 0.5539 (OUTLIER) cc_final: 0.3711 (p90) REVERT: K 276 MET cc_start: 0.7524 (tpp) cc_final: 0.7320 (tpp) REVERT: K 333 LYS cc_start: 0.8712 (tppt) cc_final: 0.8362 (tppt) REVERT: K 402 ILE cc_start: 0.8819 (pt) cc_final: 0.8524 (mm) REVERT: L 34 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7884 (tp40) REVERT: M 237 GLN cc_start: 0.6139 (pm20) cc_final: 0.5568 (pm20) REVERT: M 342 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7549 (tmtm) REVERT: M 354 ARG cc_start: 0.7986 (tpm170) cc_final: 0.7773 (tpm170) REVERT: N 85 GLU cc_start: 0.9020 (pp20) cc_final: 0.8801 (pp20) outliers start: 72 outliers final: 48 residues processed: 477 average time/residue: 0.1975 time to fit residues: 126.7340 Evaluate side-chains 490 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 433 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 326 GLU Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain K residue 379 MET Chi-restraints excluded: chain K residue 398 LYS Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 363 ASN Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 108 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 0.0570 chunk 156 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN B 25 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN G 38 HIS ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN M 243 ASN ** M 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.095395 restraints weight = 54177.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.097620 restraints weight = 30200.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.099106 restraints weight = 20002.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.100069 restraints weight = 15062.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100715 restraints weight = 12491.484| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.8916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17881 Z= 0.188 Angle : 0.903 14.734 25382 Z= 0.469 Chirality : 0.045 0.251 2864 Planarity : 0.006 0.069 2198 Dihedral : 28.532 179.608 4767 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 5.75 % Allowed : 35.78 % Favored : 58.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -2.98 (0.22), residues: 1323 helix: -1.27 (0.19), residues: 653 sheet: -2.40 (1.00), residues: 27 loop : -2.75 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 44 TYR 0.049 0.002 TYR N 23 PHE 0.032 0.002 PHE K 323 TRP 0.011 0.002 TRP K 247 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00428 (17881) covalent geometry : angle 0.90262 (25382) hydrogen bonds : bond 0.05013 ( 735) hydrogen bonds : angle 4.17750 ( 1811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 449 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: 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 73 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: A 76 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8109 (pp30) REVERT: A 106 ASP cc_start: 0.7662 (p0) cc_final: 0.7223 (p0) REVERT: A 115 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8683 (tppp) REVERT: A 131 ARG cc_start: 0.8861 (mmm160) cc_final: 0.8605 (mtp85) REVERT: B 92 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8169 (tmt170) REVERT: C 21 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6988 (ppp-140) REVERT: C 64 VAL cc_start: 0.7361 (m) cc_final: 0.7129 (m) REVERT: C 70 ASN cc_start: 0.5664 (t0) cc_final: 0.4247 (t0) REVERT: C 76 LYS cc_start: 0.8442 (tttt) cc_final: 0.7828 (tptt) REVERT: C 105 SER cc_start: 0.9489 (OUTLIER) cc_final: 0.9231 (p) REVERT: D 41 SER cc_start: 0.8586 (m) cc_final: 0.8342 (p) REVERT: D 79 GLU cc_start: 0.7342 (pp20) cc_final: 0.7087 (pp20) REVERT: D 89 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8124 (mmmm) REVERT: E 50 GLU cc_start: 0.7564 (tp30) cc_final: 0.7019 (tp30) REVERT: F 29 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7936 (mm) REVERT: F 51 TYR cc_start: 0.7849 (m-80) cc_final: 0.7630 (m-10) REVERT: F 91 LYS cc_start: 0.8758 (ttpp) cc_final: 0.8513 (ttpt) REVERT: G 93 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7981 (t0) REVERT: H 51 THR cc_start: 0.7136 (m) cc_final: 0.6836 (p) REVERT: H 93 SER cc_start: 0.8819 (t) cc_final: 0.8477 (p) REVERT: H 96 GLU cc_start: 0.7960 (pm20) cc_final: 0.7124 (pm20) REVERT: H 104 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8508 (tp) REVERT: H 119 ARG cc_start: 0.8119 (ptm160) cc_final: 0.7571 (ptm160) REVERT: H 123 LYS cc_start: 0.8202 (mppt) cc_final: 0.7835 (mppt) REVERT: K 210 GLN cc_start: 0.6888 (pp30) cc_final: 0.6399 (tt0) REVERT: K 233 TYR cc_start: 0.5584 (OUTLIER) cc_final: 0.3886 (p90) REVERT: K 300 TYR cc_start: 0.6161 (t80) cc_final: 0.4979 (t80) REVERT: K 412 ARG cc_start: 0.7290 (mpp-170) cc_final: 0.6255 (mpp80) REVERT: L 34 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7918 (tp40) REVERT: M 237 GLN cc_start: 0.6198 (pm20) cc_final: 0.5740 (pm20) REVERT: M 327 ASP cc_start: 0.6069 (m-30) cc_final: 0.5617 (m-30) REVERT: M 341 LEU cc_start: 0.8329 (pt) cc_final: 0.7789 (mt) REVERT: M 342 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7377 (tmtm) outliers start: 69 outliers final: 51 residues processed: 478 average time/residue: 0.1997 time to fit residues: 128.4151 Evaluate side-chains 493 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 432 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 271 PHE Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 326 GLU Chi-restraints excluded: chain K residue 379 MET Chi-restraints excluded: chain K residue 398 LYS Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 162 TYR Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 243 ASN Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 363 ASN Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 59 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 109 optimal weight: 0.0070 chunk 107 optimal weight: 8.9990 chunk 96 optimal weight: 0.0970 chunk 148 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN E 93 GLN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN M 163 ASN ** M 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.114108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096156 restraints weight = 54472.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.098386 restraints weight = 30676.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099892 restraints weight = 20391.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.100876 restraints weight = 15366.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101524 restraints weight = 12718.868| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.9179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17881 Z= 0.184 Angle : 0.934 18.542 25382 Z= 0.479 Chirality : 0.045 0.267 2864 Planarity : 0.006 0.065 2198 Dihedral : 28.470 179.140 4767 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 5.84 % Allowed : 36.86 % Favored : 57.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -3.02 (0.22), residues: 1323 helix: -1.32 (0.19), residues: 647 sheet: -2.43 (0.96), residues: 27 loop : -2.74 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 83 TYR 0.043 0.002 TYR N 23 PHE 0.032 0.002 PHE K 323 TRP 0.009 0.001 TRP K 353 HIS 0.005 0.001 HIS M 245 Details of bonding type rmsd covalent geometry : bond 0.00415 (17881) covalent geometry : angle 0.93416 (25382) hydrogen bonds : bond 0.04958 ( 735) hydrogen bonds : angle 4.27243 ( 1811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 434 time to evaluate : 0.582 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: A 73 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7102 (tp30) REVERT: A 76 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: A 105 GLU cc_start: 0.7724 (pp20) cc_final: 0.7389 (pp20) REVERT: A 115 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8647 (tppp) REVERT: B 92 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8134 (tmt170) REVERT: C 21 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6749 (ppp-140) REVERT: C 64 VAL cc_start: 0.7281 (m) cc_final: 0.7068 (m) REVERT: C 76 LYS cc_start: 0.8446 (tttt) cc_final: 0.7880 (tptt) REVERT: C 105 SER cc_start: 0.9482 (OUTLIER) cc_final: 0.9244 (p) REVERT: D 39 THR cc_start: 0.8429 (t) cc_final: 0.8165 (m) REVERT: D 41 SER cc_start: 0.8606 (m) cc_final: 0.8400 (p) REVERT: D 79 GLU cc_start: 0.7353 (pp20) cc_final: 0.7129 (pp20) REVERT: D 89 LYS cc_start: 0.8589 (mmmm) cc_final: 0.8116 (mmmm) REVERT: E 50 GLU cc_start: 0.7609 (tp30) cc_final: 0.7046 (tp30) REVERT: F 91 LYS cc_start: 0.8770 (ttpp) cc_final: 0.8554 (ttpt) REVERT: G 92 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.6973 (t70) REVERT: G 93 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7679 (t0) REVERT: H 51 THR cc_start: 0.7106 (m) cc_final: 0.6806 (p) REVERT: H 93 SER cc_start: 0.8771 (t) cc_final: 0.8370 (p) REVERT: H 96 GLU cc_start: 0.7908 (pm20) cc_final: 0.7197 (pm20) REVERT: H 104 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8488 (tp) REVERT: H 119 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7529 (ptm160) REVERT: H 123 LYS cc_start: 0.8221 (mppt) cc_final: 0.7854 (mppt) REVERT: K 209 LYS cc_start: 0.7183 (pptt) cc_final: 0.6931 (pptt) REVERT: K 210 GLN cc_start: 0.6722 (pp30) cc_final: 0.6490 (tt0) REVERT: K 233 TYR cc_start: 0.5646 (OUTLIER) cc_final: 0.3627 (p90) REVERT: K 238 GLU cc_start: 0.8185 (pm20) cc_final: 0.7914 (pm20) REVERT: K 300 TYR cc_start: 0.6340 (t80) cc_final: 0.5118 (t80) REVERT: K 402 ILE cc_start: 0.8765 (pt) cc_final: 0.8434 (mm) REVERT: L 34 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7926 (tp40) REVERT: M 133 TYR cc_start: 0.4774 (m-10) cc_final: 0.3818 (m-10) REVERT: M 237 GLN cc_start: 0.6202 (pm20) cc_final: 0.5863 (pm20) REVERT: M 327 ASP cc_start: 0.6048 (m-30) cc_final: 0.5598 (m-30) REVERT: M 341 LEU cc_start: 0.8364 (pt) cc_final: 0.7814 (mt) REVERT: M 342 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7315 (tmtm) REVERT: M 353 LYS cc_start: 0.7676 (pttp) cc_final: 0.7361 (ptpp) outliers start: 70 outliers final: 43 residues processed: 466 average time/residue: 0.2003 time to fit residues: 125.4485 Evaluate side-chains 475 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 422 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 271 PHE Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 379 MET Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain K residue 398 LYS Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 363 ASN Chi-restraints excluded: chain N residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 107 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN H 66 ASN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.109639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091770 restraints weight = 54028.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094004 restraints weight = 30244.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.095462 restraints weight = 20006.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096436 restraints weight = 15042.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097057 restraints weight = 12435.291| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.9343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 17881 Z= 0.298 Angle : 1.010 17.121 25382 Z= 0.526 Chirality : 0.051 0.262 2864 Planarity : 0.007 0.066 2198 Dihedral : 28.526 177.729 4767 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 23.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 5.67 % Allowed : 36.36 % Favored : 57.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.31 % 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 aren not related in a simple way. whole: -3.19 (0.22), residues: 1323 helix: -1.44 (0.19), residues: 671 sheet: -2.62 (0.93), residues: 27 loop : -2.89 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 350 TYR 0.041 0.003 TYR N 23 PHE 0.041 0.003 PHE K 194 TRP 0.010 0.002 TRP M 361 HIS 0.015 0.002 HIS K 364 Details of bonding type rmsd covalent geometry : bond 0.00679 (17881) covalent geometry : angle 1.01044 (25382) hydrogen bonds : bond 0.06056 ( 735) hydrogen bonds : angle 4.31984 ( 1811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.45 seconds wall clock time: 63 minutes 47.06 seconds (3827.06 seconds total)