Starting phenix.real_space_refine on Fri Mar 6 00:36:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kiw_0693/03_2026/6kiw_0693.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiw_0693/03_2026/6kiw_0693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kiw_0693/03_2026/6kiw_0693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiw_0693/03_2026/6kiw_0693.map" model { file = "/net/cci-nas-00/data/ceres_data/6kiw_0693/03_2026/6kiw_0693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiw_0693/03_2026/6kiw_0693.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.000 sd= 0.006 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 8458 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 289 5.49 5 S 58 5.16 5 C 11850 2.51 5 N 3670 2.21 5 O 4357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20225 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 2 Chain: "N" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2724 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "T" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1404 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain breaks: 1 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13087 SG CYS K4901 63.291 80.861 43.129 1.00136.31 S ATOM 13117 SG CYS K4906 60.436 78.974 41.905 1.00128.71 S Time building chain proxies: 4.38, per 1000 atoms: 0.22 Number of scatterers: 20225 At special positions: 0 Unit cell: (162.41, 147.15, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 58 16.00 P 289 15.00 O 4357 8.00 N 3670 7.00 C 11850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 741.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K5001 " pdb="ZN ZN K5001 " - pdb=" SG CYS K4906 " pdb="ZN ZN K5001 " - pdb=" SG CYS K4901 " 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3378 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 29 sheets defined 32.7% alpha, 11.2% beta 143 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.888A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.947A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.588A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.871A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.966A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.443A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.577A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.707A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.886A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.820A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.843A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.519A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.888A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.946A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.588A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.871A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.713A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.687A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.509A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.982A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.796A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.380A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.799A pdb=" N LEU G 115 " --> pdb=" O GLN G 112 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 116' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 53 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 4.035A pdb=" N ALA H 121 " --> pdb=" O CYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 4758 through 4767 Processing helix chain 'K' and resid 4768 through 4773 removed outlier: 4.401A pdb=" N VAL K4773 " --> pdb=" O TRP K4769 " (cutoff:3.500A) Processing helix chain 'K' and resid 4809 through 4817 removed outlier: 4.559A pdb=" N LYS K4815 " --> pdb=" O ASN K4811 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'O' and resid 22 through 34 removed outlier: 3.887A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 499 through 503 removed outlier: 3.717A pdb=" N ASP T 502 " --> pdb=" O PRO T 499 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.759A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.499A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.166A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.760A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'K' and resid 4799 through 4800 removed outlier: 4.772A pdb=" N ILE K4868 " --> pdb=" O TYR K4800 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 4803 through 4805 Processing sheet with id=AB1, first strand: chain 'N' and resid 20 through 21 removed outlier: 4.018A pdb=" N VAL N 318 " --> pdb=" O LEU N 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER N 319 " --> pdb=" O SER N 312 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER N 312 " --> pdb=" O SER N 319 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE N 310 " --> pdb=" O TRP N 321 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP N 300 " --> pdb=" O ILE N 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 27 through 29 removed outlier: 3.700A pdb=" N THR N 29 " --> pdb=" O GLY N 42 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS N 60 " --> pdb=" O ILE N 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 71 through 72 removed outlier: 3.939A pdb=" N SER N 71 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA N 84 " --> pdb=" O SER N 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'N' and resid 89 through 90 removed outlier: 3.527A pdb=" N PHE N 104 " --> pdb=" O VAL N 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 112 through 115 removed outlier: 4.041A pdb=" N LYS N 112 " --> pdb=" O CYS N 126 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL N 125 " --> pdb=" O VAL N 133 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL N 133 " --> pdb=" O VAL N 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 156 through 159 removed outlier: 4.147A pdb=" N LEU N 176 " --> pdb=" O THR N 168 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 201 through 206 removed outlier: 7.077A pdb=" N ASN N 216 " --> pdb=" O LYS N 202 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE N 204 " --> pdb=" O LEU N 214 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU N 214 " --> pdb=" O ILE N 204 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE N 206 " --> pdb=" O CYS N 212 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N CYS N 212 " --> pdb=" O PHE N 206 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN N 243 " --> pdb=" O VAL N 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 254 through 258 removed outlier: 4.069A pdb=" N LYS N 256 " --> pdb=" O GLY N 269 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL N 267 " --> pdb=" O CYS N 258 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU N 276 " --> pdb=" O LEU N 290 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 4 through 6 removed outlier: 6.462A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'R' and resid 36 through 37 Processing sheet with id=AC2, first strand: chain 'R' and resid 68 through 70 Processing sheet with id=AC3, first strand: chain 'R' and resid 90 through 93 removed outlier: 7.394A pdb=" N ALA R 105 " --> pdb=" O SER R 91 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL R 93 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL R 103 " --> pdb=" O VAL R 93 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS R 112 " --> pdb=" O SER R 104 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU R 111 " --> pdb=" O LEU R 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 134 through 137 removed outlier: 3.991A pdb=" N CYS R 134 " --> pdb=" O GLY R 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 177 through 179 removed outlier: 3.667A pdb=" N ARG R 196 " --> pdb=" O SER R 188 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 228 through 230 Processing sheet with id=AC7, first strand: chain 'R' and resid 264 through 267 removed outlier: 3.799A pdb=" N VAL R 275 " --> pdb=" O ASN R 265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER R 267 " --> pdb=" O TRP R 273 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP R 273 " --> pdb=" O SER R 267 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR R 284 " --> pdb=" O SER R 276 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 299 through 300 removed outlier: 4.091A pdb=" N LYS T 299 " --> pdb=" O VAL T 308 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL T 307 " --> pdb=" O VAL T 480 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL T 480 " --> pdb=" O VAL T 307 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR T 479 " --> pdb=" O ASP T 334 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 316 through 317 removed outlier: 3.616A pdb=" N SER T 473 " --> pdb=" O ARG T 343 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 365 through 366 removed outlier: 4.188A pdb=" N SER T 365 " --> pdb=" O PHE T 374 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE T 374 " --> pdb=" O SER T 365 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS T 380 " --> pdb=" O LYS T 373 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 395 through 396 removed outlier: 7.244A pdb=" N ILE T 447 " --> pdb=" O VAL T 458 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL T 458 " --> pdb=" O ILE T 447 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE T 449 " --> pdb=" O GLN T 456 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.20 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: 4683 1.33 - 1.45: 5751 1.45 - 1.57: 10114 1.57 - 1.70: 576 1.70 - 1.82: 83 Bond restraints: 21207 Sorted by residual: bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.47e+00 bond pdb=" C LYS F 31 " pdb=" N PRO F 32 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.23e-02 6.61e+03 3.26e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.07e+00 bond pdb=" C HIS N 67 " pdb=" N PRO N 68 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 bond pdb=" CA LEU T 392 " pdb=" CB LEU T 392 " ideal model delta sigma weight residual 1.526 1.554 -0.028 1.76e-02 3.23e+03 2.45e+00 ... (remaining 21202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 29461 2.83 - 5.65: 409 5.65 - 8.48: 28 8.48 - 11.30: 6 11.30 - 14.13: 1 Bond angle restraints: 29905 Sorted by residual: angle pdb=" N VAL K4824 " pdb=" CA VAL K4824 " pdb=" C VAL K4824 " ideal model delta sigma weight residual 112.17 104.37 7.80 9.50e-01 1.11e+00 6.75e+01 angle pdb=" C ASP B 24 " pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 121.54 132.68 -11.14 1.91e+00 2.74e-01 3.40e+01 angle pdb=" C ARG A 49 " pdb=" N GLU A 50 " pdb=" CA GLU A 50 " ideal model delta sigma weight residual 121.54 132.63 -11.09 1.91e+00 2.74e-01 3.37e+01 angle pdb=" C ARG E 49 " pdb=" N GLU E 50 " pdb=" CA GLU E 50 " ideal model delta sigma weight residual 121.54 132.62 -11.08 1.91e+00 2.74e-01 3.37e+01 angle pdb=" C GLU N 327 " pdb=" N ASN N 328 " pdb=" CA ASN N 328 " ideal model delta sigma weight residual 121.54 131.12 -9.58 1.91e+00 2.74e-01 2.51e+01 ... (remaining 29900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 10527 34.75 - 69.51: 1426 69.51 - 104.26: 21 104.26 - 139.02: 2 139.02 - 173.77: 2 Dihedral angle restraints: 11978 sinusoidal: 6738 harmonic: 5240 Sorted by residual: dihedral pdb=" CA GLU N 327 " pdb=" C GLU N 327 " pdb=" N ASN N 328 " pdb=" CA ASN N 328 " ideal model delta harmonic sigma weight residual 180.00 145.72 34.28 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA ALA N 333 " pdb=" C ALA N 333 " pdb=" N PRO N 334 " pdb=" CA PRO N 334 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA TYR N 115 " pdb=" C TYR N 115 " pdb=" N HIS N 116 " pdb=" CA HIS N 116 " ideal model delta harmonic sigma weight residual 180.00 150.56 29.44 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 11975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2267 0.046 - 0.091: 802 0.091 - 0.137: 255 0.137 - 0.182: 40 0.182 - 0.228: 7 Chirality restraints: 3371 Sorted by residual: chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA GLU E 59 " pdb=" N GLU E 59 " pdb=" C GLU E 59 " pdb=" CB GLU E 59 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3368 not shown) Planarity restraints: 2785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 50 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLU E 50 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU E 50 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE E 51 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 50 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C GLU A 50 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 50 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 51 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER R 223 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO R 224 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO R 224 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 224 " -0.037 5.00e-02 4.00e+02 ... (remaining 2782 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1397 2.73 - 3.27: 17332 3.27 - 3.81: 35509 3.81 - 4.36: 41871 4.36 - 4.90: 64146 Nonbonded interactions: 160255 Sorted by model distance: nonbonded pdb=" OG SER K4850 " pdb="ZN ZN K5001 " model vdw 2.182 2.230 nonbonded pdb=" O PHE T 464 " pdb=" OH TYR T 468 " model vdw 2.252 3.040 nonbonded pdb=" OG SER R 129 " pdb=" OD2 ASP R 150 " model vdw 2.257 3.040 nonbonded pdb=" OG SER R 175 " pdb=" OG SER R 189 " model vdw 2.269 3.040 nonbonded pdb=" OG SER R 223 " pdb=" OD1 ASN R 225 " model vdw 2.273 3.040 ... (remaining 160250 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' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 29 through 120) } 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: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 23.460 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 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 0.473 21209 Z= 0.293 Angle : 0.887 14.126 29905 Z= 0.509 Chirality : 0.051 0.228 3371 Planarity : 0.007 0.067 2785 Dihedral : 22.755 173.773 8600 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.16), residues: 1775 helix: -1.66 (0.17), residues: 567 sheet: -2.25 (0.35), residues: 182 loop : -3.45 (0.16), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 343 TYR 0.040 0.003 TYR H 37 PHE 0.016 0.002 PHE N 189 TRP 0.026 0.002 TRP R 286 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00590 (21207) covalent geometry : angle 0.88716 (29905) hydrogen bonds : bond 0.15269 ( 873) hydrogen bonds : angle 5.70818 ( 2190) metal coordination : bond 0.36987 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8680 (tt0) cc_final: 0.8349 (tt0) REVERT: B 27 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7769 (tm-30) REVERT: B 77 LYS cc_start: 0.9049 (tppt) cc_final: 0.8778 (mtmt) REVERT: B 79 LYS cc_start: 0.9008 (mttt) cc_final: 0.8667 (mttm) REVERT: B 88 TYR cc_start: 0.8010 (m-10) cc_final: 0.7747 (m-10) REVERT: C 38 ASN cc_start: 0.8392 (m110) cc_final: 0.8163 (p0) REVERT: C 90 ASP cc_start: 0.8954 (t0) cc_final: 0.8666 (t0) REVERT: C 100 VAL cc_start: 0.9486 (t) cc_final: 0.9266 (p) REVERT: D 33 SER cc_start: 0.9108 (t) cc_final: 0.8842 (m) REVERT: D 51 ILE cc_start: 0.9192 (tt) cc_final: 0.8973 (tt) REVERT: D 65 ASP cc_start: 0.8689 (t0) cc_final: 0.8029 (t0) REVERT: D 116 THR cc_start: 0.8651 (m) cc_final: 0.8356 (p) REVERT: F 82 THR cc_start: 0.9362 (p) cc_final: 0.9124 (m) REVERT: F 84 MET cc_start: 0.7780 (mmm) cc_final: 0.7094 (mmm) REVERT: G 18 SER cc_start: 0.9278 (m) cc_final: 0.8956 (t) REVERT: G 84 GLN cc_start: 0.9016 (tp40) cc_final: 0.8774 (tp40) REVERT: G 101 THR cc_start: 0.9451 (m) cc_final: 0.9149 (p) REVERT: G 110 ASN cc_start: 0.8377 (t160) cc_final: 0.8136 (p0) REVERT: H 82 LYS cc_start: 0.9135 (mttt) cc_final: 0.8635 (mttm) REVERT: K 4886 TYR cc_start: 0.6052 (m-10) cc_final: 0.5767 (m-80) REVERT: N 50 ILE cc_start: 0.8020 (mt) cc_final: 0.7717 (pt) REVERT: N 209 LYS cc_start: 0.8676 (tmtp) cc_final: 0.8399 (tttt) REVERT: R 149 PHE cc_start: 0.4278 (m-10) cc_final: 0.3567 (m-10) REVERT: R 155 ILE cc_start: 0.5056 (mt) cc_final: 0.4780 (mt) REVERT: R 173 PRO cc_start: 0.5486 (Cg_exo) cc_final: 0.5184 (Cg_endo) REVERT: T 313 TYR cc_start: 0.0721 (m-80) cc_final: -0.0487 (m-80) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1984 time to fit residues: 119.4468 Evaluate side-chains 242 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 55 GLN E 68 GLN G 110 ASN H 46 HIS K4811 ASN ** N 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 250 ASN N 324 ASN N 328 ASN R 44 HIS R 136 ASN R 295 GLN T 456 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.172863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.135267 restraints weight = 44717.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135484 restraints weight = 70889.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136176 restraints weight = 63462.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136048 restraints weight = 44826.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136941 restraints weight = 37089.215| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 21209 Z= 0.216 Angle : 0.704 11.347 29905 Z= 0.396 Chirality : 0.043 0.186 3371 Planarity : 0.006 0.079 2785 Dihedral : 27.866 173.014 5132 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.32 % Allowed : 9.61 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.18), residues: 1775 helix: 0.19 (0.21), residues: 573 sheet: -2.03 (0.33), residues: 202 loop : -3.18 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K4845 TYR 0.040 0.002 TYR T 475 PHE 0.024 0.002 PHE N 206 TRP 0.024 0.002 TRP K4769 HIS 0.015 0.001 HIS K4833 Details of bonding type rmsd covalent geometry : bond 0.00485 (21207) covalent geometry : angle 0.70445 (29905) hydrogen bonds : bond 0.06371 ( 873) hydrogen bonds : angle 4.53401 ( 2190) metal coordination : bond 0.01668 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8124 (tt0) cc_final: 0.7824 (tt0) REVERT: B 27 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7502 (tm-30) REVERT: B 79 LYS cc_start: 0.8966 (mttt) cc_final: 0.8629 (mttm) REVERT: B 88 TYR cc_start: 0.7980 (m-10) cc_final: 0.7570 (m-10) REVERT: C 20 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7607 (ttp80) REVERT: D 33 SER cc_start: 0.9026 (t) cc_final: 0.8692 (m) REVERT: D 48 ASP cc_start: 0.7034 (p0) cc_final: 0.6817 (p0) REVERT: D 73 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8502 (mm-30) REVERT: E 51 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9311 (tt) REVERT: E 59 GLU cc_start: 0.8118 (pm20) cc_final: 0.7896 (pm20) REVERT: E 74 ILE cc_start: 0.9214 (pt) cc_final: 0.8112 (pt) REVERT: F 27 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7911 (mm-40) REVERT: F 82 THR cc_start: 0.9437 (p) cc_final: 0.9098 (m) REVERT: F 84 MET cc_start: 0.7579 (mmm) cc_final: 0.7230 (mmm) REVERT: G 18 SER cc_start: 0.9018 (m) cc_final: 0.8767 (t) REVERT: G 84 GLN cc_start: 0.8992 (tp40) cc_final: 0.8658 (tp40) REVERT: G 101 THR cc_start: 0.9417 (m) cc_final: 0.9018 (p) REVERT: H 68 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7500 (mm-30) REVERT: K 4886 TYR cc_start: 0.5976 (m-10) cc_final: 0.5735 (m-80) REVERT: N 89 ILE cc_start: 0.5402 (OUTLIER) cc_final: 0.5179 (mm) REVERT: N 134 MET cc_start: 0.7459 (tmm) cc_final: 0.7019 (tmm) REVERT: N 159 PHE cc_start: 0.5569 (m-80) cc_final: 0.5309 (m-10) REVERT: N 160 ASP cc_start: 0.6097 (OUTLIER) cc_final: 0.5836 (t70) REVERT: N 209 LYS cc_start: 0.8714 (tmtp) cc_final: 0.8489 (tttt) REVERT: N 332 PHE cc_start: 0.6140 (t80) cc_final: 0.5524 (t80) REVERT: R 173 PRO cc_start: 0.5448 (Cg_exo) cc_final: 0.5188 (Cg_endo) REVERT: T 313 TYR cc_start: 0.1202 (m-80) cc_final: -0.0825 (m-80) REVERT: T 460 TYR cc_start: 0.4143 (m-80) cc_final: 0.3482 (m-80) outliers start: 36 outliers final: 20 residues processed: 299 average time/residue: 0.1460 time to fit residues: 66.5651 Evaluate side-chains 269 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain K residue 4798 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain R residue 131 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 44 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 176 optimal weight: 0.0870 chunk 137 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN D 44 GLN E 39 HIS G 84 GLN H 92 GLN R 86 HIS R 178 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.173413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136945 restraints weight = 44968.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136053 restraints weight = 78778.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137235 restraints weight = 72204.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136933 restraints weight = 49900.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137531 restraints weight = 46340.838| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21209 Z= 0.176 Angle : 0.638 13.516 29905 Z= 0.362 Chirality : 0.041 0.182 3371 Planarity : 0.004 0.052 2785 Dihedral : 27.589 172.258 5132 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.51 % Allowed : 12.12 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.19), residues: 1775 helix: 0.96 (0.22), residues: 574 sheet: -2.03 (0.32), residues: 231 loop : -3.02 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 498 TYR 0.022 0.002 TYR T 497 PHE 0.019 0.001 PHE N 189 TRP 0.025 0.002 TRP N 51 HIS 0.007 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00389 (21207) covalent geometry : angle 0.63834 (29905) hydrogen bonds : bond 0.05499 ( 873) hydrogen bonds : angle 4.04363 ( 2190) metal coordination : bond 0.00266 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 79 LYS cc_start: 0.8928 (mttt) cc_final: 0.8614 (mttm) REVERT: C 20 ARG cc_start: 0.7992 (ttm170) cc_final: 0.7604 (ttp80) REVERT: D 33 SER cc_start: 0.9008 (t) cc_final: 0.8679 (m) REVERT: D 48 ASP cc_start: 0.7116 (p0) cc_final: 0.6589 (p0) REVERT: D 65 ASP cc_start: 0.8256 (t0) cc_final: 0.8043 (t0) REVERT: F 27 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7901 (mm-40) REVERT: G 18 SER cc_start: 0.8968 (m) cc_final: 0.8671 (t) REVERT: G 84 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8646 (tp40) REVERT: G 99 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7816 (mmt90) REVERT: G 101 THR cc_start: 0.9400 (m) cc_final: 0.8836 (p) REVERT: K 4886 TYR cc_start: 0.5992 (m-10) cc_final: 0.5734 (m-80) REVERT: N 74 TRP cc_start: 0.6376 (m100) cc_final: 0.6170 (m-10) REVERT: N 134 MET cc_start: 0.7633 (tmm) cc_final: 0.7314 (tmm) REVERT: N 159 PHE cc_start: 0.5554 (m-80) cc_final: 0.5302 (m-10) REVERT: N 199 THR cc_start: 0.8518 (t) cc_final: 0.8266 (t) REVERT: N 255 LYS cc_start: 0.4555 (tptt) cc_final: 0.4233 (tptt) REVERT: N 332 PHE cc_start: 0.6148 (t80) cc_final: 0.5618 (t80) REVERT: R 234 LEU cc_start: 0.6526 (mt) cc_final: 0.6202 (mp) REVERT: T 313 TYR cc_start: 0.0971 (m-80) cc_final: -0.0905 (m-80) REVERT: T 460 TYR cc_start: 0.4268 (m-80) cc_final: 0.3582 (m-80) outliers start: 39 outliers final: 20 residues processed: 279 average time/residue: 0.1397 time to fit residues: 60.8639 Evaluate side-chains 254 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 4798 ILE Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain R residue 131 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 132 optimal weight: 20.0000 chunk 137 optimal weight: 40.0000 chunk 160 optimal weight: 8.9990 chunk 176 optimal weight: 0.1980 chunk 149 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 38 ASN E 113 HIS ** R 178 HIS ** 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 = 0.4255 r_free = 0.4255 target = 0.170587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.135343 restraints weight = 44707.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.137439 restraints weight = 74767.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136790 restraints weight = 60242.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.136543 restraints weight = 49726.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137379 restraints weight = 39280.920| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 21209 Z= 0.248 Angle : 0.700 12.089 29905 Z= 0.389 Chirality : 0.043 0.184 3371 Planarity : 0.005 0.051 2785 Dihedral : 27.509 172.488 5132 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 2.90 % Allowed : 12.57 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.19), residues: 1775 helix: 0.89 (0.21), residues: 577 sheet: -1.89 (0.32), residues: 240 loop : -2.94 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 162 TYR 0.049 0.003 TYR H 80 PHE 0.021 0.002 PHE A 84 TRP 0.031 0.002 TRP R 114 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00564 (21207) covalent geometry : angle 0.69963 (29905) hydrogen bonds : bond 0.06331 ( 873) hydrogen bonds : angle 4.21425 ( 2190) metal coordination : bond 0.00087 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9006 (mttt) cc_final: 0.8673 (mttm) REVERT: B 88 TYR cc_start: 0.8030 (m-10) cc_final: 0.7646 (m-10) REVERT: C 20 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7642 (ttp80) REVERT: D 33 SER cc_start: 0.9093 (t) cc_final: 0.8774 (m) REVERT: D 48 ASP cc_start: 0.7321 (p0) cc_final: 0.6762 (p0) REVERT: D 65 ASP cc_start: 0.8510 (t70) cc_final: 0.8164 (t0) REVERT: D 98 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9006 (mp) REVERT: F 27 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8152 (mm-40) REVERT: G 18 SER cc_start: 0.8970 (m) cc_final: 0.8734 (t) REVERT: G 99 ARG cc_start: 0.8030 (mmm160) cc_final: 0.7787 (mmt90) REVERT: H 36 ILE cc_start: 0.8665 (pt) cc_final: 0.8380 (mt) REVERT: K 4886 TYR cc_start: 0.6152 (m-10) cc_final: 0.5873 (m-80) REVERT: N 74 TRP cc_start: 0.6494 (m100) cc_final: 0.6277 (m-10) REVERT: N 134 MET cc_start: 0.7790 (tmm) cc_final: 0.7504 (tmm) REVERT: N 255 LYS cc_start: 0.4560 (tptt) cc_final: 0.4336 (tptt) REVERT: N 332 PHE cc_start: 0.6038 (t80) cc_final: 0.5347 (t80) REVERT: T 313 TYR cc_start: 0.1136 (m-80) cc_final: -0.0943 (m-80) REVERT: T 336 MET cc_start: -0.2768 (mmt) cc_final: -0.2998 (mmm) REVERT: T 460 TYR cc_start: 0.4290 (m-80) cc_final: 0.3651 (m-80) outliers start: 45 outliers final: 30 residues processed: 267 average time/residue: 0.1396 time to fit residues: 57.8202 Evaluate side-chains 261 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 4798 ILE Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 226 ASP Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain R residue 131 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 142 optimal weight: 3.9990 chunk 137 optimal weight: 30.0000 chunk 133 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS G 84 GLN ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.171491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135239 restraints weight = 44375.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136751 restraints weight = 75201.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.136789 restraints weight = 67090.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.136419 restraints weight = 51466.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137116 restraints weight = 40741.592| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21209 Z= 0.198 Angle : 0.649 11.789 29905 Z= 0.364 Chirality : 0.041 0.162 3371 Planarity : 0.004 0.049 2785 Dihedral : 27.349 172.097 5132 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.48 % Allowed : 12.38 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.19), residues: 1775 helix: 1.14 (0.22), residues: 576 sheet: -1.90 (0.32), residues: 244 loop : -2.87 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 30 TYR 0.045 0.002 TYR H 80 PHE 0.017 0.001 PHE N 189 TRP 0.036 0.002 TRP R 114 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00448 (21207) covalent geometry : angle 0.64940 (29905) hydrogen bonds : bond 0.05671 ( 873) hydrogen bonds : angle 3.96525 ( 2190) metal coordination : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8324 (mmm) cc_final: 0.8008 (mmm) REVERT: B 79 LYS cc_start: 0.8963 (mttt) cc_final: 0.8637 (mttm) REVERT: B 88 TYR cc_start: 0.7893 (m-10) cc_final: 0.7535 (m-10) REVERT: C 20 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7617 (ttp80) REVERT: D 33 SER cc_start: 0.8983 (t) cc_final: 0.8687 (m) REVERT: D 48 ASP cc_start: 0.7562 (p0) cc_final: 0.7046 (p0) REVERT: D 65 ASP cc_start: 0.8473 (t70) cc_final: 0.8145 (t0) REVERT: E 59 GLU cc_start: 0.8219 (pm20) cc_final: 0.7979 (pm20) REVERT: E 74 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8981 (mm) REVERT: F 63 GLU cc_start: 0.8024 (tt0) cc_final: 0.7746 (tt0) REVERT: G 18 SER cc_start: 0.8961 (m) cc_final: 0.8683 (t) REVERT: G 84 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8314 (tm-30) REVERT: H 36 ILE cc_start: 0.8613 (pt) cc_final: 0.8304 (mt) REVERT: K 4886 TYR cc_start: 0.6185 (m-10) cc_final: 0.5926 (m-80) REVERT: N 51 TRP cc_start: 0.6320 (OUTLIER) cc_final: 0.6036 (m100) REVERT: N 74 TRP cc_start: 0.6521 (m100) cc_final: 0.6314 (m-10) REVERT: N 134 MET cc_start: 0.7912 (tmm) cc_final: 0.7687 (tmm) REVERT: N 255 LYS cc_start: 0.4721 (tptt) cc_final: 0.4498 (tptt) REVERT: N 332 PHE cc_start: 0.6128 (t80) cc_final: 0.5365 (t80) REVERT: R 64 SER cc_start: 0.3872 (OUTLIER) cc_final: 0.3612 (m) REVERT: T 313 TYR cc_start: 0.1018 (m-80) cc_final: -0.1018 (m-80) REVERT: T 336 MET cc_start: -0.2890 (mmt) cc_final: -0.3114 (mmm) REVERT: T 460 TYR cc_start: 0.4319 (m-80) cc_final: 0.3685 (m-80) outliers start: 54 outliers final: 32 residues processed: 275 average time/residue: 0.1396 time to fit residues: 59.4997 Evaluate side-chains 267 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 4798 ILE Chi-restraints excluded: chain N residue 51 TRP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 131 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 116 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 111 optimal weight: 0.3980 chunk 169 optimal weight: 20.0000 chunk 4 optimal weight: 0.1980 chunk 178 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.169870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133533 restraints weight = 43915.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.135465 restraints weight = 79329.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.135089 restraints weight = 65574.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136166 restraints weight = 43371.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136209 restraints weight = 39534.654| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21209 Z= 0.242 Angle : 0.697 13.481 29905 Z= 0.387 Chirality : 0.043 0.174 3371 Planarity : 0.005 0.050 2785 Dihedral : 27.366 172.299 5132 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.68 % Allowed : 13.54 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.19), residues: 1775 helix: 1.03 (0.21), residues: 571 sheet: -1.67 (0.33), residues: 211 loop : -2.83 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 154 TYR 0.044 0.002 TYR H 80 PHE 0.019 0.002 PHE A 84 TRP 0.041 0.002 TRP R 114 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00554 (21207) covalent geometry : angle 0.69712 (29905) hydrogen bonds : bond 0.06369 ( 873) hydrogen bonds : angle 4.13708 ( 2190) metal coordination : bond 0.00152 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 240 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: A 96 SER cc_start: 0.9185 (p) cc_final: 0.8957 (t) REVERT: B 79 LYS cc_start: 0.9024 (mttt) cc_final: 0.8647 (mttm) REVERT: B 88 TYR cc_start: 0.8031 (m-10) cc_final: 0.7752 (m-10) REVERT: C 20 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7625 (ttp80) REVERT: D 33 SER cc_start: 0.9054 (t) cc_final: 0.8740 (m) REVERT: D 48 ASP cc_start: 0.7523 (p0) cc_final: 0.6978 (p0) REVERT: D 65 ASP cc_start: 0.8532 (t70) cc_final: 0.8024 (t0) REVERT: E 59 GLU cc_start: 0.8169 (pm20) cc_final: 0.7927 (pm20) REVERT: F 63 GLU cc_start: 0.8078 (tt0) cc_final: 0.7759 (tt0) REVERT: F 84 MET cc_start: 0.8087 (tpp) cc_final: 0.7847 (tpp) REVERT: G 18 SER cc_start: 0.9005 (m) cc_final: 0.8748 (t) REVERT: G 84 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: G 101 THR cc_start: 0.9366 (m) cc_final: 0.8713 (p) REVERT: H 36 ILE cc_start: 0.8630 (pt) cc_final: 0.8406 (mt) REVERT: H 48 ASP cc_start: 0.8020 (p0) cc_final: 0.7248 (p0) REVERT: K 4886 TYR cc_start: 0.6148 (m-10) cc_final: 0.5874 (m-80) REVERT: N 51 TRP cc_start: 0.6354 (OUTLIER) cc_final: 0.5933 (m100) REVERT: N 74 TRP cc_start: 0.6685 (m100) cc_final: 0.6474 (m-10) REVERT: N 134 MET cc_start: 0.7902 (tmm) cc_final: 0.7682 (tmm) REVERT: T 313 TYR cc_start: 0.0910 (m-80) cc_final: -0.1150 (m-10) REVERT: T 336 MET cc_start: -0.2888 (mmt) cc_final: -0.3119 (mmm) REVERT: T 460 TYR cc_start: 0.4345 (m-80) cc_final: 0.3718 (m-80) outliers start: 57 outliers final: 38 residues processed: 273 average time/residue: 0.1358 time to fit residues: 57.2294 Evaluate side-chains 269 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 4798 ILE Chi-restraints excluded: chain N residue 51 TRP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 226 ASP Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 83 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.172640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.138555 restraints weight = 44486.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138518 restraints weight = 64821.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137918 restraints weight = 52562.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.138182 restraints weight = 37543.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138376 restraints weight = 34659.505| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21209 Z= 0.158 Angle : 0.634 12.403 29905 Z= 0.354 Chirality : 0.040 0.164 3371 Planarity : 0.004 0.048 2785 Dihedral : 27.213 172.099 5132 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.26 % Allowed : 15.99 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.19), residues: 1775 helix: 1.43 (0.22), residues: 577 sheet: -1.53 (0.34), residues: 212 loop : -2.79 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 30 TYR 0.032 0.002 TYR D 37 PHE 0.021 0.001 PHE N 189 TRP 0.035 0.002 TRP R 114 HIS 0.004 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00348 (21207) covalent geometry : angle 0.63380 (29905) hydrogen bonds : bond 0.05195 ( 873) hydrogen bonds : angle 3.74798 ( 2190) metal coordination : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.9048 (p) cc_final: 0.8771 (t) REVERT: B 59 LYS cc_start: 0.8862 (tppt) cc_final: 0.8513 (tptt) REVERT: B 79 LYS cc_start: 0.8970 (mttt) cc_final: 0.8645 (mttm) REVERT: B 84 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7274 (tmm) REVERT: B 88 TYR cc_start: 0.7860 (m-10) cc_final: 0.7490 (m-10) REVERT: C 20 ARG cc_start: 0.7939 (ttm170) cc_final: 0.7578 (ttp80) REVERT: D 33 SER cc_start: 0.8895 (t) cc_final: 0.8670 (m) REVERT: D 48 ASP cc_start: 0.7599 (p0) cc_final: 0.7112 (p0) REVERT: D 65 ASP cc_start: 0.8389 (t70) cc_final: 0.8102 (t0) REVERT: E 42 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.8517 (ttm110) REVERT: F 63 GLU cc_start: 0.8184 (tt0) cc_final: 0.7876 (tt0) REVERT: G 18 SER cc_start: 0.8992 (m) cc_final: 0.8706 (t) REVERT: G 84 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8305 (tm-30) REVERT: G 101 THR cc_start: 0.9369 (m) cc_final: 0.8720 (p) REVERT: H 36 ILE cc_start: 0.8518 (pt) cc_final: 0.8266 (mt) REVERT: H 48 ASP cc_start: 0.7795 (p0) cc_final: 0.7020 (p0) REVERT: K 4886 TYR cc_start: 0.6057 (m-10) cc_final: 0.5750 (m-80) REVERT: N 51 TRP cc_start: 0.6217 (OUTLIER) cc_final: 0.5699 (m100) REVERT: N 134 MET cc_start: 0.7868 (tmm) cc_final: 0.7605 (tmm) REVERT: N 304 HIS cc_start: 0.7559 (t-90) cc_final: 0.7288 (t-90) REVERT: O 1 MET cc_start: 0.4262 (tpp) cc_final: 0.3264 (mmp) REVERT: R 149 PHE cc_start: 0.3868 (m-10) cc_final: 0.3646 (m-80) REVERT: T 313 TYR cc_start: 0.0709 (m-80) cc_final: -0.1388 (m-10) REVERT: T 336 MET cc_start: -0.2771 (mmt) cc_final: -0.3024 (mmm) REVERT: T 460 TYR cc_start: 0.4321 (m-80) cc_final: 0.3667 (m-80) outliers start: 35 outliers final: 27 residues processed: 255 average time/residue: 0.1491 time to fit residues: 58.2104 Evaluate side-chains 256 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain N residue 51 TRP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 7 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 189 optimal weight: 30.0000 chunk 128 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 177 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.172755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.136768 restraints weight = 44514.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.136198 restraints weight = 72293.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136509 restraints weight = 56958.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136627 restraints weight = 39825.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137037 restraints weight = 36688.772| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21209 Z= 0.166 Angle : 0.630 12.224 29905 Z= 0.352 Chirality : 0.040 0.227 3371 Planarity : 0.004 0.049 2785 Dihedral : 27.138 172.610 5132 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.26 % Allowed : 16.05 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.20), residues: 1775 helix: 1.55 (0.22), residues: 580 sheet: -1.45 (0.33), residues: 221 loop : -2.75 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.033 0.002 TYR H 80 PHE 0.020 0.001 PHE N 332 TRP 0.048 0.002 TRP N 74 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00370 (21207) covalent geometry : angle 0.63049 (29905) hydrogen bonds : bond 0.05080 ( 873) hydrogen bonds : angle 3.67207 ( 2190) metal coordination : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.9049 (p) cc_final: 0.8693 (t) REVERT: A 120 MET cc_start: 0.8194 (mmm) cc_final: 0.7933 (mmp) REVERT: B 79 LYS cc_start: 0.8967 (mttt) cc_final: 0.8634 (mttm) REVERT: B 84 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7351 (tmm) REVERT: B 88 TYR cc_start: 0.7873 (m-10) cc_final: 0.7528 (m-10) REVERT: C 20 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7572 (ttp80) REVERT: D 33 SER cc_start: 0.8910 (t) cc_final: 0.8589 (m) REVERT: D 48 ASP cc_start: 0.7624 (p0) cc_final: 0.7177 (p0) REVERT: D 65 ASP cc_start: 0.8310 (t70) cc_final: 0.8006 (t0) REVERT: E 42 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8491 (ttm110) REVERT: F 63 GLU cc_start: 0.7851 (tt0) cc_final: 0.7512 (tt0) REVERT: F 96 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8437 (p) REVERT: G 18 SER cc_start: 0.9024 (m) cc_final: 0.8737 (t) REVERT: G 84 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8291 (tm-30) REVERT: G 101 THR cc_start: 0.9372 (m) cc_final: 0.8713 (p) REVERT: H 36 ILE cc_start: 0.8567 (pt) cc_final: 0.8366 (mt) REVERT: H 48 ASP cc_start: 0.7800 (p0) cc_final: 0.7071 (p0) REVERT: K 4886 TYR cc_start: 0.6054 (m-10) cc_final: 0.5757 (m-80) REVERT: N 51 TRP cc_start: 0.6127 (OUTLIER) cc_final: 0.5710 (m100) REVERT: N 304 HIS cc_start: 0.7452 (t-90) cc_final: 0.7203 (t-90) REVERT: O 1 MET cc_start: 0.4357 (tpp) cc_final: 0.3363 (mmp) REVERT: T 313 TYR cc_start: 0.0658 (m-80) cc_final: -0.1388 (m-10) REVERT: T 336 MET cc_start: -0.2883 (mmt) cc_final: -0.3114 (mmm) REVERT: T 460 TYR cc_start: 0.4341 (m-80) cc_final: 0.3678 (m-80) outliers start: 35 outliers final: 24 residues processed: 251 average time/residue: 0.1371 time to fit residues: 53.2733 Evaluate side-chains 250 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain N residue 51 TRP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 122 optimal weight: 0.4980 chunk 123 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.175007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.138483 restraints weight = 44434.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.138823 restraints weight = 69549.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139445 restraints weight = 66784.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139226 restraints weight = 45739.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140288 restraints weight = 38823.352| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21209 Z= 0.141 Angle : 0.613 12.217 29905 Z= 0.343 Chirality : 0.040 0.259 3371 Planarity : 0.004 0.049 2785 Dihedral : 27.032 172.638 5132 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.87 % Allowed : 17.02 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.20), residues: 1775 helix: 1.78 (0.22), residues: 581 sheet: -1.18 (0.36), residues: 206 loop : -2.70 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.026 0.001 TYR H 80 PHE 0.022 0.001 PHE N 189 TRP 0.038 0.002 TRP K4769 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00309 (21207) covalent geometry : angle 0.61284 (29905) hydrogen bonds : bond 0.04404 ( 873) hydrogen bonds : angle 3.47094 ( 2190) metal coordination : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.8976 (p) cc_final: 0.8649 (t) REVERT: A 120 MET cc_start: 0.8163 (mmm) cc_final: 0.7892 (mmp) REVERT: B 43 VAL cc_start: 0.9144 (t) cc_final: 0.8934 (p) REVERT: B 59 LYS cc_start: 0.8715 (tppt) cc_final: 0.8180 (tptp) REVERT: B 72 TYR cc_start: 0.9278 (m-80) cc_final: 0.8285 (m-80) REVERT: B 79 LYS cc_start: 0.8918 (mttt) cc_final: 0.8584 (mttm) REVERT: B 84 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7103 (tmm) REVERT: B 88 TYR cc_start: 0.7854 (m-10) cc_final: 0.6299 (m-10) REVERT: C 20 ARG cc_start: 0.7918 (ttm170) cc_final: 0.7531 (ttp80) REVERT: D 33 SER cc_start: 0.8949 (t) cc_final: 0.8623 (m) REVERT: D 39 TYR cc_start: 0.7896 (t80) cc_final: 0.7662 (t80) REVERT: D 48 ASP cc_start: 0.7515 (p0) cc_final: 0.7084 (p0) REVERT: D 65 ASP cc_start: 0.8332 (t70) cc_final: 0.8129 (t70) REVERT: F 96 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8374 (p) REVERT: G 18 SER cc_start: 0.8980 (m) cc_final: 0.8677 (t) REVERT: G 74 LYS cc_start: 0.8564 (mtmt) cc_final: 0.8308 (ttmt) REVERT: G 84 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8274 (tm-30) REVERT: H 36 ILE cc_start: 0.8553 (pt) cc_final: 0.8322 (mt) REVERT: H 48 ASP cc_start: 0.7749 (p0) cc_final: 0.7018 (p0) REVERT: H 98 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8227 (mt) REVERT: K 4820 GLN cc_start: 0.6150 (mp10) cc_final: 0.5667 (tp40) REVERT: K 4886 TYR cc_start: 0.6053 (m-10) cc_final: 0.5774 (m-80) REVERT: N 51 TRP cc_start: 0.6131 (OUTLIER) cc_final: 0.5433 (m100) REVERT: N 134 MET cc_start: 0.7631 (tmm) cc_final: 0.7115 (tpp) REVERT: N 304 HIS cc_start: 0.7412 (t-90) cc_final: 0.7208 (t-90) REVERT: N 348 ARG cc_start: 0.0724 (OUTLIER) cc_final: 0.0371 (ptp-170) REVERT: O 1 MET cc_start: 0.4117 (tpp) cc_final: 0.3129 (mmp) REVERT: T 313 TYR cc_start: 0.0674 (m-80) cc_final: -0.1525 (m-10) REVERT: T 336 MET cc_start: -0.2869 (mmt) cc_final: -0.3103 (mmm) outliers start: 29 outliers final: 19 residues processed: 241 average time/residue: 0.1373 time to fit residues: 50.9441 Evaluate side-chains 235 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain N residue 51 TRP Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 348 ARG Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain T residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 37 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.174616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.137721 restraints weight = 44697.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137829 restraints weight = 75424.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138296 restraints weight = 69970.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.138950 restraints weight = 45123.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139237 restraints weight = 41242.637| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21209 Z= 0.152 Angle : 0.626 13.235 29905 Z= 0.348 Chirality : 0.040 0.201 3371 Planarity : 0.004 0.049 2785 Dihedral : 27.026 172.774 5132 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.68 % Allowed : 17.54 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.20), residues: 1775 helix: 1.83 (0.22), residues: 582 sheet: -1.12 (0.36), residues: 211 loop : -2.68 (0.17), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.029 0.002 TYR H 80 PHE 0.038 0.001 PHE R 222 TRP 0.047 0.003 TRP N 35 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00337 (21207) covalent geometry : angle 0.62588 (29905) hydrogen bonds : bond 0.04608 ( 873) hydrogen bonds : angle 3.55476 ( 2190) metal coordination : bond 0.00058 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.9046 (p) cc_final: 0.8701 (t) REVERT: A 120 MET cc_start: 0.8181 (mmm) cc_final: 0.7937 (mmm) REVERT: B 72 TYR cc_start: 0.9259 (m-80) cc_final: 0.8269 (m-80) REVERT: B 79 LYS cc_start: 0.8934 (mttt) cc_final: 0.8578 (mttm) REVERT: B 84 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7472 (tpt) REVERT: B 88 TYR cc_start: 0.7825 (m-10) cc_final: 0.7327 (m-10) REVERT: C 20 ARG cc_start: 0.7932 (ttm170) cc_final: 0.7546 (ttp80) REVERT: D 33 SER cc_start: 0.8926 (t) cc_final: 0.8606 (m) REVERT: D 48 ASP cc_start: 0.7572 (p0) cc_final: 0.7124 (p0) REVERT: D 65 ASP cc_start: 0.8228 (t70) cc_final: 0.7956 (t70) REVERT: F 96 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8377 (p) REVERT: G 18 SER cc_start: 0.8984 (m) cc_final: 0.8679 (t) REVERT: G 74 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8306 (ttmt) REVERT: G 84 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8328 (tm-30) REVERT: H 36 ILE cc_start: 0.8602 (pt) cc_final: 0.8348 (mt) REVERT: H 48 ASP cc_start: 0.7797 (p0) cc_final: 0.7050 (p0) REVERT: H 98 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8264 (mt) REVERT: K 4796 MET cc_start: 0.2721 (tpp) cc_final: 0.1016 (mmp) REVERT: K 4886 TYR cc_start: 0.6034 (m-10) cc_final: 0.5748 (m-80) REVERT: N 51 TRP cc_start: 0.6122 (OUTLIER) cc_final: 0.5333 (m100) REVERT: N 134 MET cc_start: 0.7610 (tmm) cc_final: 0.7088 (tpp) REVERT: N 304 HIS cc_start: 0.7399 (t-90) cc_final: 0.7144 (t-90) REVERT: N 348 ARG cc_start: 0.0750 (OUTLIER) cc_final: 0.0369 (ptp-170) REVERT: O 1 MET cc_start: 0.4230 (tpp) cc_final: 0.3235 (mmp) REVERT: R 243 TYR cc_start: 0.2356 (t80) cc_final: 0.2093 (t80) REVERT: T 313 TYR cc_start: 0.0678 (m-80) cc_final: -0.1510 (m-10) REVERT: T 336 MET cc_start: -0.2852 (mmt) cc_final: -0.3092 (mmm) outliers start: 26 outliers final: 21 residues processed: 233 average time/residue: 0.1289 time to fit residues: 46.9040 Evaluate side-chains 236 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain N residue 51 TRP Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 348 ARG Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 497 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 84 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 170 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** K4821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.172290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137219 restraints weight = 44556.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139691 restraints weight = 73470.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138553 restraints weight = 59543.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138478 restraints weight = 48306.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139175 restraints weight = 37953.954| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21209 Z= 0.200 Angle : 0.669 12.251 29905 Z= 0.369 Chirality : 0.041 0.219 3371 Planarity : 0.004 0.050 2785 Dihedral : 27.094 171.961 5132 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.00 % Allowed : 17.28 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.20), residues: 1775 helix: 1.55 (0.22), residues: 582 sheet: -1.05 (0.36), residues: 210 loop : -2.64 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.043 0.002 TYR D 80 PHE 0.033 0.002 PHE R 222 TRP 0.046 0.003 TRP N 35 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00455 (21207) covalent geometry : angle 0.66899 (29905) hydrogen bonds : bond 0.05526 ( 873) hydrogen bonds : angle 3.78287 ( 2190) metal coordination : bond 0.00130 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2685.83 seconds wall clock time: 47 minutes 17.57 seconds (2837.57 seconds total)