Starting phenix.real_space_refine on Wed Jun 18 05:38:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2z_38023/06_2025/8x2z_38023.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2z_38023/06_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_38023/06_2025/8x2z_38023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2z_38023/06_2025/8x2z_38023.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2z_38023/06_2025/8x2z_38023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2z_38023/06_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-5710/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: 9.73, per 1000 atoms: 0.57 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: 4.04 Conformation dependent library (CDL) restraints added in 1.8 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: 6.94 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: 6.81 Time building geometry restraints manager: 4.91 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: 1.560 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.620 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.910 ------------------------------------------------------------------------------- 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 : 1.425 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: 0.3751 time to fit residues: 287.3169 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 : 1.417 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095275 restraints weight = 53909.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.097553 restraints weight = 28930.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.099053 restraints weight = 18706.785| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 : 1.368 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: 0.7821 (pp20) cc_final: 0.7416 (pp20) REVERT: A 97 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7071 (mt-10) REVERT: B 55 ARG cc_start: 0.8393 (mpp80) cc_final: 0.8124 (mtm-85) REVERT: C 32 LYS cc_start: 0.8401 (ttmm) cc_final: 0.7965 (ttmm) REVERT: C 37 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8175 (ttt-90) REVERT: C 63 GLU cc_start: 0.6303 (pm20) cc_final: 0.5820 (pm20) REVERT: C 76 LYS cc_start: 0.7729 (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: 0.8075 (t80) cc_final: 0.7144 (t80) REVERT: D 74 GLU cc_start: 0.6957 (tp30) cc_final: 0.6607 (tp30) REVERT: D 96 GLU cc_start: 0.7153 (pp20) cc_final: 0.6810 (tm-30) REVERT: E 42 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6246 (pmmt) REVERT: E 50 GLU cc_start: 0.6918 (tp30) cc_final: 0.6518 (tp30) REVERT: E 62 ILE cc_start: 0.8262 (tp) cc_final: 0.7758 (tp) REVERT: E 82 LEU cc_start: 0.7601 (mp) cc_final: 0.6587 (mp) REVERT: F 27 GLN cc_start: 0.7854 (mm110) cc_final: 0.7425 (mp10) REVERT: F 60 SER cc_start: 0.8170 (m) cc_final: 0.7416 (t) REVERT: F 72 TYR cc_start: 0.8364 (m-80) cc_final: 0.8118 (m-80) REVERT: F 74 GLU cc_start: 0.7513 (pp20) cc_final: 0.7274 (pp20) REVERT: F 79 LYS cc_start: 0.7564 (ptmm) cc_final: 0.7059 (tppt) REVERT: F 87 VAL cc_start: 0.8040 (m) cc_final: 0.7810 (p) REVERT: G 24 LEU cc_start: 0.7861 (mm) cc_final: 0.7613 (mp) REVERT: G 57 LEU cc_start: 0.8644 (tt) cc_final: 0.8300 (tp) REVERT: H 51 THR cc_start: 0.6559 (m) cc_final: 0.6279 (p) REVERT: H 70 ASN cc_start: 0.8436 (t0) cc_final: 0.8196 (t0) REVERT: H 118 THR cc_start: 0.7940 (m) cc_final: 0.7662 (t) REVERT: H 119 ARG cc_start: 0.8031 (ptm-80) cc_final: 0.7534 (ttt-90) REVERT: K 172 MET cc_start: 0.6481 (tmm) cc_final: 0.6085 (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: 0.7396 (tpt-90) REVERT: K 333 LYS cc_start: 0.8581 (tmtm) cc_final: 0.8210 (tmtm) REVERT: K 350 ARG cc_start: 0.7300 (mmm-85) cc_final: 0.6679 (mmm-85) REVERT: K 356 THR cc_start: 0.7491 (m) cc_final: 0.7113 (p) REVERT: K 379 MET cc_start: 0.5249 (tmt) cc_final: 0.4520 (tmt) REVERT: K 393 ILE cc_start: 0.5519 (OUTLIER) cc_final: 0.5291 (pp) REVERT: L 31 ASN cc_start: 0.7868 (p0) cc_final: 0.6866 (p0) REVERT: L 33 GLN cc_start: 0.8170 (pm20) cc_final: 0.7433 (mp10) REVERT: L 34 GLN cc_start: 0.8423 (mm110) cc_final: 0.8056 (mp10) REVERT: M 133 TYR cc_start: 0.5134 (m-80) cc_final: 0.4585 (m-80) REVERT: M 169 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7324 (mt-10) REVERT: M 209 MET cc_start: 0.5519 (pp-130) cc_final: 0.5243 (pp-130) REVERT: M 232 PHE cc_start: 0.6709 (p90) cc_final: 0.6230 (p90) REVERT: M 279 TRP cc_start: 0.7592 (t-100) cc_final: 0.7009 (t-100) REVERT: N 13 ASP cc_start: 0.5934 (p0) cc_final: 0.5421 (p0) REVERT: N 23 TYR cc_start: 0.5867 (m-80) cc_final: 0.5463 (m-80) outliers start: 83 outliers final: 39 residues processed: 511 average time/residue: 0.3710 time to fit residues: 260.2136 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 : 1.397 ------------------------------------------------------------------------------- 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: 0.9980 chunk 115 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 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: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** 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 222 HIS ** 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 = 0.3908 r_free = 0.3908 target = 0.112632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095424 restraints weight = 54778.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.097647 restraints weight = 29350.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.099141 restraints weight = 19018.786| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17881 Z= 0.197 Angle : 0.860 16.276 25382 Z= 0.464 Chirality : 0.046 0.216 2864 Planarity : 0.007 0.108 2198 Dihedral : 29.052 170.394 4783 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 7.84 % Allowed : 24.94 % Favored : 67.22 % 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: -3.68 (0.20), residues: 1323 helix: -1.81 (0.18), residues: 640 sheet: -1.78 (0.92), residues: 22 loop : -3.19 (0.21), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 130 HIS 0.017 0.002 HIS K 222 PHE 0.039 0.002 PHE M 217 TYR 0.050 0.003 TYR N 23 ARG 0.013 0.001 ARG G 83 Details of bonding type rmsd hydrogen bonds : bond 0.05349 ( 735) hydrogen bonds : angle 4.26769 ( 1811) covalent geometry : bond 0.00435 (17881) covalent geometry : angle 0.85953 (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 569 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 475 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7405 (mt-10) REVERT: A 125 LYS cc_start: 0.8396 (ptmm) cc_final: 0.8175 (ptmm) REVERT: B 45 ARG cc_start: 0.7356 (mmm-85) cc_final: 0.7122 (mmm160) REVERT: C 21 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.6151 (ppp-140) REVERT: C 32 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8160 (ttmm) REVERT: C 63 GLU cc_start: 0.6658 (pm20) cc_final: 0.6327 (pm20) REVERT: D 41 SER cc_start: 0.8657 (p) cc_final: 0.8444 (m) REVERT: D 44 ILE cc_start: 0.8458 (pp) cc_final: 0.7179 (pt) REVERT: D 64 ILE cc_start: 0.7774 (mm) cc_final: 0.7368 (mm) REVERT: D 68 PHE cc_start: 0.8251 (t80) cc_final: 0.7983 (t80) REVERT: D 74 GLU cc_start: 0.7196 (tp30) cc_final: 0.6699 (tp30) REVERT: D 82 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8221 (mmmt) REVERT: D 96 GLU cc_start: 0.7181 (pp20) cc_final: 0.6963 (tm-30) REVERT: D 111 LYS cc_start: 0.7718 (mtmm) cc_final: 0.7425 (mtmm) REVERT: E 121 LYS cc_start: 0.8343 (mttp) cc_final: 0.8030 (mttt) REVERT: E 128 ARG cc_start: 0.8715 (mtp85) cc_final: 0.8436 (mtp180) REVERT: F 60 SER cc_start: 0.8149 (m) cc_final: 0.7514 (t) REVERT: F 72 TYR cc_start: 0.8535 (m-80) cc_final: 0.8328 (m-80) REVERT: G 38 HIS cc_start: 0.7268 (t70) cc_final: 0.6742 (t-90) REVERT: G 59 TYR cc_start: 0.6386 (p90) cc_final: 0.6142 (p90) REVERT: H 49 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7382 (tmmt) REVERT: H 51 THR cc_start: 0.7110 (m) cc_final: 0.6689 (p) REVERT: H 74 GLU cc_start: 0.7905 (tp30) cc_final: 0.7202 (tp30) REVERT: H 119 ARG cc_start: 0.8036 (ptm-80) cc_final: 0.7613 (ttt-90) REVERT: K 252 CYS cc_start: 0.8070 (p) cc_final: 0.7347 (t) REVERT: K 300 TYR cc_start: 0.6136 (t80) cc_final: 0.4266 (t80) REVERT: K 321 ILE cc_start: 0.8515 (tt) cc_final: 0.8257 (tp) REVERT: K 322 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6430 (pm20) REVERT: K 347 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7497 (tt) REVERT: K 373 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8527 (mp) REVERT: K 379 MET cc_start: 0.6048 (tmt) cc_final: 0.5520 (tmt) REVERT: K 406 ASN cc_start: 0.6889 (m110) cc_final: 0.6566 (m110) REVERT: M 149 LYS cc_start: 0.6237 (ptmt) cc_final: 0.6009 (pttt) REVERT: M 155 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7610 (mm-30) REVERT: M 209 MET cc_start: 0.5374 (pp-130) cc_final: 0.5097 (pp-130) REVERT: M 215 LEU cc_start: 0.8425 (pp) cc_final: 0.8187 (pp) REVERT: M 232 PHE cc_start: 0.6813 (p90) cc_final: 0.6502 (p90) REVERT: M 278 TYR cc_start: 0.7006 (t80) cc_final: 0.6441 (t80) REVERT: N 32 ASP cc_start: 0.8257 (m-30) cc_final: 0.8001 (m-30) REVERT: N 85 GLU cc_start: 0.8646 (pp20) cc_final: 0.8266 (pp20) outliers start: 94 outliers final: 42 residues processed: 517 average time/residue: 0.4029 time to fit residues: 286.4768 Evaluate side-chains 493 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 446 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 86 GLN Chi-restraints excluded: chain G residue 89 ILE 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 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: 2.9990 chunk 131 optimal weight: 2.9990 chunk 22 optimal weight: 0.0000 chunk 93 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 overall best weight: 0.4942 ------------------------------------------------------------------------------- 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** D 59 GLN D 87 ASN E 68 GLN ** 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.113935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.096715 restraints weight = 54141.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.098898 restraints weight = 29997.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.100385 restraints weight = 19755.420| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17881 Z= 0.175 Angle : 0.832 12.146 25382 Z= 0.445 Chirality : 0.044 0.225 2864 Planarity : 0.005 0.076 2198 Dihedral : 28.807 172.484 4779 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 7.34 % Allowed : 28.44 % Favored : 64.22 % 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: -3.36 (0.21), residues: 1323 helix: -1.52 (0.19), residues: 636 sheet: -1.79 (1.01), residues: 22 loop : -3.03 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 247 HIS 0.006 0.001 HIS K 222 PHE 0.031 0.002 PHE M 217 TYR 0.028 0.002 TYR K 311 ARG 0.007 0.001 ARG N 22 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 735) hydrogen bonds : angle 4.14931 ( 1811) covalent geometry : bond 0.00383 (17881) covalent geometry : angle 0.83159 (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 553 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 465 time to evaluate : 1.333 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: 0.8436 (mtp85) cc_final: 0.8090 (mtp-110) REVERT: A 50 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 106 ASP cc_start: 0.7611 (p0) cc_final: 0.7326 (p0) REVERT: B 70 VAL cc_start: 0.8688 (m) cc_final: 0.8434 (p) REVERT: C 21 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.6353 (ppp-140) REVERT: C 32 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8277 (ttmm) REVERT: C 52 TYR cc_start: 0.7923 (t80) cc_final: 0.7698 (t80) REVERT: C 105 SER cc_start: 0.9248 (OUTLIER) cc_final: 0.8947 (p) REVERT: D 44 ILE cc_start: 0.8660 (pp) cc_final: 0.8433 (pt) REVERT: D 64 ILE cc_start: 0.7870 (mm) cc_final: 0.7478 (mm) REVERT: D 73 PHE cc_start: 0.8689 (t80) cc_final: 0.8456 (t80) REVERT: D 79 GLU cc_start: 0.7523 (pp20) cc_final: 0.7241 (pp20) REVERT: D 82 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8211 (mmmt) REVERT: D 111 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7464 (mtmm) REVERT: E 59 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: E 128 ARG cc_start: 0.8839 (mtp85) cc_final: 0.8539 (mtp180) REVERT: F 60 SER cc_start: 0.8122 (m) cc_final: 0.7544 (t) REVERT: F 72 TYR cc_start: 0.8599 (m-80) cc_final: 0.8314 (m-80) REVERT: F 91 LYS cc_start: 0.8456 (ttpp) cc_final: 0.8193 (ttpt) REVERT: G 32 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8162 (mtpp) REVERT: G 38 HIS cc_start: 0.7155 (t70) cc_final: 0.6601 (t70) REVERT: G 44 ARG cc_start: 0.6933 (tmm-80) cc_final: 0.6220 (tmm-80) REVERT: H 38 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6593 (pp20) REVERT: H 51 THR cc_start: 0.7154 (m) cc_final: 0.6698 (p) REVERT: H 74 GLU cc_start: 0.7783 (tp30) cc_final: 0.7131 (tp30) REVERT: H 96 GLU cc_start: 0.8122 (pm20) cc_final: 0.7685 (pm20) REVERT: H 108 GLU cc_start: 0.7440 (mp0) cc_final: 0.7239 (mp0) REVERT: H 119 ARG cc_start: 0.8093 (ptm-80) cc_final: 0.7589 (tmm160) REVERT: K 252 CYS cc_start: 0.8074 (p) cc_final: 0.7426 (t) REVERT: K 333 LYS cc_start: 0.8766 (tppt) cc_final: 0.8408 (tppt) REVERT: L 33 GLN cc_start: 0.8186 (pm20) cc_final: 0.7390 (mp10) REVERT: L 34 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7859 (mp10) REVERT: M 149 LYS cc_start: 0.6501 (ptmt) cc_final: 0.6292 (pttt) REVERT: M 209 MET cc_start: 0.5358 (pp-130) cc_final: 0.5036 (pp-130) REVERT: M 215 LEU cc_start: 0.8469 (pp) cc_final: 0.8206 (pp) REVERT: M 232 PHE cc_start: 0.6999 (p90) cc_final: 0.6108 (p90) REVERT: M 279 TRP cc_start: 0.7554 (t-100) cc_final: 0.7105 (t-100) REVERT: M 345 LYS cc_start: 0.7838 (mttt) cc_final: 0.7623 (mmtm) REVERT: N 22 ARG cc_start: 0.7739 (mmm160) cc_final: 0.6732 (mmm160) REVERT: N 85 GLU cc_start: 0.8694 (pp20) cc_final: 0.8106 (pp20) outliers start: 88 outliers final: 45 residues processed: 507 average time/residue: 0.3753 time to fit residues: 259.0660 Evaluate side-chains 478 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 430 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 122 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 C residue 17 SER Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 83 ARG 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 123 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain G residue 112 ILE 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 H residue 118 THR 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 L residue 28 THR Chi-restraints excluded: chain M residue 163 ASN 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 1 MET Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 87 CYS 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: 0.8980 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.112830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.095195 restraints weight = 54815.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.097474 restraints weight = 30096.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.099004 restraints weight = 19694.929| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17881 Z= 0.190 Angle : 0.851 13.023 25382 Z= 0.452 Chirality : 0.045 0.223 2864 Planarity : 0.006 0.089 2198 Dihedral : 28.719 174.895 4771 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 7.09 % Allowed : 31.03 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -3.23 (0.21), residues: 1323 helix: -1.42 (0.19), residues: 638 sheet: -1.42 (1.13), residues: 22 loop : -2.97 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 247 HIS 0.004 0.001 HIS A 113 PHE 0.035 0.002 PHE M 217 TYR 0.044 0.002 TYR N 23 ARG 0.013 0.001 ARG G 83 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 735) hydrogen bonds : angle 4.10805 ( 1811) covalent geometry : bond 0.00425 (17881) covalent geometry : angle 0.85061 (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 545 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 460 time to evaluate : 1.421 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 49 ARG cc_start: 0.8393 (mtp85) cc_final: 0.8042 (mtp-110) REVERT: A 50 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 76 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: A 77 ASP cc_start: 0.8324 (p0) cc_final: 0.7773 (p0) REVERT: B 37 LEU cc_start: 0.9062 (tp) cc_final: 0.8850 (mt) REVERT: B 92 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.6645 (tpt-90) REVERT: C 21 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6843 (ppp-140) REVERT: C 63 GLU cc_start: 0.6987 (pm20) cc_final: 0.6779 (pm20) REVERT: C 76 LYS cc_start: 0.8155 (tttt) cc_final: 0.7595 (tttt) REVERT: C 105 SER cc_start: 0.9412 (OUTLIER) cc_final: 0.9161 (p) REVERT: D 74 GLU cc_start: 0.7290 (tp30) cc_final: 0.6808 (tp30) REVERT: D 79 GLU cc_start: 0.7619 (pp20) cc_final: 0.7088 (pp20) REVERT: D 82 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8236 (mmmt) REVERT: E 66 PRO cc_start: 0.8044 (Cg_exo) cc_final: 0.7740 (Cg_endo) REVERT: E 128 ARG cc_start: 0.8892 (mtp85) cc_final: 0.8644 (mtp180) REVERT: F 44 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8505 (mtpp) REVERT: F 53 GLU cc_start: 0.7287 (pm20) cc_final: 0.6929 (pm20) REVERT: F 91 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8360 (ttpt) REVERT: F 92 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8583 (tmt-80) REVERT: G 38 HIS cc_start: 0.7463 (t70) cc_final: 0.6833 (t-90) REVERT: G 44 ARG cc_start: 0.7180 (tmm-80) cc_final: 0.6954 (tmm-80) REVERT: G 80 ILE cc_start: 0.7197 (pt) cc_final: 0.6823 (pt) REVERT: H 51 THR cc_start: 0.7200 (m) cc_final: 0.6787 (p) REVERT: H 74 GLU cc_start: 0.7821 (tp30) cc_final: 0.7166 (tp30) REVERT: H 96 GLU cc_start: 0.8127 (pm20) cc_final: 0.7841 (pm20) REVERT: H 119 ARG cc_start: 0.8107 (ptm-80) cc_final: 0.7606 (tmm160) REVERT: K 233 TYR cc_start: 0.5296 (OUTLIER) cc_final: 0.3471 (p90) REVERT: K 319 LEU cc_start: 0.8727 (pp) cc_final: 0.8403 (pp) REVERT: K 333 LYS cc_start: 0.8892 (tppt) cc_final: 0.8440 (tppt) REVERT: K 347 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7832 (tt) REVERT: K 379 MET cc_start: 0.5951 (tmt) cc_final: 0.5492 (tmt) REVERT: M 130 TRP cc_start: 0.7456 (m-90) cc_final: 0.7108 (m100) REVERT: M 155 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7726 (mm-30) REVERT: M 197 GLU cc_start: 0.7814 (mm-30) cc_final: 0.6378 (mp0) REVERT: M 209 MET cc_start: 0.5435 (pp-130) cc_final: 0.5130 (pp-130) REVERT: M 215 LEU cc_start: 0.8464 (pp) cc_final: 0.8160 (pp) REVERT: N 31 ASN cc_start: 0.5526 (p0) cc_final: 0.4972 (p0) REVERT: N 85 GLU cc_start: 0.8772 (pp20) cc_final: 0.8321 (pp20) outliers start: 85 outliers final: 41 residues processed: 503 average time/residue: 0.4073 time to fit residues: 274.4477 Evaluate side-chains 484 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 436 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 125 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 17 SER 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 95 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 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 F residue 29 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG 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 83 LEU 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 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 347 LEU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 242 ILE Chi-restraints excluded: chain M residue 267 LEU Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 87 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** 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** ** D 87 ASN ** 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 401 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** ** 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 = 0.3786 r_free = 0.3786 target = 0.105744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.088112 restraints weight = 53572.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090373 restraints weight = 29235.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.091878 restraints weight = 19042.051| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.8752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 17881 Z= 0.332 Angle : 1.003 18.593 25382 Z= 0.540 Chirality : 0.054 0.266 2864 Planarity : 0.007 0.083 2198 Dihedral : 29.118 177.493 4769 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 28.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 8.26 % Allowed : 31.11 % Favored : 60.63 % 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: -3.24 (0.21), residues: 1323 helix: -1.40 (0.18), residues: 641 sheet: -1.62 (1.17), residues: 22 loop : -3.01 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP M 279 HIS 0.009 0.002 HIS F 75 PHE 0.040 0.003 PHE E 67 TYR 0.048 0.003 TYR K 352 ARG 0.009 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.07255 ( 735) hydrogen bonds : angle 4.44944 ( 1811) covalent geometry : bond 0.00741 (17881) covalent geometry : angle 1.00330 (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 579 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 480 time to evaluate : 1.542 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 49 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8189 (mtp-110) REVERT: A 50 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7089 (mt-10) REVERT: A 76 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8341 (pp30) REVERT: A 83 ARG cc_start: 0.6362 (mtt180) cc_final: 0.5992 (mtt90) REVERT: A 105 GLU cc_start: 0.7820 (pp20) cc_final: 0.7573 (pp20) REVERT: A 106 ASP cc_start: 0.7778 (p0) cc_final: 0.7448 (p0) REVERT: B 27 GLN cc_start: 0.7840 (pm20) cc_final: 0.7450 (pm20) REVERT: B 55 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.8085 (ttm110) REVERT: B 59 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.7992 (tptp) REVERT: B 72 TYR cc_start: 0.8953 (m-10) cc_final: 0.8748 (m-80) REVERT: B 79 LYS cc_start: 0.7674 (pttp) cc_final: 0.7472 (pttp) REVERT: B 92 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.6985 (tpt-90) REVERT: C 59 TYR cc_start: 0.6876 (m-10) cc_final: 0.6526 (m-10) REVERT: C 74 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7525 (m-30) REVERT: C 105 SER cc_start: 0.9397 (OUTLIER) cc_final: 0.9079 (p) REVERT: D 51 THR cc_start: 0.8709 (t) cc_final: 0.8368 (p) REVERT: D 60 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8405 (mtpp) REVERT: D 79 GLU cc_start: 0.7184 (pp20) cc_final: 0.6915 (pp20) REVERT: D 82 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8021 (mmmt) REVERT: D 86 TYR cc_start: 0.7928 (p90) cc_final: 0.7151 (p90) REVERT: D 102 ARG cc_start: 0.8726 (mtp-110) cc_final: 0.8511 (ttp80) REVERT: E 59 GLU cc_start: 0.8291 (pm20) cc_final: 0.7904 (pm20) REVERT: E 128 ARG cc_start: 0.8908 (mtp85) cc_final: 0.8686 (mtp180) REVERT: F 98 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7490 (t80) REVERT: G 38 HIS cc_start: 0.7689 (t-90) cc_final: 0.7301 (t70) REVERT: G 44 ARG cc_start: 0.7319 (tmm-80) cc_final: 0.7056 (tmm-80) REVERT: G 78 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7957 (ttmm) REVERT: G 103 ILE cc_start: 0.9324 (pt) cc_final: 0.9118 (pt) REVERT: H 37 LYS cc_start: 0.8713 (tptp) cc_final: 0.8455 (tptp) REVERT: H 74 GLU cc_start: 0.7989 (tp30) cc_final: 0.7419 (tp30) REVERT: H 96 GLU cc_start: 0.7974 (pm20) cc_final: 0.7394 (pm20) REVERT: H 119 ARG cc_start: 0.8237 (ptm-80) cc_final: 0.7808 (tmm160) REVERT: K 233 TYR cc_start: 0.6043 (OUTLIER) cc_final: 0.4057 (p90) REVERT: K 237 PHE cc_start: 0.6759 (p90) cc_final: 0.6505 (p90) REVERT: K 247 TRP cc_start: 0.7237 (t60) cc_final: 0.6993 (t60) REVERT: K 322 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: K 347 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8133 (tt) REVERT: K 379 MET cc_start: 0.6425 (tmt) cc_final: 0.6128 (tmt) REVERT: K 384 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8108 (mm) REVERT: K 436 PHE cc_start: 0.6732 (p90) cc_final: 0.6452 (p90) REVERT: M 196 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7648 (p90) REVERT: M 209 MET cc_start: 0.5618 (pp-130) cc_final: 0.5259 (pp-130) REVERT: M 215 LEU cc_start: 0.8709 (pp) cc_final: 0.8380 (pp) REVERT: M 217 PHE cc_start: 0.6120 (p90) cc_final: 0.5763 (p90) REVERT: M 226 LYS cc_start: 0.8431 (pmtt) cc_final: 0.8224 (pmtt) REVERT: N 9 GLN cc_start: 0.8774 (pm20) cc_final: 0.8319 (pm20) REVERT: N 13 ASP cc_start: 0.7094 (p0) cc_final: 0.6811 (p0) REVERT: N 23 TYR cc_start: 0.6446 (m-80) cc_final: 0.6208 (m-80) outliers start: 99 outliers final: 51 residues processed: 518 average time/residue: 0.3996 time to fit residues: 278.6764 Evaluate side-chains 512 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 450 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 68 GLN 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 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 123 LYS 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 82 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU 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 100 ARG Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain K residue 229 TYR 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 275 CYS Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 305 ILE Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain K residue 322 GLU Chi-restraints excluded: chain K residue 326 GLU Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain M residue 145 THR Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 242 ILE Chi-restraints excluded: chain M residue 338 HIS Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 82 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 123 optimal weight: 0.1980 chunk 143 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 9 optimal weight: 0.0570 chunk 150 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN 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 ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.111350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093573 restraints weight = 54014.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.095818 restraints weight = 30049.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.097336 restraints weight = 19789.769| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.8949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17881 Z= 0.188 Angle : 0.902 14.083 25382 Z= 0.475 Chirality : 0.046 0.256 2864 Planarity : 0.006 0.084 2198 Dihedral : 28.795 174.422 4769 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 5.67 % Allowed : 36.28 % Favored : 58.05 % 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: -3.01 (0.22), residues: 1323 helix: -1.21 (0.19), residues: 631 sheet: -1.99 (1.08), residues: 27 loop : -2.85 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 279 HIS 0.011 0.001 HIS M 248 PHE 0.033 0.002 PHE M 217 TYR 0.031 0.002 TYR N 23 ARG 0.016 0.001 ARG K 395 Details of bonding type rmsd hydrogen bonds : bond 0.05307 ( 735) hydrogen bonds : angle 4.27387 ( 1811) covalent geometry : bond 0.00430 (17881) covalent geometry : angle 0.90247 (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 533 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 465 time to evaluate : 1.362 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: A 42 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8199 (mmtp) REVERT: A 49 ARG cc_start: 0.8356 (mtp85) cc_final: 0.8058 (mtp-110) REVERT: A 50 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7274 (mt-10) REVERT: A 74 ILE cc_start: 0.8841 (tt) cc_final: 0.8514 (tp) REVERT: A 76 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8294 (pp30) REVERT: A 106 ASP cc_start: 0.7729 (p0) cc_final: 0.7266 (p0) REVERT: B 27 GLN cc_start: 0.7823 (pm20) cc_final: 0.7482 (pm20) REVERT: B 40 ARG cc_start: 0.8976 (tpp80) cc_final: 0.8771 (ttt90) REVERT: B 59 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8074 (tptp) REVERT: B 92 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.6962 (tpt-90) REVERT: B 97 LEU cc_start: 0.9021 (mp) cc_final: 0.8797 (mt) REVERT: C 76 LYS cc_start: 0.8452 (tttt) cc_final: 0.7790 (tptt) REVERT: C 105 SER cc_start: 0.9423 (m) cc_final: 0.9164 (p) REVERT: D 51 THR cc_start: 0.8665 (t) cc_final: 0.8280 (p) REVERT: D 79 GLU cc_start: 0.7399 (pp20) cc_final: 0.7078 (pp20) REVERT: D 82 LYS cc_start: 0.8451 (mtpp) cc_final: 0.8251 (mmmt) REVERT: D 83 LEU cc_start: 0.8781 (tp) cc_final: 0.8534 (tp) REVERT: D 96 GLU cc_start: 0.7889 (tp30) cc_final: 0.7635 (tp30) REVERT: E 59 GLU cc_start: 0.8204 (pm20) cc_final: 0.7951 (pm20) REVERT: E 128 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8632 (mtp180) REVERT: F 31 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6750 (tttm) REVERT: F 98 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.7324 (t80) REVERT: G 38 HIS cc_start: 0.7659 (t-90) cc_final: 0.7006 (t-90) REVERT: G 63 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7582 (mt-10) REVERT: G 86 GLN cc_start: 0.5778 (OUTLIER) cc_final: 0.5551 (mt0) REVERT: G 100 ARG cc_start: 0.6011 (OUTLIER) cc_final: 0.5739 (tmt90) REVERT: H 74 GLU cc_start: 0.7798 (tp30) cc_final: 0.7042 (tp30) REVERT: H 93 SER cc_start: 0.8862 (t) cc_final: 0.8575 (p) REVERT: H 96 GLU cc_start: 0.7942 (pm20) cc_final: 0.6970 (pm20) REVERT: H 119 ARG cc_start: 0.8158 (ptm-80) cc_final: 0.7650 (tmm160) REVERT: K 233 TYR cc_start: 0.5616 (OUTLIER) cc_final: 0.3897 (p90) REVERT: K 247 TRP cc_start: 0.6987 (t60) cc_final: 0.6663 (t60) REVERT: K 319 LEU cc_start: 0.8759 (pp) cc_final: 0.8011 (mp) REVERT: K 347 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8043 (tt) REVERT: K 376 MET cc_start: 0.7103 (mmm) cc_final: 0.6706 (mmm) REVERT: K 379 MET cc_start: 0.6432 (tmt) cc_final: 0.5974 (tmt) REVERT: K 385 LEU cc_start: 0.8574 (pt) cc_final: 0.8075 (pp) REVERT: K 386 HIS cc_start: 0.8430 (t-90) cc_final: 0.8125 (t70) REVERT: K 412 ARG cc_start: 0.7362 (mpp-170) cc_final: 0.6828 (mpp80) REVERT: K 425 ASP cc_start: 0.7376 (p0) cc_final: 0.6931 (p0) REVERT: K 436 PHE cc_start: 0.6642 (p90) cc_final: 0.6420 (p90) REVERT: L 34 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8035 (tp40) REVERT: M 209 MET cc_start: 0.5490 (pp-130) cc_final: 0.5117 (pp-130) REVERT: M 215 LEU cc_start: 0.8603 (pp) cc_final: 0.8348 (pp) REVERT: M 229 MET cc_start: 0.0975 (pmm) cc_final: 0.0582 (pmm) REVERT: M 327 ASP cc_start: 0.6570 (m-30) cc_final: 0.6187 (m-30) REVERT: M 341 LEU cc_start: 0.8336 (pt) cc_final: 0.7859 (mt) REVERT: M 342 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6967 (tmtm) REVERT: M 354 ARG cc_start: 0.7912 (tpm170) cc_final: 0.7695 (tpm170) REVERT: M 360 ASN cc_start: 0.7907 (t0) cc_final: 0.7660 (t0) REVERT: N 85 GLU cc_start: 0.9020 (pp20) cc_final: 0.8811 (pp20) outliers start: 68 outliers final: 33 residues processed: 493 average time/residue: 0.4033 time to fit residues: 266.8085 Evaluate side-chains 486 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 443 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 76 GLN Chi-restraints excluded: chain A residue 124 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 100 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 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 31 LYS Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 100 ARG Chi-restraints excluded: chain H residue 86 TYR Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain K residue 233 TYR 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 326 GLU Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 150 PHE Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 191 ILE Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 242 ILE Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 347 LEU 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: 1.9990 chunk 132 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** H 52 HIS ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.109653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.091822 restraints weight = 54187.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.094117 restraints weight = 30275.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095612 restraints weight = 19919.634| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.9253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17881 Z= 0.211 Angle : 0.927 14.403 25382 Z= 0.488 Chirality : 0.047 0.257 2864 Planarity : 0.006 0.083 2198 Dihedral : 28.718 178.075 4769 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 5.67 % Allowed : 36.45 % Favored : 57.88 % 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: -2.95 (0.21), residues: 1323 helix: -1.10 (0.19), residues: 628 sheet: -2.15 (1.04), residues: 27 loop : -2.88 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 279 HIS 0.007 0.001 HIS M 248 PHE 0.034 0.002 PHE M 217 TYR 0.036 0.002 TYR N 23 ARG 0.010 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.05603 ( 735) hydrogen bonds : angle 4.21040 ( 1811) covalent geometry : bond 0.00481 (17881) covalent geometry : angle 0.92739 (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 524 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 456 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8263 (mtp85) cc_final: 0.7977 (mtp-110) REVERT: A 50 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 74 ILE cc_start: 0.8825 (tt) cc_final: 0.8205 (tp) REVERT: A 106 ASP cc_start: 0.7829 (p0) cc_final: 0.7611 (p0) REVERT: A 129 ARG cc_start: 0.8652 (tpt90) cc_final: 0.8332 (tpt-90) REVERT: A 131 ARG cc_start: 0.8981 (mtp85) cc_final: 0.8694 (mtp85) REVERT: B 53 GLU cc_start: 0.7474 (pm20) cc_final: 0.7246 (pm20) REVERT: B 59 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8076 (tptp) REVERT: B 72 TYR cc_start: 0.8975 (m-10) cc_final: 0.8744 (m-80) REVERT: B 92 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7012 (tpt-90) REVERT: C 76 LYS cc_start: 0.8484 (tttt) cc_final: 0.7894 (tptt) REVERT: C 105 SER cc_start: 0.9445 (m) cc_final: 0.9131 (p) REVERT: D 51 THR cc_start: 0.8685 (t) cc_final: 0.8312 (p) REVERT: D 79 GLU cc_start: 0.7330 (pp20) cc_final: 0.6934 (pp20) REVERT: D 82 LYS cc_start: 0.8496 (mtpp) cc_final: 0.7894 (tptp) REVERT: D 83 LEU cc_start: 0.8769 (tp) cc_final: 0.8245 (tp) REVERT: D 86 TYR cc_start: 0.7898 (p90) cc_final: 0.7302 (p90) REVERT: D 96 GLU cc_start: 0.7892 (tp30) cc_final: 0.7604 (tp30) REVERT: E 59 GLU cc_start: 0.8223 (pm20) cc_final: 0.7972 (pm20) REVERT: F 29 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7953 (mm) REVERT: F 31 LYS cc_start: 0.7290 (tmmt) cc_final: 0.7056 (tttm) REVERT: F 39 ARG cc_start: 0.8185 (mtt90) cc_final: 0.7821 (mtt90) REVERT: F 98 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7323 (t80) REVERT: G 38 HIS cc_start: 0.7688 (t-90) cc_final: 0.6998 (t-90) REVERT: H 74 GLU cc_start: 0.7818 (tp30) cc_final: 0.7095 (tp30) REVERT: H 119 ARG cc_start: 0.8148 (ptm-80) cc_final: 0.7721 (tmm-80) REVERT: K 218 CYS cc_start: 0.7292 (t) cc_final: 0.6788 (t) REVERT: K 233 TYR cc_start: 0.5873 (OUTLIER) cc_final: 0.3975 (p90) REVERT: K 347 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8087 (tt) REVERT: K 379 MET cc_start: 0.6381 (tmt) cc_final: 0.5698 (tmt) REVERT: K 384 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.7630 (mm) REVERT: K 386 HIS cc_start: 0.8382 (t-90) cc_final: 0.8073 (t70) REVERT: K 412 ARG cc_start: 0.7146 (mpp-170) cc_final: 0.6388 (mpp80) REVERT: K 436 PHE cc_start: 0.6578 (p90) cc_final: 0.6347 (p90) REVERT: L 34 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8069 (tp40) REVERT: M 209 MET cc_start: 0.5525 (pp-130) cc_final: 0.5200 (pp-130) REVERT: M 226 LYS cc_start: 0.8508 (pmtt) cc_final: 0.8248 (pmtt) REVERT: M 232 PHE cc_start: 0.7014 (p90) cc_final: 0.6709 (p90) REVERT: M 247 THR cc_start: 0.3035 (t) cc_final: 0.2634 (t) REVERT: M 327 ASP cc_start: 0.6557 (m-30) cc_final: 0.6193 (m-30) REVERT: M 341 LEU cc_start: 0.8378 (pt) cc_final: 0.7831 (mt) REVERT: M 354 ARG cc_start: 0.7902 (tpm170) cc_final: 0.7616 (tpm170) outliers start: 68 outliers final: 43 residues processed: 482 average time/residue: 0.3960 time to fit residues: 255.8389 Evaluate side-chains 498 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 448 time to evaluate : 1.889 ------------------------------------------------------------------------------- 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 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 77 VAL Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 58 THR 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 34 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 60 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 86 TYR Chi-restraints excluded: chain K residue 165 ARG 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 326 GLU Chi-restraints excluded: chain K residue 328 SER Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 242 ILE Chi-restraints excluded: chain M residue 243 ASN Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain N residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 20 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS ** K 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.109576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.091769 restraints weight = 54681.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.094074 restraints weight = 30193.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095589 restraints weight = 19765.725| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.9584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17881 Z= 0.214 Angle : 0.967 19.008 25382 Z= 0.502 Chirality : 0.048 0.292 2864 Planarity : 0.006 0.080 2198 Dihedral : 28.671 177.610 4769 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 4.92 % Allowed : 38.28 % Favored : 56.80 % 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: -2.97 (0.21), residues: 1323 helix: -1.15 (0.19), residues: 625 sheet: -2.42 (0.99), residues: 27 loop : -2.84 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP M 279 HIS 0.007 0.001 HIS F 75 PHE 0.039 0.002 PHE M 217 TYR 0.033 0.002 TYR K 352 ARG 0.011 0.001 ARG K 395 Details of bonding type rmsd hydrogen bonds : bond 0.05591 ( 735) hydrogen bonds : angle 4.23169 ( 1811) covalent geometry : bond 0.00488 (17881) covalent geometry : angle 0.96650 (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 528 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 469 time to evaluate : 1.497 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 49 ARG cc_start: 0.8253 (mtp85) cc_final: 0.8009 (mtp-110) REVERT: A 50 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7258 (mt-10) REVERT: A 74 ILE cc_start: 0.8744 (tt) cc_final: 0.8321 (tp) REVERT: A 105 GLU cc_start: 0.7929 (pp20) cc_final: 0.7590 (pp20) REVERT: A 129 ARG cc_start: 0.8638 (tpt90) cc_final: 0.8234 (tpt-90) REVERT: A 131 ARG cc_start: 0.8928 (mtp85) cc_final: 0.8607 (mtp85) REVERT: B 35 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8604 (mtp85) REVERT: B 53 GLU cc_start: 0.7495 (pm20) cc_final: 0.7235 (pm20) REVERT: B 59 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8088 (tptp) REVERT: C 21 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7371 (ttp80) REVERT: C 76 LYS cc_start: 0.8556 (tttt) cc_final: 0.7960 (tptt) REVERT: C 105 SER cc_start: 0.9498 (m) cc_final: 0.9180 (p) REVERT: D 82 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8034 (mmmt) REVERT: D 83 LEU cc_start: 0.8758 (tp) cc_final: 0.8149 (tp) REVERT: D 86 TYR cc_start: 0.7892 (p90) cc_final: 0.7377 (p90) REVERT: D 89 LYS cc_start: 0.8552 (mmmm) cc_final: 0.8097 (mmmm) REVERT: E 59 GLU cc_start: 0.8250 (pm20) cc_final: 0.7953 (pm20) REVERT: E 121 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7818 (mmtm) REVERT: F 27 GLN cc_start: 0.7966 (mp10) cc_final: 0.7673 (mp10) REVERT: F 31 LYS cc_start: 0.7351 (tmmt) cc_final: 0.7107 (tttm) REVERT: F 39 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7895 (mtt90) REVERT: F 53 GLU cc_start: 0.7227 (pm20) cc_final: 0.6119 (pm20) REVERT: F 98 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7400 (t80) REVERT: G 38 HIS cc_start: 0.7685 (t-90) cc_final: 0.7001 (t-90) REVERT: G 44 ARG cc_start: 0.7481 (tmm-80) cc_final: 0.7228 (tmm-80) REVERT: G 93 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8224 (t0) REVERT: H 46 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8035 (ttpp) REVERT: H 74 GLU cc_start: 0.7778 (tp30) cc_final: 0.7166 (tp30) REVERT: H 119 ARG cc_start: 0.8195 (ptm-80) cc_final: 0.7901 (ptm-80) REVERT: H 123 LYS cc_start: 0.8085 (mppt) cc_final: 0.7821 (mppt) REVERT: K 218 CYS cc_start: 0.7399 (t) cc_final: 0.7032 (t) REVERT: K 233 TYR cc_start: 0.5767 (OUTLIER) cc_final: 0.3738 (p90) REVERT: K 247 TRP cc_start: 0.7002 (t60) cc_final: 0.6667 (t60) REVERT: K 298 ASP cc_start: 0.8010 (p0) cc_final: 0.7610 (p0) REVERT: K 316 TYR cc_start: 0.4425 (m-10) cc_final: 0.4057 (m-10) REVERT: K 333 LYS cc_start: 0.9000 (tppt) cc_final: 0.8625 (tppt) REVERT: K 347 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8084 (tt) REVERT: K 379 MET cc_start: 0.6249 (tmt) cc_final: 0.5944 (tmt) REVERT: K 386 HIS cc_start: 0.8351 (t-90) cc_final: 0.8056 (t70) REVERT: K 412 ARG cc_start: 0.7172 (mpp-170) cc_final: 0.6376 (mpp80) REVERT: K 436 PHE cc_start: 0.6640 (p90) cc_final: 0.6404 (p90) REVERT: L 34 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8107 (tp40) REVERT: M 215 LEU cc_start: 0.8679 (pp) cc_final: 0.8399 (tt) REVERT: M 226 LYS cc_start: 0.8509 (pmtt) cc_final: 0.8219 (pmtt) REVERT: M 247 THR cc_start: 0.3168 (t) cc_final: 0.2746 (t) REVERT: M 279 TRP cc_start: 0.8154 (t-100) cc_final: 0.7156 (t60) REVERT: M 327 ASP cc_start: 0.6618 (m-30) cc_final: 0.6194 (m-30) REVERT: M 354 ARG cc_start: 0.7910 (tpm170) cc_final: 0.7560 (tpm170) REVERT: N 22 ARG cc_start: 0.7696 (mmm160) cc_final: 0.7394 (tpm170) REVERT: N 103 LYS cc_start: 0.7931 (mmtm) cc_final: 0.7664 (mmtm) outliers start: 59 outliers final: 40 residues processed: 491 average time/residue: 0.4224 time to fit residues: 282.0031 Evaluate side-chains 506 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 459 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 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 21 ARG 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 100 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 60 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 H residue 83 LEU Chi-restraints excluded: chain H residue 86 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 326 GLU Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 167 ARG Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 242 ILE Chi-restraints excluded: chain M residue 243 ASN Chi-restraints excluded: chain M residue 347 LEU 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: 0.9980 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 128 optimal weight: 0.0870 chunk 150 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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** B 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS M 243 ASN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.111036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.093514 restraints weight = 54622.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.095713 restraints weight = 30792.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.097200 restraints weight = 20484.489| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.9779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17881 Z= 0.196 Angle : 0.981 16.961 25382 Z= 0.507 Chirality : 0.047 0.241 2864 Planarity : 0.006 0.081 2198 Dihedral : 28.571 178.422 4769 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 4.09 % Allowed : 39.53 % Favored : 56.38 % 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: -2.92 (0.22), residues: 1323 helix: -1.10 (0.19), residues: 615 sheet: -2.86 (0.82), residues: 33 loop : -2.78 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP M 279 HIS 0.007 0.001 HIS M 248 PHE 0.023 0.002 PHE M 232 TYR 0.037 0.002 TYR M 276 ARG 0.009 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.05308 ( 735) hydrogen bonds : angle 4.24366 ( 1811) covalent geometry : bond 0.00445 (17881) covalent geometry : angle 0.98076 (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 504 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 455 time to evaluate : 1.347 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 49 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7708 (mtp85) REVERT: A 50 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7249 (mt-10) REVERT: A 73 GLU cc_start: 0.7235 (tp30) cc_final: 0.6790 (tp30) REVERT: A 93 GLN cc_start: 0.7162 (tt0) cc_final: 0.6772 (tt0) REVERT: A 97 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7216 (tp30) REVERT: A 105 GLU cc_start: 0.7803 (pp20) cc_final: 0.7515 (pp20) REVERT: A 122 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8364 (ttmm) REVERT: B 35 ARG cc_start: 0.8857 (ttm-80) cc_final: 0.8601 (mtp85) REVERT: B 59 LYS cc_start: 0.8826 (ptmm) cc_final: 0.8062 (tptp) REVERT: C 21 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7426 (ttp80) REVERT: C 76 LYS cc_start: 0.8457 (tttt) cc_final: 0.7881 (tptt) REVERT: C 99 ILE cc_start: 0.7947 (mp) cc_final: 0.7734 (mp) REVERT: C 105 SER cc_start: 0.9495 (m) cc_final: 0.9172 (p) REVERT: D 82 LYS cc_start: 0.8456 (mtpp) cc_final: 0.7803 (tptp) REVERT: D 83 LEU cc_start: 0.8805 (tp) cc_final: 0.8223 (tp) REVERT: D 86 TYR cc_start: 0.7896 (p90) cc_final: 0.7377 (p90) REVERT: D 89 LYS cc_start: 0.8526 (mmmm) cc_final: 0.8086 (mmmm) REVERT: E 59 GLU cc_start: 0.8299 (pm20) cc_final: 0.8050 (pm20) REVERT: E 121 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7825 (mmtm) REVERT: E 131 ARG cc_start: 0.8413 (tpp80) cc_final: 0.8146 (tpp80) REVERT: F 29 ILE cc_start: 0.8275 (pp) cc_final: 0.8015 (mm) REVERT: F 39 ARG cc_start: 0.8179 (mtt90) cc_final: 0.7847 (mtt90) REVERT: F 53 GLU cc_start: 0.7253 (pm20) cc_final: 0.6283 (pm20) REVERT: F 98 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7225 (t80) REVERT: G 25 GLN cc_start: 0.8188 (mt0) cc_final: 0.7937 (mt0) REVERT: G 38 HIS cc_start: 0.7760 (t-90) cc_final: 0.7048 (t-90) REVERT: G 44 ARG cc_start: 0.7499 (tmm-80) cc_final: 0.7283 (tmm-80) REVERT: G 93 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8281 (t0) REVERT: H 74 GLU cc_start: 0.7775 (tp30) cc_final: 0.7170 (tp30) REVERT: H 119 ARG cc_start: 0.8154 (ptm-80) cc_final: 0.7950 (ptm-80) REVERT: H 123 LYS cc_start: 0.8088 (mppt) cc_final: 0.7809 (mppt) REVERT: K 218 CYS cc_start: 0.7343 (t) cc_final: 0.6988 (t) REVERT: K 233 TYR cc_start: 0.5693 (OUTLIER) cc_final: 0.3756 (p90) REVERT: K 238 GLU cc_start: 0.8062 (pm20) cc_final: 0.7751 (pm20) REVERT: K 247 TRP cc_start: 0.7073 (t60) cc_final: 0.6842 (t60) REVERT: K 322 GLU cc_start: 0.7417 (pm20) cc_final: 0.6957 (pm20) REVERT: K 333 LYS cc_start: 0.8946 (tppt) cc_final: 0.8544 (tppt) REVERT: K 347 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8030 (tt) REVERT: K 379 MET cc_start: 0.6262 (tmt) cc_final: 0.5936 (tmt) REVERT: K 386 HIS cc_start: 0.8359 (t-90) cc_final: 0.8072 (t70) REVERT: K 389 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7762 (mmtt) REVERT: K 412 ARG cc_start: 0.7136 (mpp-170) cc_final: 0.6538 (mpp80) REVERT: L 34 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8123 (tp40) REVERT: M 168 ASP cc_start: 0.6703 (p0) cc_final: 0.5989 (p0) REVERT: M 210 ASP cc_start: 0.4534 (p0) cc_final: 0.3956 (t0) REVERT: M 215 LEU cc_start: 0.8642 (pp) cc_final: 0.8374 (tt) REVERT: M 247 THR cc_start: 0.3082 (t) cc_final: 0.2656 (t) REVERT: M 279 TRP cc_start: 0.8255 (t-100) cc_final: 0.7259 (t60) REVERT: M 327 ASP cc_start: 0.6354 (m-30) cc_final: 0.6009 (m-30) REVERT: M 341 LEU cc_start: 0.8344 (pt) cc_final: 0.7774 (mt) REVERT: M 342 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.6902 (tmtm) REVERT: M 354 ARG cc_start: 0.7753 (tpm170) cc_final: 0.7518 (tpm170) REVERT: N 17 LEU cc_start: 0.7653 (pp) cc_final: 0.7343 (tp) REVERT: N 22 ARG cc_start: 0.7502 (mmm160) cc_final: 0.7286 (tpm170) REVERT: N 106 LYS cc_start: 0.7660 (pttp) cc_final: 0.7410 (pttm) outliers start: 49 outliers final: 34 residues processed: 475 average time/residue: 0.3878 time to fit residues: 249.7346 Evaluate side-chains 490 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 449 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 130 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 ILE 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 95 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 E residue 56 LYS Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 60 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 H residue 83 LEU Chi-restraints excluded: chain H residue 86 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 313 ARG Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 150 PHE Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 349 LEU 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: 0.5980 chunk 91 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 25 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN F 27 GLN 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 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.110934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.093465 restraints weight = 54713.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095635 restraints weight = 31047.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.097101 restraints weight = 20648.025| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.9940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17881 Z= 0.199 Angle : 0.972 15.579 25382 Z= 0.505 Chirality : 0.048 0.264 2864 Planarity : 0.008 0.202 2198 Dihedral : 28.555 179.836 4769 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 4.42 % Allowed : 39.95 % Favored : 55.63 % 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: -2.91 (0.22), residues: 1323 helix: -1.16 (0.19), residues: 632 sheet: -2.92 (0.81), residues: 33 loop : -2.71 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 279 HIS 0.007 0.001 HIS M 248 PHE 0.020 0.002 PHE M 232 TYR 0.030 0.002 TYR K 352 ARG 0.009 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.05351 ( 735) hydrogen bonds : angle 4.29575 ( 1811) covalent geometry : bond 0.00454 (17881) covalent geometry : angle 0.97162 (25382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6836.85 seconds wall clock time: 118 minutes 53.47 seconds (7133.47 seconds total)