Starting phenix.real_space_refine on Wed May 21 02:34:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2z_38023/05_2025/8x2z_38023.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2z_38023/05_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_38023/05_2025/8x2z_38023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2z_38023/05_2025/8x2z_38023.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2z_38023/05_2025/8x2z_38023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2z_38023/05_2025/8x2z_38023.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.52, per 1000 atoms: 0.56 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: 4.18 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 7.32 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: 6.59 Time building geometry restraints manager: 4.93 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.150 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.760 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.003 TRP K 353 HIS 0.013 0.003 HIS F 75 PHE 0.044 0.004 PHE M 171 TYR 0.048 0.005 TYR N 23 ARG 0.027 0.001 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.15719 ( 735) hydrogen bonds : angle 6.57463 ( 1811) covalent geometry : bond 0.00709 (17881) covalent geometry : angle 1.28371 (25382) *********************** 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 : 1.462 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: 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: 0.3671 time to fit residues: 281.4611 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 : 1.516 ------------------------------------------------------------------------------- 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 132 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 80 optimal weight: 0.0060 chunk 63 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS D 59 GLN F 27 GLN G 84 HIS H 66 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 210 GLN K 222 HIS ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 363 ASN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.112429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095258 restraints weight = 53909.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.097546 restraints weight = 28963.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.099058 restraints weight = 18725.482| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3873 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= 0.207 Angle : 0.898 17.478 25382 Z= 0.488 Chirality : 0.047 0.242 2864 Planarity : 0.007 0.132 2198 Dihedral : 29.312 171.714 4790 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 6.92 % Allowed : 23.19 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.19), residues: 1323 helix: -2.31 (0.17), residues: 620 sheet: -1.63 (1.07), residues: 22 loop : -3.29 (0.20), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 130 HIS 0.007 0.001 HIS C 111 PHE 0.030 0.003 PHE K 323 TYR 0.044 0.003 TYR D 86 ARG 0.010 0.001 ARG G 83 Details of bonding type rmsd hydrogen bonds : bond 0.05669 ( 735) hydrogen bonds : angle 4.55775 ( 1811) covalent geometry : bond 0.00442 (17881) covalent geometry : angle 0.89803 (25382) *********************** 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 554 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 471 time to evaluate : 1.418 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 59 GLU cc_start: 0.7823 (pp20) cc_final: 0.7418 (pp20) REVERT: A 97 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7074 (mt-10) REVERT: B 55 ARG cc_start: 0.8397 (mpp80) cc_final: 0.8127 (mtm-85) REVERT: C 32 LYS cc_start: 0.8402 (ttmm) cc_final: 0.7967 (ttmm) REVERT: C 37 ARG cc_start: 0.8389 (ttp80) cc_final: 0.8178 (ttt-90) REVERT: C 63 GLU cc_start: 0.6306 (pm20) cc_final: 0.5821 (pm20) REVERT: C 76 LYS cc_start: 0.7731 (tttt) cc_final: 0.7387 (tttt) REVERT: D 44 ILE cc_start: 0.8412 (pp) cc_final: 0.7977 (pt) REVERT: D 68 PHE cc_start: 0.8076 (t80) cc_final: 0.7144 (t80) REVERT: D 74 GLU cc_start: 0.6965 (tp30) cc_final: 0.6611 (tp30) REVERT: D 96 GLU cc_start: 0.7157 (pp20) cc_final: 0.6811 (tm-30) REVERT: E 42 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6246 (pmmt) REVERT: E 50 GLU cc_start: 0.6922 (tp30) cc_final: 0.6520 (tp30) REVERT: E 62 ILE cc_start: 0.8263 (tp) cc_final: 0.7756 (tp) REVERT: E 82 LEU cc_start: 0.7605 (mp) cc_final: 0.6588 (mp) REVERT: F 27 GLN cc_start: 0.7856 (mm110) cc_final: 0.7425 (mp10) REVERT: F 60 SER cc_start: 0.8166 (m) cc_final: 0.7414 (t) REVERT: F 72 TYR cc_start: 0.8366 (m-80) cc_final: 0.8120 (m-80) REVERT: F 74 GLU cc_start: 0.7514 (pp20) cc_final: 0.7275 (pp20) REVERT: F 79 LYS cc_start: 0.7567 (ptmm) cc_final: 0.7059 (tppt) REVERT: F 87 VAL cc_start: 0.8042 (m) cc_final: 0.7812 (p) REVERT: G 24 LEU cc_start: 0.7867 (mm) cc_final: 0.7619 (mp) REVERT: G 57 LEU cc_start: 0.8644 (tt) cc_final: 0.8301 (tp) REVERT: H 51 THR cc_start: 0.6559 (m) cc_final: 0.6279 (p) REVERT: H 70 ASN cc_start: 0.8439 (t0) cc_final: 0.8199 (t0) REVERT: H 118 THR cc_start: 0.7942 (m) cc_final: 0.7665 (t) REVERT: H 119 ARG cc_start: 0.8033 (ptm-80) cc_final: 0.7537 (ttt-90) REVERT: K 172 MET cc_start: 0.6484 (tmm) cc_final: 0.6087 (tmm) REVERT: K 210 GLN cc_start: 0.5953 (OUTLIER) cc_final: 0.5735 (pp30) REVERT: K 242 ARG cc_start: 0.7896 (tpt-90) cc_final: 0.7395 (tpt-90) REVERT: K 333 LYS cc_start: 0.8583 (tmtm) cc_final: 0.8210 (tmtm) REVERT: K 350 ARG cc_start: 0.7303 (mmm-85) cc_final: 0.6681 (mmm-85) REVERT: K 356 THR cc_start: 0.7494 (m) cc_final: 0.7116 (p) REVERT: K 379 MET cc_start: 0.5253 (tmt) cc_final: 0.4523 (tmt) REVERT: K 393 ILE cc_start: 0.5520 (OUTLIER) cc_final: 0.5291 (pp) REVERT: L 31 ASN cc_start: 0.7868 (p0) cc_final: 0.6867 (p0) REVERT: L 33 GLN cc_start: 0.8171 (pm20) cc_final: 0.7432 (mp10) REVERT: L 34 GLN cc_start: 0.8424 (mm110) cc_final: 0.8055 (mp10) REVERT: M 133 TYR cc_start: 0.5140 (m-80) cc_final: 0.4589 (m-80) REVERT: M 169 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7325 (mt-10) REVERT: M 209 MET cc_start: 0.5524 (pp-130) cc_final: 0.5247 (pp-130) REVERT: M 232 PHE cc_start: 0.6711 (p90) cc_final: 0.6231 (p90) REVERT: M 279 TRP cc_start: 0.7595 (t-100) cc_final: 0.7011 (t-100) REVERT: N 13 ASP cc_start: 0.5937 (p0) cc_final: 0.5422 (p0) REVERT: N 23 TYR cc_start: 0.5872 (m-80) cc_final: 0.5468 (m-80) outliers start: 83 outliers final: 39 residues processed: 511 average time/residue: 0.3629 time to fit residues: 254.0944 Evaluate side-chains 476 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 434 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 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 81 THR Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 42 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 F residue 98 TYR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 49 LYS 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 97 ILE Chi-restraints excluded: chain K residue 181 TYR Chi-restraints excluded: chain K residue 210 GLN Chi-restraints excluded: chain K residue 222 HIS Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 393 ILE Chi-restraints excluded: chain K residue 432 LYS 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 275 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 66 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 85 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN K 406 ASN ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 HIS ** 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 = 0.3899 r_free = 0.3899 target = 0.112084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094719 restraints weight = 54694.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.097030 restraints weight = 29468.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.098512 restraints weight = 19097.020| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17881 Z= 0.215 Angle : 0.870 16.517 25382 Z= 0.472 Chirality : 0.046 0.217 2864 Planarity : 0.007 0.110 2198 Dihedral : 29.079 170.124 4783 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 7.92 % Allowed : 24.69 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.20), residues: 1323 helix: -1.83 (0.18), residues: 647 sheet: -1.87 (0.90), residues: 22 loop : -3.25 (0.21), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 130 HIS 0.024 0.002 HIS K 222 PHE 0.038 0.002 PHE M 217 TYR 0.049 0.003 TYR N 23 ARG 0.013 0.001 ARG G 83 Details of bonding type rmsd hydrogen bonds : bond 0.05518 ( 735) hydrogen bonds : angle 4.28982 ( 1811) covalent geometry : bond 0.00472 (17881) covalent geometry : angle 0.87019 (25382) *********************** 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 574 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 479 time to evaluate : 1.356 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 40 ARG cc_start: 0.7288 (tpp80) cc_final: 0.7062 (mmm160) REVERT: A 50 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7419 (mt-10) REVERT: A 125 LYS cc_start: 0.8480 (ptmm) cc_final: 0.8273 (ptmm) REVERT: C 21 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6572 (ppp-140) REVERT: C 32 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8215 (ttmm) REVERT: C 63 GLU cc_start: 0.6735 (pm20) cc_final: 0.6454 (pm20) REVERT: C 105 SER cc_start: 0.9253 (OUTLIER) cc_final: 0.8880 (p) REVERT: D 44 ILE cc_start: 0.8493 (pp) cc_final: 0.8065 (pt) REVERT: D 64 ILE cc_start: 0.7837 (mm) cc_final: 0.7420 (mm) REVERT: D 74 GLU cc_start: 0.7254 (tp30) cc_final: 0.6742 (tp30) REVERT: D 82 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8255 (mmmt) REVERT: D 96 GLU cc_start: 0.7131 (pp20) cc_final: 0.6930 (tm-30) REVERT: D 111 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7442 (mtmm) REVERT: E 50 GLU cc_start: 0.7277 (tp30) cc_final: 0.7014 (tp30) REVERT: E 121 LYS cc_start: 0.8359 (mttp) cc_final: 0.7991 (mttt) REVERT: E 122 LYS cc_start: 0.7711 (pptt) cc_final: 0.7468 (pttp) REVERT: E 128 ARG cc_start: 0.8763 (mtp85) cc_final: 0.8497 (mtp85) REVERT: F 60 SER cc_start: 0.8210 (m) cc_final: 0.7616 (t) REVERT: F 91 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8155 (ttpt) REVERT: G 38 HIS cc_start: 0.7437 (t70) cc_final: 0.6974 (t-90) REVERT: G 80 ILE cc_start: 0.7115 (pt) cc_final: 0.6811 (pt) REVERT: H 51 THR cc_start: 0.7099 (m) cc_final: 0.6624 (p) REVERT: H 74 GLU cc_start: 0.7898 (tp30) cc_final: 0.7211 (tp30) REVERT: H 119 ARG cc_start: 0.8048 (ptm-80) cc_final: 0.7675 (ttp80) REVERT: K 252 CYS cc_start: 0.8088 (p) cc_final: 0.7361 (t) REVERT: K 300 TYR cc_start: 0.6270 (t80) cc_final: 0.4415 (t80) REVERT: K 321 ILE cc_start: 0.8517 (tt) cc_final: 0.8250 (tp) REVERT: K 322 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6575 (pm20) REVERT: K 347 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7586 (tt) REVERT: K 373 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8573 (mp) REVERT: K 379 MET cc_start: 0.6099 (tmt) cc_final: 0.5594 (tmt) REVERT: M 155 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7755 (mm-30) REVERT: M 209 MET cc_start: 0.5367 (pp-130) cc_final: 0.5070 (pp-130) REVERT: M 215 LEU cc_start: 0.8467 (pp) cc_final: 0.8258 (pp) REVERT: M 232 PHE cc_start: 0.6873 (p90) cc_final: 0.6553 (p90) REVERT: M 278 TYR cc_start: 0.7033 (t80) cc_final: 0.6461 (t80) REVERT: N 85 GLU cc_start: 0.8684 (pp20) cc_final: 0.8266 (pp20) outliers start: 95 outliers final: 43 residues processed: 521 average time/residue: 0.3717 time to fit residues: 264.7352 Evaluate side-chains 499 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 451 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE 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 57 LEU Chi-restraints excluded: chain C residue 83 ARG 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 118 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain F residue 49 LEU 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 75 LEU Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE 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 97 ILE Chi-restraints excluded: chain K residue 222 HIS Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 301 ASN 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 373 ILE Chi-restraints excluded: chain K residue 432 LYS Chi-restraints excluded: chain M residue 174 GLU 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 1 MET Chi-restraints excluded: chain N residue 87 CYS 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 111 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 93 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 87 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS H 66 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS M 163 ASN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095638 restraints weight = 54353.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097871 restraints weight = 30098.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.099357 restraints weight = 19820.986| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17881 Z= 0.184 Angle : 0.836 12.801 25382 Z= 0.448 Chirality : 0.045 0.224 2864 Planarity : 0.006 0.145 2198 Dihedral : 28.853 172.431 4775 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 7.26 % Allowed : 29.27 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.21), residues: 1323 helix: -1.49 (0.19), residues: 635 sheet: -2.01 (0.95), residues: 22 loop : -3.12 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 247 HIS 0.005 0.001 HIS K 222 PHE 0.031 0.002 PHE M 217 TYR 0.036 0.002 TYR N 23 ARG 0.011 0.001 ARG G 83 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 735) hydrogen bonds : angle 4.14307 ( 1811) covalent geometry : bond 0.00409 (17881) covalent geometry : angle 0.83580 (25382) *********************** 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 563 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 476 time to evaluate : 1.289 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: A 49 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8116 (mtp-110) REVERT: A 50 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 72 ARG cc_start: 0.8481 (mtt90) cc_final: 0.8207 (mtt90) REVERT: A 76 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8253 (pm20) REVERT: A 106 ASP cc_start: 0.7642 (p0) cc_final: 0.7340 (p0) REVERT: C 21 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6591 (ppp-140) REVERT: C 32 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8207 (ttmm) REVERT: C 51 ILE cc_start: 0.5507 (OUTLIER) cc_final: 0.5271 (tt) REVERT: C 59 TYR cc_start: 0.6846 (m-10) cc_final: 0.6607 (m-10) REVERT: C 79 ARG cc_start: 0.7185 (ttp80) cc_final: 0.6963 (ttp80) REVERT: C 105 SER cc_start: 0.9317 (OUTLIER) cc_final: 0.8997 (p) REVERT: D 44 ILE cc_start: 0.8665 (pp) cc_final: 0.8383 (pt) REVERT: D 62 MET cc_start: 0.8105 (tpp) cc_final: 0.7751 (mmm) REVERT: D 64 ILE cc_start: 0.7920 (mm) cc_final: 0.7525 (mm) REVERT: D 79 GLU cc_start: 0.7505 (pp20) cc_final: 0.7222 (pp20) REVERT: D 82 LYS cc_start: 0.8515 (mtpp) cc_final: 0.8239 (mmmt) REVERT: D 111 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7439 (mtmm) REVERT: E 50 GLU cc_start: 0.7357 (tp30) cc_final: 0.7111 (tp30) REVERT: E 59 GLU cc_start: 0.8229 (pm20) cc_final: 0.8003 (pm20) REVERT: E 128 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8574 (mtp180) REVERT: F 51 TYR cc_start: 0.8485 (m-80) cc_final: 0.8279 (m-10) REVERT: F 60 SER cc_start: 0.8206 (m) cc_final: 0.7895 (t) REVERT: F 91 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8277 (ttpt) REVERT: F 98 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7180 (t80) REVERT: G 21 ARG cc_start: 0.8108 (ppt170) cc_final: 0.7660 (ppt170) REVERT: G 38 HIS cc_start: 0.7393 (t70) cc_final: 0.6788 (t-90) REVERT: H 46 LYS cc_start: 0.8306 (tttm) cc_final: 0.8007 (ttpp) REVERT: H 49 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7434 (tmmt) REVERT: H 51 THR cc_start: 0.7170 (m) cc_final: 0.6762 (p) REVERT: H 74 GLU cc_start: 0.7812 (tp30) cc_final: 0.7170 (tp30) REVERT: H 119 ARG cc_start: 0.8084 (ptm-80) cc_final: 0.7560 (tmm160) REVERT: K 252 CYS cc_start: 0.8175 (p) cc_final: 0.7488 (t) REVERT: K 322 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6343 (pm20) REVERT: K 333 LYS cc_start: 0.8802 (tppt) cc_final: 0.8448 (tppt) REVERT: L 33 GLN cc_start: 0.8198 (pm20) cc_final: 0.7399 (mp10) REVERT: L 34 GLN cc_start: 0.8491 (mm-40) cc_final: 0.7825 (mp10) REVERT: M 209 MET cc_start: 0.5342 (pp-130) cc_final: 0.5047 (pp-130) REVERT: M 215 LEU cc_start: 0.8464 (pp) cc_final: 0.8191 (pp) REVERT: M 232 PHE cc_start: 0.7031 (p90) cc_final: 0.6163 (p90) REVERT: M 279 TRP cc_start: 0.7664 (t-100) cc_final: 0.7147 (t-100) REVERT: M 345 LYS cc_start: 0.7780 (mttt) cc_final: 0.7311 (mmtp) REVERT: N 22 ARG cc_start: 0.7666 (mmm160) cc_final: 0.6713 (mmm160) REVERT: N 85 GLU cc_start: 0.8764 (pp20) cc_final: 0.8159 (pp20) outliers start: 87 outliers final: 41 residues processed: 518 average time/residue: 0.3715 time to fit residues: 260.7441 Evaluate side-chains 487 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 439 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 115 LYS 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 51 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 83 ARG 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 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain F residue 50 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 F residue 98 TYR 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 49 LYS Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain K residue 217 LYS Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 275 CYS 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 K residue 432 LYS Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 108 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS G 38 HIS H 52 HIS H 66 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 363 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 = 0.3789 r_free = 0.3789 target = 0.105836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.088554 restraints weight = 53658.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.090735 restraints weight = 29626.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092173 restraints weight = 19335.077| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.8482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17881 Z= 0.324 Angle : 0.987 14.264 25382 Z= 0.534 Chirality : 0.054 0.253 2864 Planarity : 0.007 0.096 2198 Dihedral : 29.212 176.238 4769 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 28.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 9.17 % Allowed : 29.94 % Favored : 60.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.21), residues: 1323 helix: -1.46 (0.18), residues: 638 sheet: -2.15 (1.02), residues: 27 loop : -3.05 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP K 353 HIS 0.007 0.002 HIS G 84 PHE 0.038 0.003 PHE M 217 TYR 0.054 0.003 TYR K 352 ARG 0.012 0.001 ARG M 335 Details of bonding type rmsd hydrogen bonds : bond 0.07304 ( 735) hydrogen bonds : angle 4.51287 ( 1811) covalent geometry : bond 0.00732 (17881) covalent geometry : angle 0.98743 (25382) *********************** 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 598 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 488 time to evaluate : 1.484 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: A 42 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8273 (mmtp) REVERT: A 49 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8214 (mtp-110) REVERT: A 50 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7234 (mt-10) REVERT: A 76 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8409 (pp30) REVERT: B 49 LEU cc_start: 0.9028 (mt) cc_final: 0.8683 (mp) REVERT: B 55 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.7907 (ttm110) REVERT: B 59 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7888 (tptp) REVERT: B 60 SER cc_start: 0.8500 (p) cc_final: 0.8233 (p) REVERT: B 92 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.6928 (tpt-90) REVERT: C 32 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8244 (ttmm) REVERT: C 59 TYR cc_start: 0.6850 (m-10) cc_final: 0.6541 (m-10) REVERT: C 105 SER cc_start: 0.9418 (OUTLIER) cc_final: 0.9176 (p) REVERT: D 41 SER cc_start: 0.8702 (m) cc_final: 0.8395 (p) REVERT: D 44 ILE cc_start: 0.8599 (pp) cc_final: 0.8209 (pt) REVERT: D 51 THR cc_start: 0.8684 (t) cc_final: 0.8333 (p) REVERT: D 79 GLU cc_start: 0.7445 (pp20) cc_final: 0.7022 (pp20) REVERT: D 82 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8005 (mmmt) REVERT: D 86 TYR cc_start: 0.7942 (p90) cc_final: 0.7042 (p90) REVERT: D 97 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8410 (tt) REVERT: D 102 ARG cc_start: 0.8731 (mtp-110) cc_final: 0.8526 (ttp80) REVERT: D 119 ARG cc_start: 0.8605 (ptm-80) cc_final: 0.8368 (ptm-80) REVERT: E 50 GLU cc_start: 0.7631 (tp30) cc_final: 0.7103 (tp30) REVERT: E 53 ARG cc_start: 0.8250 (ptm-80) cc_final: 0.8032 (ptm-80) REVERT: E 74 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8502 (tt) REVERT: E 128 ARG cc_start: 0.8925 (mtp85) cc_final: 0.8710 (mtp180) REVERT: F 31 LYS cc_start: 0.7659 (tmmt) cc_final: 0.7087 (tttm) REVERT: F 36 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7896 (mtm-85) REVERT: F 92 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8656 (tmt-80) REVERT: F 98 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7283 (t80) REVERT: G 21 ARG cc_start: 0.8315 (ppt170) cc_final: 0.7544 (ppt170) REVERT: G 38 HIS cc_start: 0.7769 (t-90) cc_final: 0.7374 (t70) REVERT: H 49 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7656 (tmmt) REVERT: H 74 GLU cc_start: 0.8009 (tp30) cc_final: 0.7410 (tp30) REVERT: H 119 ARG cc_start: 0.8198 (ptm-80) cc_final: 0.7781 (tmm160) REVERT: K 233 TYR cc_start: 0.5744 (OUTLIER) cc_final: 0.3635 (p90) REVERT: K 237 PHE cc_start: 0.6822 (p90) cc_final: 0.6472 (p90) REVERT: K 272 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8206 (tp) REVERT: K 279 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7876 (tpt90) REVERT: K 304 CYS cc_start: 0.7392 (p) cc_final: 0.7106 (p) REVERT: K 319 LEU cc_start: 0.8752 (pt) cc_final: 0.8470 (pp) REVERT: K 322 GLU cc_start: 0.7404 (pm20) cc_final: 0.6884 (pm20) REVERT: K 347 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8068 (tt) REVERT: K 379 MET cc_start: 0.6473 (tmt) cc_final: 0.6146 (tmt) REVERT: K 401 HIS cc_start: 0.6698 (p-80) cc_final: 0.6398 (p-80) REVERT: K 436 PHE cc_start: 0.6756 (p90) cc_final: 0.6555 (p90) REVERT: L 34 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8136 (tp40) REVERT: L 35 GLU cc_start: 0.8356 (pm20) cc_final: 0.8150 (pm20) REVERT: M 189 PHE cc_start: 0.7640 (m-10) cc_final: 0.7418 (m-10) REVERT: M 197 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7472 (mp0) REVERT: M 209 MET cc_start: 0.5637 (pp-130) cc_final: 0.5330 (pp-130) REVERT: M 215 LEU cc_start: 0.8565 (pp) cc_final: 0.8290 (pp) REVERT: M 217 PHE cc_start: 0.6860 (p90) cc_final: 0.6539 (p90) REVERT: M 238 LEU cc_start: 0.8145 (tm) cc_final: 0.7506 (tm) REVERT: M 267 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.5156 (mp) REVERT: M 341 LEU cc_start: 0.8457 (pt) cc_final: 0.7928 (mt) REVERT: M 342 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7361 (tmtm) REVERT: N 13 ASP cc_start: 0.7044 (p0) cc_final: 0.6787 (p0) REVERT: N 25 LEU cc_start: 0.6589 (mm) cc_final: 0.6373 (tp) REVERT: N 31 ASN cc_start: 0.5989 (p0) cc_final: 0.5535 (p0) outliers start: 110 outliers final: 51 residues processed: 537 average time/residue: 0.4059 time to fit residues: 297.0031 Evaluate side-chains 519 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 452 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 72 ARG Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE 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 38 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 45 VAL 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 49 LYS Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 272 LEU Chi-restraints excluded: chain K residue 275 CYS Chi-restraints excluded: chain K residue 279 ARG Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 242 ILE Chi-restraints excluded: chain M residue 265 ILE Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain M residue 290 GLU 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 108 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 53 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS H 52 HIS K 301 ASN M 163 ASN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.110032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.092323 restraints weight = 54287.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.094581 restraints weight = 29974.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096090 restraints weight = 19660.856| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.8708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17881 Z= 0.195 Angle : 0.885 12.837 25382 Z= 0.472 Chirality : 0.046 0.247 2864 Planarity : 0.006 0.081 2198 Dihedral : 28.972 174.240 4769 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 7.51 % Allowed : 33.03 % Favored : 59.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.21), residues: 1323 helix: -1.31 (0.19), residues: 646 sheet: -2.00 (1.08), residues: 27 loop : -2.87 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 279 HIS 0.005 0.001 HIS F 75 PHE 0.031 0.002 PHE M 217 TYR 0.037 0.002 TYR K 352 ARG 0.015 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.05456 ( 735) hydrogen bonds : angle 4.29654 ( 1811) covalent geometry : bond 0.00441 (17881) covalent geometry : angle 0.88454 (25382) *********************** 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 560 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 470 time to evaluate : 1.460 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 49 ARG cc_start: 0.8380 (mtp85) cc_final: 0.8069 (mtp-110) REVERT: A 50 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7325 (mt-10) REVERT: A 69 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7287 (mtm180) REVERT: A 73 GLU cc_start: 0.7040 (tp30) cc_final: 0.6733 (tp30) REVERT: A 74 ILE cc_start: 0.8832 (tt) cc_final: 0.8466 (tp) REVERT: A 105 GLU cc_start: 0.7677 (pp20) cc_final: 0.7421 (pp20) REVERT: A 106 ASP cc_start: 0.7645 (p0) cc_final: 0.7107 (p0) REVERT: A 115 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8783 (tppp) REVERT: B 59 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8016 (tptp) REVERT: B 92 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7051 (tpt-90) REVERT: C 74 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7042 (m-30) REVERT: C 76 LYS cc_start: 0.8372 (tttt) cc_final: 0.7721 (tptt) REVERT: C 86 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7453 (mp10) REVERT: C 105 SER cc_start: 0.9385 (m) cc_final: 0.9109 (p) REVERT: D 79 GLU cc_start: 0.7461 (pp20) cc_final: 0.7022 (pp20) REVERT: D 82 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8078 (mmmt) REVERT: D 83 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.7983 (tp) REVERT: D 86 TYR cc_start: 0.7675 (p90) cc_final: 0.7302 (p90) REVERT: D 102 ARG cc_start: 0.8779 (mtp-110) cc_final: 0.8525 (ttp80) REVERT: E 50 GLU cc_start: 0.7618 (tp30) cc_final: 0.6981 (tp30) REVERT: E 51 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8680 (tt) REVERT: E 53 ARG cc_start: 0.8129 (ptm-80) cc_final: 0.7908 (ptm-80) REVERT: E 128 ARG cc_start: 0.8965 (mtp85) cc_final: 0.8713 (mtp180) REVERT: F 51 TYR cc_start: 0.8272 (m-80) cc_final: 0.8018 (m-10) REVERT: F 98 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7294 (t80) REVERT: G 21 ARG cc_start: 0.8246 (ppt170) cc_final: 0.7664 (ppt170) REVERT: G 38 HIS cc_start: 0.7672 (t-90) cc_final: 0.6896 (t-90) REVERT: H 37 LYS cc_start: 0.8569 (tptp) cc_final: 0.8237 (tptp) REVERT: H 38 GLU cc_start: 0.7359 (tp30) cc_final: 0.6893 (tp30) REVERT: H 49 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7605 (tmmt) REVERT: H 74 GLU cc_start: 0.7790 (tp30) cc_final: 0.6880 (tp30) REVERT: H 96 GLU cc_start: 0.7941 (pm20) cc_final: 0.7395 (pp20) REVERT: H 104 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8676 (tp) REVERT: H 119 ARG cc_start: 0.8123 (ptm-80) cc_final: 0.7873 (ptm-80) REVERT: K 175 TYR cc_start: 0.6497 (m-80) cc_final: 0.6184 (m-80) REVERT: K 218 CYS cc_start: 0.7247 (t) cc_final: 0.6843 (t) REVERT: K 233 TYR cc_start: 0.5549 (OUTLIER) cc_final: 0.3932 (p90) REVERT: K 267 ASP cc_start: 0.6570 (t70) cc_final: 0.6269 (t70) REVERT: K 279 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7652 (tpt90) REVERT: K 322 GLU cc_start: 0.7563 (pm20) cc_final: 0.7179 (pm20) REVERT: K 346 LEU cc_start: 0.7660 (pt) cc_final: 0.7418 (pt) REVERT: K 347 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8123 (tt) REVERT: K 379 MET cc_start: 0.6189 (tmt) cc_final: 0.5842 (tmt) REVERT: K 386 HIS cc_start: 0.8404 (t-90) cc_final: 0.8163 (t70) REVERT: K 401 HIS cc_start: 0.6749 (p-80) cc_final: 0.6397 (p-80) REVERT: K 436 PHE cc_start: 0.6641 (p90) cc_final: 0.6368 (p90) REVERT: L 40 GLU cc_start: 0.8008 (pp20) cc_final: 0.7478 (pp20) REVERT: M 209 MET cc_start: 0.5657 (pp-130) cc_final: 0.5291 (pp-130) REVERT: M 217 PHE cc_start: 0.6350 (p90) cc_final: 0.6068 (p90) REVERT: M 238 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7645 (tm) REVERT: M 342 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7504 (tmtm) REVERT: N 13 ASP cc_start: 0.6762 (p0) cc_final: 0.6423 (p0) REVERT: N 31 ASN cc_start: 0.5962 (p0) cc_final: 0.5695 (p0) outliers start: 90 outliers final: 36 residues processed: 508 average time/residue: 0.3871 time to fit residues: 263.3692 Evaluate side-chains 497 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 446 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 124 ILE 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 91 LYS 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 83 ARG 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 D residue 38 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 98 TYR 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 H residue 49 LYS 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 275 CYS Chi-restraints excluded: chain K residue 279 ARG Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 289 TYR Chi-restraints excluded: chain K residue 301 ASN Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 242 ILE Chi-restraints excluded: chain M residue 279 TRP Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 82 LEU 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 12 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 123 optimal weight: 0.0050 chunk 143 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 150 optimal weight: 2.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 HIS H 52 HIS H 66 ASN M 163 ASN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 363 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 = 0.3897 r_free = 0.3897 target = 0.111908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.094242 restraints weight = 54322.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.096496 restraints weight = 30268.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.098009 restraints weight = 19986.857| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.8979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17881 Z= 0.182 Angle : 0.908 14.454 25382 Z= 0.475 Chirality : 0.046 0.262 2864 Planarity : 0.006 0.082 2198 Dihedral : 28.757 176.311 4769 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 5.59 % Allowed : 35.70 % Favored : 58.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.21), residues: 1323 helix: -1.33 (0.19), residues: 645 sheet: -1.73 (1.17), residues: 22 loop : -2.80 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 279 HIS 0.005 0.001 HIS H 52 PHE 0.030 0.002 PHE M 217 TYR 0.032 0.002 TYR D 45 ARG 0.014 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.05178 ( 735) hydrogen bonds : angle 4.27945 ( 1811) covalent geometry : bond 0.00409 (17881) covalent geometry : angle 0.90791 (25382) *********************** 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 516 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 449 time to evaluate : 1.315 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: A 49 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7952 (mtp-110) REVERT: A 50 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 73 GLU cc_start: 0.7028 (tp30) cc_final: 0.6671 (tp30) REVERT: A 74 ILE cc_start: 0.8862 (tt) cc_final: 0.8470 (tp) REVERT: A 106 ASP cc_start: 0.7730 (p0) cc_final: 0.7472 (p0) REVERT: A 115 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8756 (tppp) REVERT: A 129 ARG cc_start: 0.8359 (tpt90) cc_final: 0.8126 (tpt-90) REVERT: A 131 ARG cc_start: 0.8851 (mtp85) cc_final: 0.8636 (mtp85) REVERT: B 59 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8044 (tptp) REVERT: C 74 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: C 76 LYS cc_start: 0.8510 (tttt) cc_final: 0.7873 (tptt) REVERT: C 99 ILE cc_start: 0.7967 (mp) cc_final: 0.7724 (mp) REVERT: C 105 SER cc_start: 0.9414 (m) cc_final: 0.9051 (p) REVERT: D 79 GLU cc_start: 0.7488 (pp20) cc_final: 0.7179 (pp20) REVERT: D 86 TYR cc_start: 0.7628 (p90) cc_final: 0.7365 (p90) REVERT: D 95 ARG cc_start: 0.8205 (ptm160) cc_final: 0.7943 (ptm160) REVERT: D 96 GLU cc_start: 0.8017 (tp30) cc_final: 0.7781 (tp30) REVERT: E 50 GLU cc_start: 0.7613 (tp30) cc_final: 0.6946 (tp30) REVERT: E 51 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8597 (tt) REVERT: E 53 ARG cc_start: 0.8080 (ptm-80) cc_final: 0.7845 (ptm-80) REVERT: E 128 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8588 (mtp180) REVERT: F 29 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7788 (mm) REVERT: F 98 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7258 (t80) REVERT: G 21 ARG cc_start: 0.8166 (ppt170) cc_final: 0.7673 (ppt170) REVERT: G 38 HIS cc_start: 0.7715 (t-90) cc_final: 0.6925 (t-90) REVERT: H 37 LYS cc_start: 0.8538 (tptp) cc_final: 0.8140 (tptp) REVERT: H 38 GLU cc_start: 0.7059 (tp30) cc_final: 0.6548 (tp30) REVERT: H 48 LEU cc_start: 0.8181 (pp) cc_final: 0.7923 (pp) REVERT: H 49 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7541 (tmmt) REVERT: H 74 GLU cc_start: 0.7762 (tp30) cc_final: 0.6962 (tp30) REVERT: H 104 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8588 (tp) REVERT: K 233 TYR cc_start: 0.5852 (OUTLIER) cc_final: 0.3945 (p90) REVERT: K 267 ASP cc_start: 0.6596 (t70) cc_final: 0.6308 (t70) REVERT: K 346 LEU cc_start: 0.7643 (pt) cc_final: 0.7274 (pt) REVERT: K 347 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8040 (tt) REVERT: K 379 MET cc_start: 0.6214 (tmt) cc_final: 0.5688 (tmt) REVERT: K 401 HIS cc_start: 0.6672 (p-80) cc_final: 0.6350 (p-80) REVERT: K 436 PHE cc_start: 0.6672 (p90) cc_final: 0.6403 (p90) REVERT: M 133 TYR cc_start: 0.4509 (m-80) cc_final: 0.4212 (m-80) REVERT: M 209 MET cc_start: 0.5528 (pp-130) cc_final: 0.5156 (pp-130) REVERT: M 217 PHE cc_start: 0.6388 (p90) cc_final: 0.6108 (p90) REVERT: M 327 ASP cc_start: 0.6465 (m-30) cc_final: 0.6134 (m-30) REVERT: M 342 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7388 (tmtm) REVERT: N 13 ASP cc_start: 0.6872 (p0) cc_final: 0.6655 (p0) outliers start: 67 outliers final: 39 residues processed: 482 average time/residue: 0.3910 time to fit residues: 253.4307 Evaluate side-chains 475 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 425 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 124 ILE 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 C residue 67 LEU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 77 VAL 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 D residue 38 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 109 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 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 H residue 49 LYS 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 211 TYR 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 289 TYR Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 167 ARG 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 82 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 155 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 132 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN H 52 HIS ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 363 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 = 0.3894 r_free = 0.3894 target = 0.111805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.094115 restraints weight = 53994.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.096345 restraints weight = 30285.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.097844 restraints weight = 20015.581| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.9208 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= 0.186 Angle : 0.913 14.454 25382 Z= 0.478 Chirality : 0.046 0.250 2864 Planarity : 0.006 0.082 2198 Dihedral : 28.610 177.989 4769 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 6.01 % Allowed : 36.03 % Favored : 57.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.21), residues: 1323 helix: -1.38 (0.19), residues: 656 sheet: -2.52 (0.90), residues: 33 loop : -2.76 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP M 279 HIS 0.006 0.001 HIS H 52 PHE 0.027 0.002 PHE M 189 TYR 0.024 0.002 TYR M 162 ARG 0.012 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.05164 ( 735) hydrogen bonds : angle 4.24045 ( 1811) covalent geometry : bond 0.00420 (17881) covalent geometry : angle 0.91270 (25382) *********************** 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 523 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 451 time to evaluate : 1.353 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 49 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7924 (mtp-110) REVERT: A 50 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 69 ARG cc_start: 0.7469 (mtm180) cc_final: 0.6940 (ptt-90) REVERT: A 73 GLU cc_start: 0.7037 (tp30) cc_final: 0.6767 (tp30) REVERT: A 105 GLU cc_start: 0.7821 (pp20) cc_final: 0.7556 (pp20) REVERT: A 106 ASP cc_start: 0.7748 (p0) cc_final: 0.7005 (p0) REVERT: A 131 ARG cc_start: 0.8894 (mtp85) cc_final: 0.8500 (mtp85) REVERT: B 34 ILE cc_start: 0.8808 (pt) cc_final: 0.8509 (mt) REVERT: B 59 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.7970 (tptp) REVERT: B 92 ARG cc_start: 0.8201 (tpt-90) cc_final: 0.7819 (tmt170) REVERT: C 74 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: C 76 LYS cc_start: 0.8424 (tttt) cc_final: 0.7852 (tptt) REVERT: C 99 ILE cc_start: 0.7969 (mp) cc_final: 0.7748 (mp) REVERT: C 105 SER cc_start: 0.9379 (m) cc_final: 0.9117 (p) REVERT: D 79 GLU cc_start: 0.7429 (pp20) cc_final: 0.7172 (pp20) REVERT: E 50 GLU cc_start: 0.7641 (tp30) cc_final: 0.6939 (tp30) REVERT: E 51 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8687 (tt) REVERT: E 53 ARG cc_start: 0.8110 (ptm-80) cc_final: 0.7858 (ptm-80) REVERT: F 44 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8546 (mtmm) REVERT: F 98 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7365 (t80) REVERT: G 38 HIS cc_start: 0.7802 (t-90) cc_final: 0.6928 (t-90) REVERT: G 93 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8289 (t0) REVERT: H 37 LYS cc_start: 0.8598 (tptp) cc_final: 0.8198 (tptp) REVERT: H 48 LEU cc_start: 0.8184 (pp) cc_final: 0.7958 (pp) REVERT: H 49 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7466 (tmmt) REVERT: H 74 GLU cc_start: 0.7844 (tp30) cc_final: 0.6967 (tp30) REVERT: H 96 GLU cc_start: 0.7686 (pp20) cc_final: 0.7454 (pp20) REVERT: H 104 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8626 (tp) REVERT: H 123 LYS cc_start: 0.8215 (mppt) cc_final: 0.7869 (mppt) REVERT: K 218 CYS cc_start: 0.7125 (t) cc_final: 0.6708 (t) REVERT: K 233 TYR cc_start: 0.5830 (OUTLIER) cc_final: 0.3851 (p90) REVERT: K 242 ARG cc_start: 0.7928 (ttt90) cc_final: 0.7711 (ttt90) REVERT: K 267 ASP cc_start: 0.6831 (t70) cc_final: 0.6460 (t70) REVERT: K 319 LEU cc_start: 0.8588 (pp) cc_final: 0.8162 (mp) REVERT: K 333 LYS cc_start: 0.8946 (tppt) cc_final: 0.8642 (tppt) REVERT: K 347 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8039 (tt) REVERT: K 349 TYR cc_start: 0.4800 (p90) cc_final: 0.1706 (p90) REVERT: K 379 MET cc_start: 0.6098 (tmt) cc_final: 0.5658 (tmt) REVERT: K 389 LYS cc_start: 0.8220 (mptt) cc_final: 0.7738 (mmmt) REVERT: K 401 HIS cc_start: 0.6792 (p-80) cc_final: 0.6508 (p-80) REVERT: K 406 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7279 (m-40) REVERT: K 436 PHE cc_start: 0.6646 (p90) cc_final: 0.6423 (p90) REVERT: L 34 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7974 (tp40) REVERT: M 209 MET cc_start: 0.5532 (pp-130) cc_final: 0.5159 (pp-130) REVERT: M 217 PHE cc_start: 0.6348 (p90) cc_final: 0.6114 (p90) REVERT: M 232 PHE cc_start: 0.7060 (p90) cc_final: 0.6541 (p90) REVERT: M 279 TRP cc_start: 0.8270 (t-100) cc_final: 0.7534 (t60) REVERT: M 327 ASP cc_start: 0.6390 (m-30) cc_final: 0.5974 (m-30) REVERT: M 342 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7399 (tmtm) REVERT: M 345 LYS cc_start: 0.7865 (tppt) cc_final: 0.7571 (tmtt) REVERT: N 13 ASP cc_start: 0.6777 (p0) cc_final: 0.6561 (p0) outliers start: 72 outliers final: 41 residues processed: 487 average time/residue: 0.3870 time to fit residues: 253.3594 Evaluate side-chains 488 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 436 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain A residue 124 ILE 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 C residue 67 LEU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 77 VAL 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 D residue 38 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 130 LEU 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 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 49 LYS 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 211 TYR 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 289 TYR Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 406 ASN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 225 ILE 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 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 20 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN H 52 HIS H 66 ASN ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 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 = 0.3836 r_free = 0.3836 target = 0.108460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.090625 restraints weight = 54362.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.092885 restraints weight = 30276.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.094388 restraints weight = 19883.404| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.9582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17881 Z= 0.239 Angle : 0.964 14.386 25382 Z= 0.508 Chirality : 0.049 0.250 2864 Planarity : 0.006 0.077 2198 Dihedral : 28.697 179.847 4769 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 6.26 % Allowed : 36.36 % Favored : 57.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.22), residues: 1323 helix: -1.25 (0.19), residues: 657 sheet: -2.68 (0.89), residues: 33 loop : -2.75 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP M 279 HIS 0.010 0.001 HIS M 248 PHE 0.032 0.002 PHE E 67 TYR 0.026 0.002 TYR K 214 ARG 0.011 0.001 ARG M 235 Details of bonding type rmsd hydrogen bonds : bond 0.05982 ( 735) hydrogen bonds : angle 4.27650 ( 1811) covalent geometry : bond 0.00546 (17881) covalent geometry : angle 0.96423 (25382) *********************** 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 522 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 447 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 69 ARG cc_start: 0.7485 (mtm180) cc_final: 0.6976 (ptt-90) REVERT: A 73 GLU cc_start: 0.7143 (tp30) cc_final: 0.6928 (tp30) REVERT: A 105 GLU cc_start: 0.7812 (pp20) cc_final: 0.7505 (pp20) REVERT: A 106 ASP cc_start: 0.7767 (p0) cc_final: 0.7261 (p0) REVERT: A 115 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8735 (tppp) REVERT: B 59 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8143 (tptp) REVERT: B 92 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.6916 (tpt-90) REVERT: C 76 LYS cc_start: 0.8456 (tttt) cc_final: 0.7881 (tptt) REVERT: C 105 SER cc_start: 0.9347 (m) cc_final: 0.9055 (p) REVERT: D 79 GLU cc_start: 0.7357 (pp20) cc_final: 0.6982 (pp20) REVERT: D 89 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8240 (mmmm) REVERT: E 50 GLU cc_start: 0.7635 (tp30) cc_final: 0.6926 (tp30) REVERT: E 51 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8780 (tt) REVERT: E 53 ARG cc_start: 0.8169 (ptm-80) cc_final: 0.7922 (ptm-80) REVERT: F 29 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8114 (mm) REVERT: F 98 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7276 (t80) REVERT: G 38 HIS cc_start: 0.7744 (t-90) cc_final: 0.7067 (t-90) REVERT: G 93 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8240 (t0) REVERT: H 37 LYS cc_start: 0.8750 (tptp) cc_final: 0.8415 (tptp) REVERT: H 74 GLU cc_start: 0.7861 (tp30) cc_final: 0.6992 (tp30) REVERT: H 104 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8716 (tp) REVERT: H 123 LYS cc_start: 0.8176 (mppt) cc_final: 0.7845 (mppt) REVERT: K 171 ILE cc_start: 0.5661 (OUTLIER) cc_final: 0.5199 (tt) REVERT: K 218 CYS cc_start: 0.7478 (t) cc_final: 0.7046 (t) REVERT: K 233 TYR cc_start: 0.5857 (OUTLIER) cc_final: 0.3976 (p90) REVERT: K 238 GLU cc_start: 0.8281 (pm20) cc_final: 0.7986 (pm20) REVERT: K 319 LEU cc_start: 0.8738 (pp) cc_final: 0.8309 (mp) REVERT: K 349 TYR cc_start: 0.5099 (p90) cc_final: 0.1937 (p90) REVERT: K 350 ARG cc_start: 0.7247 (ttm-80) cc_final: 0.5896 (ttm-80) REVERT: K 379 MET cc_start: 0.5981 (tmt) cc_final: 0.5769 (tmt) REVERT: K 401 HIS cc_start: 0.6893 (p-80) cc_final: 0.6519 (p-80) REVERT: K 436 PHE cc_start: 0.6709 (p90) cc_final: 0.6449 (p90) REVERT: L 34 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7931 (tp40) REVERT: M 209 MET cc_start: 0.5800 (pp-130) cc_final: 0.5350 (pp-130) REVERT: M 279 TRP cc_start: 0.8381 (t-100) cc_final: 0.7742 (t60) REVERT: M 327 ASP cc_start: 0.6431 (m-30) cc_final: 0.6034 (m-30) REVERT: M 341 LEU cc_start: 0.8341 (pt) cc_final: 0.7790 (mt) REVERT: M 342 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7180 (tmtm) REVERT: N 13 ASP cc_start: 0.6974 (p0) cc_final: 0.6717 (p0) outliers start: 75 outliers final: 47 residues processed: 480 average time/residue: 0.4046 time to fit residues: 263.6815 Evaluate side-chains 496 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 439 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 77 VAL 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 109 LEU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 24 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 102 THR 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 171 ILE Chi-restraints excluded: chain K residue 211 TYR Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 264 LEU 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 306 LEU Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 297 PHE Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 347 LEU 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 122 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.109484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091668 restraints weight = 54388.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093937 restraints weight = 30236.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095455 restraints weight = 19901.748| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.9766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17881 Z= 0.212 Angle : 0.976 14.405 25382 Z= 0.507 Chirality : 0.048 0.248 2864 Planarity : 0.006 0.067 2198 Dihedral : 28.667 179.053 4769 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.00 % Allowed : 38.62 % Favored : 56.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.22), residues: 1323 helix: -1.35 (0.18), residues: 654 sheet: -2.56 (0.99), residues: 27 loop : -2.66 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP M 279 HIS 0.008 0.001 HIS M 248 PHE 0.034 0.002 PHE M 217 TYR 0.025 0.002 TYR K 214 ARG 0.019 0.001 ARG M 335 Details of bonding type rmsd hydrogen bonds : bond 0.05529 ( 735) hydrogen bonds : angle 4.20368 ( 1811) covalent geometry : bond 0.00488 (17881) covalent geometry : angle 0.97643 (25382) ********************** 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 499 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 439 time to evaluate : 1.441 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: A 50 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7309 (mt-10) REVERT: A 69 ARG cc_start: 0.7488 (mtm180) cc_final: 0.7004 (ptt-90) REVERT: A 73 GLU cc_start: 0.7206 (tp30) cc_final: 0.6975 (tp30) REVERT: A 105 GLU cc_start: 0.7820 (pp20) cc_final: 0.7480 (pp20) REVERT: A 106 ASP cc_start: 0.7818 (p0) cc_final: 0.7545 (p0) REVERT: A 115 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8829 (tppp) REVERT: A 129 ARG cc_start: 0.8486 (tpt90) cc_final: 0.8273 (tpt-90) REVERT: B 92 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.6862 (tpt-90) REVERT: C 76 LYS cc_start: 0.8553 (tttt) cc_final: 0.7966 (tptt) REVERT: C 105 SER cc_start: 0.9336 (m) cc_final: 0.9036 (p) REVERT: D 79 GLU cc_start: 0.7376 (pp20) cc_final: 0.6990 (pp20) REVERT: D 89 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8213 (mmmm) REVERT: E 50 GLU cc_start: 0.7677 (tp30) cc_final: 0.7021 (tp30) REVERT: E 51 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8721 (tt) REVERT: E 53 ARG cc_start: 0.8157 (ptm-80) cc_final: 0.7905 (ptm-80) REVERT: F 27 GLN cc_start: 0.7953 (mp-120) cc_final: 0.7561 (mp10) REVERT: F 29 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8024 (mm) REVERT: F 44 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8545 (mtmm) REVERT: F 51 TYR cc_start: 0.8013 (m-80) cc_final: 0.7628 (m-10) REVERT: F 98 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7283 (t80) REVERT: G 30 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.8079 (tpp80) REVERT: G 38 HIS cc_start: 0.7716 (t-90) cc_final: 0.7105 (t-90) REVERT: G 93 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8326 (t0) REVERT: H 37 LYS cc_start: 0.8796 (tptp) cc_final: 0.8484 (tptp) REVERT: H 74 GLU cc_start: 0.7851 (tp30) cc_final: 0.7171 (tp30) REVERT: H 104 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8604 (tp) REVERT: H 123 LYS cc_start: 0.8168 (mppt) cc_final: 0.7836 (mppt) REVERT: K 163 ARG cc_start: 0.7411 (mmp80) cc_final: 0.7154 (mmp80) REVERT: K 171 ILE cc_start: 0.5797 (OUTLIER) cc_final: 0.5369 (tt) REVERT: K 233 TYR cc_start: 0.5860 (OUTLIER) cc_final: 0.3858 (p90) REVERT: K 248 CYS cc_start: 0.8426 (m) cc_final: 0.7997 (m) REVERT: K 276 MET cc_start: 0.7724 (tpp) cc_final: 0.7480 (tpp) REVERT: K 319 LEU cc_start: 0.8686 (pp) cc_final: 0.8172 (mp) REVERT: K 349 TYR cc_start: 0.5158 (p90) cc_final: 0.2215 (p90) REVERT: K 379 MET cc_start: 0.6314 (tmt) cc_final: 0.5649 (tmt) REVERT: K 401 HIS cc_start: 0.6985 (p-80) cc_final: 0.6704 (p-80) REVERT: K 406 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7489 (m-40) REVERT: K 412 ARG cc_start: 0.7120 (mpp-170) cc_final: 0.6838 (mpp-170) REVERT: K 436 PHE cc_start: 0.6692 (p90) cc_final: 0.6490 (p90) REVERT: L 34 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7943 (tp40) REVERT: M 209 MET cc_start: 0.5658 (pp-130) cc_final: 0.5244 (pp-130) REVERT: M 279 TRP cc_start: 0.8213 (t-100) cc_final: 0.7728 (t60) REVERT: M 327 ASP cc_start: 0.6438 (m-30) cc_final: 0.6041 (m-30) REVERT: M 342 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7379 (tmtm) REVERT: M 354 ARG cc_start: 0.8151 (tpm170) cc_final: 0.7913 (tpm170) REVERT: N 13 ASP cc_start: 0.7048 (p0) cc_final: 0.6841 (p0) REVERT: N 31 ASN cc_start: 0.6240 (p0) cc_final: 0.5823 (p0) outliers start: 60 outliers final: 44 residues processed: 464 average time/residue: 0.3868 time to fit residues: 241.7122 Evaluate side-chains 493 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 439 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 29 ILE 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 67 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 83 ARG 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 C residue 109 LEU Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 86 TYR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 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 92 ARG Chi-restraints excluded: chain F residue 98 TYR 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 102 THR 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 171 ILE Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 264 LEU 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 306 LEU Chi-restraints excluded: chain K residue 313 ARG Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain K residue 406 ASN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 297 PHE Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 347 LEU 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 83 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 129 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 146 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.111053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093701 restraints weight = 54385.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095792 restraints weight = 30604.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.097212 restraints weight = 20395.990| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.9989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17881 Z= 0.193 Angle : 0.967 15.713 25382 Z= 0.500 Chirality : 0.047 0.245 2864 Planarity : 0.006 0.067 2198 Dihedral : 28.548 179.682 4769 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 5.17 % Allowed : 39.03 % Favored : 55.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.22), residues: 1323 helix: -1.29 (0.19), residues: 634 sheet: -2.45 (1.00), residues: 27 loop : -2.61 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP M 279 HIS 0.008 0.001 HIS M 248 PHE 0.027 0.002 PHE M 189 TYR 0.027 0.002 TYR K 211 ARG 0.016 0.001 ARG M 335 Details of bonding type rmsd hydrogen bonds : bond 0.05172 ( 735) hydrogen bonds : angle 4.20014 ( 1811) covalent geometry : bond 0.00443 (17881) covalent geometry : angle 0.96741 (25382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6461.11 seconds wall clock time: 113 minutes 46.65 seconds (6826.65 seconds total)