Starting phenix.real_space_refine on Sun Sep 13 23:59:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kiw_0693/09_2026/6kiw_0693.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiw_0693/09_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_0693/09_2026/6kiw_0693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiw_0693/09_2026/6kiw_0693.map" model { file = "/net/cci-nas-00/data/ceres_data/6kiw_0693/09_2026/6kiw_0693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiw_0693/09_2026/6kiw_0693.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6kiw_0693/09_2026/6kiw_0693.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kiw_0693/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 3.52, per 1000 atoms: 0.17 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: 1.39 Conformation dependent library (CDL) restraints added in 591.3 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: 2.43 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: 3.43 Time building geometry restraints manager: 1.98 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=" C5' DA I 120 " pdb=" C4' DA I 120 " ideal model delta sigma weight residual 1.512 1.538 -0.026 7.00e-03 2.04e+04 1.38e+01 bond pdb=" C1' DT J 50 " pdb=" N1 DT J 50 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.26e+01 bond pdb=" C5' DA I 131 " pdb=" C4' DA I 131 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.23e+01 bond pdb=" C5' DG I 19 " pdb=" C4' DG I 19 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.21e+01 bond pdb=" C3' DA I 39 " pdb=" C2' DA I 39 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 ... (remaining 21202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 29361 2.83 - 5.65: 509 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=" O4' DG I 4 " pdb=" C4' DG I 4 " pdb=" C3' DG I 4 " ideal model delta sigma weight residual 106.00 101.78 4.22 6.00e-01 2.78e+00 4.96e+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 ... (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: 2105 0.046 - 0.091: 909 0.091 - 0.137: 303 0.137 - 0.182: 46 0.182 - 0.228: 8 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.090 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: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 : 0.008 0.473 21209 Z= 0.534 Angle : 0.972 14.126 29905 Z= 0.719 Chirality : 0.055 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/Z covalent geometry : bond 0.00672 / 0.52 (21207) covalent geometry : angle 0.97192 / 0.72 (29905) hydrogen bonds : bond 0.15269 / 10.03 ( 873) hydrogen bonds : angle 5.70818 / 3.99 ( 2190) metal coordination : bond 0.36987 / 24.99 ( 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 : 0.646 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: 0.8348 (tt0) REVERT: B 27 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7767 (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: 0.8668 (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: 0.8164 (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 51 ILE cc_start: 0.9192 (tt) cc_final: 0.8981 (tt) REVERT: D 65 ASP cc_start: 0.8689 (t0) cc_final: 0.8032 (t0) REVERT: D 116 THR cc_start: 0.8651 (m) cc_final: 0.8354 (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: 0.7095 (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: 0.8775 (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: 0.8138 (p0) REVERT: H 82 LYS cc_start: 0.9135 (mttt) cc_final: 0.8636 (mttm) REVERT: K 4886 TYR cc_start: 0.6052 (m-10) cc_final: 0.5768 (m-80) REVERT: N 50 ILE cc_start: 0.8020 (mt) cc_final: 0.7716 (pt) REVERT: N 209 LYS cc_start: 0.8676 (tmtp) cc_final: 0.8398 (tttt) REVERT: R 149 PHE cc_start: 0.4278 (m-10) cc_final: 0.3569 (m-10) REVERT: R 155 ILE cc_start: 0.5056 (mt) cc_final: 0.4781 (mt) REVERT: R 173 PRO cc_start: 0.5486 (Cg_exo) cc_final: 0.5185 (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: 0.1825 time to fit residues: 110.8284 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 : 0.625 ------------------------------------------------------------------------------- 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: 30.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0270 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 overall best weight: 2.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 68 GLN D 46 HIS E 55 GLN E 68 GLN G 110 ASN H 46 HIS ** K4820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 250 ASN N 324 ASN ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 HIS R 136 ASN R 295 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.173739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.136405 restraints weight = 44773.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.136083 restraints weight = 74746.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137111 restraints weight = 63252.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136741 restraints weight = 46051.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137303 restraints weight = 40862.324| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21209 Z= 0.195 Angle : 0.761 11.561 29905 Z= 0.427 Chirality : 0.050 0.233 3371 Planarity : 0.006 0.082 2785 Dihedral : 28.145 168.587 5132 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 1.87 % Allowed : 10.06 % 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: -2.81 (0.18), residues: 1775 helix: 0.11 (0.21), residues: 574 sheet: -1.98 (0.35), residues: 196 loop : -3.23 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 196 TYR 0.043 0.002 TYR T 475 PHE 0.025 0.002 PHE N 206 TRP 0.025 0.002 TRP K4769 HIS 0.008 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (21207) covalent geometry : angle 0.76106 / 0.43 (29905) hydrogen bonds : bond 0.07048 / 4.60 ( 873) hydrogen bonds : angle 4.69987 / 3.23 ( 2190) metal coordination : bond 0.01509 / 1.08 ( 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 307 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 278 time to evaluate : 0.444 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: 0.8070 (tt0) cc_final: 0.7829 (tt0) REVERT: B 79 LYS cc_start: 0.8962 (mttt) cc_final: 0.8672 (mttm) REVERT: B 88 TYR cc_start: 0.7858 (m-10) cc_final: 0.6242 (m-10) REVERT: C 20 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7580 (ttp80) REVERT: D 80 TYR cc_start: 0.7686 (m-10) cc_final: 0.7449 (m-10) REVERT: E 59 GLU cc_start: 0.8073 (pm20) cc_final: 0.7814 (pm20) REVERT: E 74 ILE cc_start: 0.9387 (pt) cc_final: 0.8092 (pt) REVERT: F 27 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7940 (mm-40) REVERT: F 82 THR cc_start: 0.9404 (p) cc_final: 0.9076 (m) REVERT: G 18 SER cc_start: 0.8870 (m) cc_final: 0.8572 (t) REVERT: G 84 GLN cc_start: 0.8974 (tp40) cc_final: 0.8733 (tp40) REVERT: G 101 THR cc_start: 0.9399 (m) cc_final: 0.9057 (p) REVERT: G 110 ASN cc_start: 0.8337 (t0) cc_final: 0.8114 (p0) REVERT: K 4886 TYR cc_start: 0.5841 (m-10) cc_final: 0.5629 (m-80) REVERT: N 89 ILE cc_start: 0.5308 (OUTLIER) cc_final: 0.5090 (mm) REVERT: N 159 PHE cc_start: 0.5402 (m-80) cc_final: 0.4968 (m-10) REVERT: N 197 ASN cc_start: 0.7157 (t0) cc_final: 0.6953 (t0) REVERT: N 332 PHE cc_start: 0.6048 (t80) cc_final: 0.5444 (t80) REVERT: R 173 PRO cc_start: 0.5601 (Cg_exo) cc_final: 0.5400 (Cg_endo) REVERT: T 313 TYR cc_start: 0.1245 (m-80) cc_final: -0.0660 (m-80) REVERT: T 336 MET cc_start: -0.1489 (mmm) cc_final: -0.1948 (mmt) REVERT: T 460 TYR cc_start: 0.4167 (m-80) cc_final: 0.3524 (m-80) outliers start: 29 outliers final: 14 residues processed: 294 average time/residue: 0.1364 time to fit residues: 61.6235 Evaluate side-chains 251 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain R residue 64 SER 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: 2.9990 chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 84 optimal weight: 40.0000 chunk 38 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 38 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS H 92 GLN ** K4807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K4811 ASN N 328 ASN R 86 HIS R 178 HIS R 265 ASN T 456 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.171998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135851 restraints weight = 44928.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136771 restraints weight = 82889.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137275 restraints weight = 69779.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137025 restraints weight = 53037.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.137882 restraints weight = 41889.582| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21209 Z= 0.227 Angle : 0.754 13.632 29905 Z= 0.420 Chirality : 0.050 0.241 3371 Planarity : 0.005 0.060 2785 Dihedral : 28.040 168.029 5132 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 2.71 % Allowed : 11.73 % Favored : 85.56 % 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: -2.53 (0.18), residues: 1775 helix: 0.57 (0.21), residues: 571 sheet: -2.06 (0.36), residues: 194 loop : -3.14 (0.17), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K4777 TYR 0.042 0.002 TYR H 80 PHE 0.025 0.002 PHE N 206 TRP 0.021 0.002 TRP K4769 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 (21207) covalent geometry : angle 0.75383 / 0.42 (29905) hydrogen bonds : bond 0.07065 / 4.63 ( 873) hydrogen bonds : angle 4.55916 / 3.15 ( 2190) metal coordination : bond 0.00312 / 0.21 ( 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 277 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 0.559 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: 0.8372 (tt0) cc_final: 0.7996 (tt0) REVERT: B 79 LYS cc_start: 0.8942 (mttt) cc_final: 0.8611 (mttm) REVERT: B 88 TYR cc_start: 0.8077 (m-10) cc_final: 0.7538 (m-10) REVERT: C 20 ARG cc_start: 0.7992 (ttm170) cc_final: 0.7611 (ttp80) REVERT: D 48 ASP cc_start: 0.6989 (p0) cc_final: 0.6663 (p0) REVERT: D 65 ASP cc_start: 0.8276 (t0) cc_final: 0.7962 (t0) REVERT: F 27 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7946 (mm-40) REVERT: G 18 SER cc_start: 0.8992 (m) cc_final: 0.8745 (t) REVERT: G 84 GLN cc_start: 0.8980 (tp40) cc_final: 0.8720 (tp40) REVERT: G 101 THR cc_start: 0.9403 (m) cc_final: 0.8963 (p) REVERT: K 4886 TYR cc_start: 0.5998 (m-10) cc_final: 0.5711 (m-80) REVERT: N 74 TRP cc_start: 0.6384 (m100) cc_final: 0.6123 (m-10) REVERT: N 89 ILE cc_start: 0.5478 (OUTLIER) cc_final: 0.5218 (mm) REVERT: N 124 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5862 (tt) REVERT: N 134 MET cc_start: 0.7712 (tmm) cc_final: 0.7433 (tmm) REVERT: N 159 PHE cc_start: 0.5467 (m-80) cc_final: 0.5129 (m-10) REVERT: N 197 ASN cc_start: 0.7107 (t0) cc_final: 0.6865 (t0) REVERT: N 332 PHE cc_start: 0.6088 (t80) cc_final: 0.5468 (t80) REVERT: T 313 TYR cc_start: 0.1264 (m-80) cc_final: -0.0725 (m-80) REVERT: T 460 TYR cc_start: 0.4118 (m-80) cc_final: 0.3534 (m-80) outliers start: 42 outliers final: 28 residues processed: 264 average time/residue: 0.1337 time to fit residues: 55.3615 Evaluate side-chains 255 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 62 ILE Chi-restraints excluded: chain D residue 33 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 80 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 K residue 4807 ASN Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 108 SER 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 343 VAL Chi-restraints excluded: chain R residue 64 SER 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: 5.9990 chunk 137 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN D 44 GLN E 113 HIS G 84 GLN G 110 ASN K4794 HIS ** K4807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.169164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134073 restraints weight = 44815.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.136605 restraints weight = 91069.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136395 restraints weight = 62700.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137625 restraints weight = 42873.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137752 restraints weight = 37492.025| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 21209 Z= 0.324 Angle : 0.854 13.967 29905 Z= 0.463 Chirality : 0.053 0.245 3371 Planarity : 0.006 0.057 2785 Dihedral : 27.994 167.363 5132 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 3.42 % Allowed : 13.02 % Favored : 83.56 % 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: -2.61 (0.18), residues: 1775 helix: 0.27 (0.20), residues: 577 sheet: -1.96 (0.36), residues: 202 loop : -3.09 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 63 TYR 0.039 0.003 TYR H 80 PHE 0.030 0.002 PHE A 84 TRP 0.027 0.002 TRP R 114 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.32 (21207) covalent geometry : angle 0.85377 / 0.46 (29905) hydrogen bonds : bond 0.07923 / 5.21 ( 873) hydrogen bonds : angle 4.80939 / 3.33 ( 2190) metal coordination : bond 0.00242 / 0.17 ( 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: 53 poor density : 231 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8537 (tt0) cc_final: 0.8309 (tt0) REVERT: B 79 LYS cc_start: 0.8981 (mttt) cc_final: 0.8646 (mttm) REVERT: B 84 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7102 (tmm) REVERT: B 88 TYR cc_start: 0.8086 (m-10) cc_final: 0.7755 (m-10) REVERT: C 20 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7588 (ttp80) REVERT: C 24 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8218 (mm-40) REVERT: D 48 ASP cc_start: 0.7259 (p0) cc_final: 0.6898 (p0) REVERT: D 65 ASP cc_start: 0.8682 (t70) cc_final: 0.8173 (t0) REVERT: F 27 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8118 (mm-40) REVERT: G 64 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: G 84 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8385 (tm-30) REVERT: G 101 THR cc_start: 0.9422 (m) cc_final: 0.8823 (p) REVERT: K 4886 TYR cc_start: 0.6191 (m-10) cc_final: 0.5946 (m-80) REVERT: N 74 TRP cc_start: 0.6572 (m100) cc_final: 0.6237 (m-10) REVERT: N 89 ILE cc_start: 0.5721 (OUTLIER) cc_final: 0.5476 (mm) REVERT: N 124 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5208 (tt) REVERT: N 134 MET cc_start: 0.7849 (tmm) cc_final: 0.7539 (tmm) REVERT: N 159 PHE cc_start: 0.5926 (m-80) cc_final: 0.5669 (m-80) REVERT: N 197 ASN cc_start: 0.7093 (t0) cc_final: 0.6872 (t0) REVERT: T 313 TYR cc_start: 0.1397 (m-80) cc_final: -0.0736 (m-80) REVERT: T 460 TYR cc_start: 0.4138 (m-80) cc_final: 0.3547 (m-80) outliers start: 53 outliers final: 32 residues processed: 266 average time/residue: 0.1416 time to fit residues: 59.1401 Evaluate side-chains 255 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 84 MET 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 33 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 52 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 64 GLU 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 89 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 R residue 64 SER Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain T residue 501 SER 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: 5.9990 chunk 133 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 29 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** K4807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.171795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136135 restraints weight = 44467.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.137975 restraints weight = 82311.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138174 restraints weight = 67677.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138103 restraints weight = 50224.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140362 restraints weight = 39882.158| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21209 Z= 0.184 Angle : 0.699 13.005 29905 Z= 0.394 Chirality : 0.048 0.224 3371 Planarity : 0.005 0.052 2785 Dihedral : 27.803 166.850 5132 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.39 % Allowed : 14.96 % Favored : 82.66 % 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: -2.19 (0.19), residues: 1775 helix: 0.85 (0.21), residues: 578 sheet: -1.94 (0.34), residues: 215 loop : -2.94 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 154 TYR 0.040 0.002 TYR H 80 PHE 0.019 0.001 PHE N 206 TRP 0.035 0.002 TRP R 114 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (21207) covalent geometry : angle 0.69856 / 0.39 (29905) hydrogen bonds : bond 0.06482 / 4.23 ( 873) hydrogen bonds : angle 4.26678 / 2.93 ( 2190) metal coordination : bond 0.00079 / 0.05 ( 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 273 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8254 (tt0) cc_final: 0.8031 (tt0) REVERT: A 120 MET cc_start: 0.8237 (mmm) cc_final: 0.7828 (mmp) REVERT: B 79 LYS cc_start: 0.8967 (mttt) cc_final: 0.8634 (mttm) REVERT: B 84 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6953 (tmm) REVERT: B 88 TYR cc_start: 0.7929 (m-10) cc_final: 0.7549 (m-10) REVERT: C 20 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7515 (ttp80) REVERT: C 24 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7853 (mm-40) REVERT: D 48 ASP cc_start: 0.7219 (p0) cc_final: 0.6748 (p0) REVERT: D 65 ASP cc_start: 0.8584 (t70) cc_final: 0.8099 (t0) REVERT: F 27 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7938 (mm-40) REVERT: F 84 MET cc_start: 0.7790 (tpp) cc_final: 0.7503 (tpp) REVERT: G 64 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7806 (tp30) REVERT: G 84 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8275 (tm-30) REVERT: G 101 THR cc_start: 0.9363 (m) cc_final: 0.8773 (p) REVERT: K 4786 TYR cc_start: 0.4878 (m-10) cc_final: 0.4677 (m-10) REVERT: K 4886 TYR cc_start: 0.6073 (m-10) cc_final: 0.5792 (m-80) REVERT: N 74 TRP cc_start: 0.6496 (m100) cc_final: 0.6204 (m-10) REVERT: N 89 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5381 (mm) REVERT: N 124 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5195 (tt) REVERT: N 134 MET cc_start: 0.7848 (tmm) cc_final: 0.7610 (tmm) REVERT: N 206 PHE cc_start: 0.6874 (m-10) cc_final: 0.6535 (m-10) REVERT: T 313 TYR cc_start: 0.1357 (m-80) cc_final: -0.0800 (m-80) REVERT: T 460 TYR cc_start: 0.4156 (m-80) cc_final: 0.3568 (m-80) outliers start: 37 outliers final: 21 residues processed: 258 average time/residue: 0.1336 time to fit residues: 54.3276 Evaluate side-chains 244 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 84 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 33 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 G residue 16 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 79 ILE 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 89 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 R residue 131 TYR Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 116 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 118 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 4 optimal weight: 0.0370 chunk 178 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 89 ASN ** 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 = 0.4262 r_free = 0.4262 target = 0.171084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136699 restraints weight = 44222.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139579 restraints weight = 81453.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.138647 restraints weight = 59171.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138339 restraints weight = 52854.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.138952 restraints weight = 41375.414| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21209 Z= 0.209 Angle : 0.719 12.257 29905 Z= 0.400 Chirality : 0.048 0.221 3371 Planarity : 0.005 0.050 2785 Dihedral : 27.746 167.338 5132 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 3.16 % Allowed : 14.83 % Favored : 82.01 % 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: -2.13 (0.19), residues: 1775 helix: 0.89 (0.21), residues: 577 sheet: -1.82 (0.35), residues: 207 loop : -2.92 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 154 TYR 0.048 0.002 TYR H 80 PHE 0.020 0.002 PHE N 206 TRP 0.037 0.002 TRP R 114 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (21207) covalent geometry : angle 0.71934 / 0.40 (29905) hydrogen bonds : bond 0.06620 / 4.31 ( 873) hydrogen bonds : angle 4.28454 / 2.95 ( 2190) metal coordination : bond 0.00158 / 0.11 ( 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 279 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8190 (tt0) cc_final: 0.7982 (tt0) REVERT: B 79 LYS cc_start: 0.8935 (mttt) cc_final: 0.8596 (mttm) REVERT: B 84 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.6958 (tmm) REVERT: B 88 TYR cc_start: 0.7936 (m-10) cc_final: 0.7567 (m-10) REVERT: C 20 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7516 (ttp80) REVERT: D 48 ASP cc_start: 0.7393 (p0) cc_final: 0.6921 (p0) REVERT: D 65 ASP cc_start: 0.8541 (t70) cc_final: 0.8036 (t0) REVERT: F 27 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7901 (mm-40) REVERT: F 96 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8337 (p) REVERT: G 84 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8549 (tt0) REVERT: K 4886 TYR cc_start: 0.6171 (m-10) cc_final: 0.5892 (m-80) REVERT: N 74 TRP cc_start: 0.6613 (m100) cc_final: 0.6318 (m-10) REVERT: N 134 MET cc_start: 0.7903 (tmm) cc_final: 0.7698 (tmm) REVERT: T 313 TYR cc_start: 0.1207 (m-80) cc_final: -0.0852 (m-80) REVERT: T 460 TYR cc_start: 0.4287 (m-80) cc_final: 0.3745 (m-80) outliers start: 49 outliers final: 33 residues processed: 264 average time/residue: 0.1428 time to fit residues: 59.1224 Evaluate side-chains 257 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 57 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 73 THR 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 16 THR Chi-restraints excluded: chain G residue 79 ILE 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 123 VAL Chi-restraints excluded: chain N residue 217 THR 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 R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 265 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 83 optimal weight: 30.0000 chunk 89 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 129 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 156 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 overall best weight: 2.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 ASN ** 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 = 0.4275 r_free = 0.4275 target = 0.172169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136542 restraints weight = 44569.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136379 restraints weight = 82530.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136769 restraints weight = 63894.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137432 restraints weight = 42400.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.137632 restraints weight = 40389.179| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21209 Z= 0.175 Angle : 0.678 13.965 29905 Z= 0.382 Chirality : 0.047 0.217 3371 Planarity : 0.004 0.048 2785 Dihedral : 27.631 167.549 5132 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.03 % Allowed : 15.09 % Favored : 81.88 % 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: -1.92 (0.19), residues: 1775 helix: 1.22 (0.22), residues: 576 sheet: -1.67 (0.35), residues: 205 loop : -2.90 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K4763 TYR 0.038 0.002 TYR H 80 PHE 0.014 0.001 PHE A 84 TRP 0.038 0.002 TRP K4769 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (21207) covalent geometry : angle 0.67838 / 0.38 (29905) hydrogen bonds : bond 0.06049 / 3.92 ( 873) hydrogen bonds : angle 4.04534 / 2.78 ( 2190) metal coordination : bond 0.00105 / 0.07 ( 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 284 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 0.648 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 120 MET cc_start: 0.8199 (mmm) cc_final: 0.7841 (mmp) REVERT: B 79 LYS cc_start: 0.8943 (mttt) cc_final: 0.8591 (mttm) REVERT: B 84 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7000 (tmm) REVERT: B 88 TYR cc_start: 0.7820 (m-10) cc_final: 0.7483 (m-10) REVERT: C 20 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7511 (ttp80) REVERT: D 48 ASP cc_start: 0.7499 (p0) cc_final: 0.7031 (p0) REVERT: D 65 ASP cc_start: 0.8482 (t70) cc_final: 0.7958 (t0) REVERT: F 27 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8061 (tp40) REVERT: F 96 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8286 (p) REVERT: G 84 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8346 (tm-30) REVERT: N 51 TRP cc_start: 0.6520 (OUTLIER) cc_final: 0.5908 (m100) REVERT: N 74 TRP cc_start: 0.6671 (m100) cc_final: 0.6345 (m-10) REVERT: N 348 ARG cc_start: 0.0469 (OUTLIER) cc_final: 0.0017 (ptp-170) REVERT: T 313 TYR cc_start: 0.1004 (m-80) cc_final: -0.1043 (m-80) REVERT: T 460 TYR cc_start: 0.4310 (m-80) cc_final: 0.3756 (m-80) outliers start: 47 outliers final: 30 residues processed: 265 average time/residue: 0.1417 time to fit residues: 58.7671 Evaluate side-chains 257 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 74 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 D residue 33 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 118 THR 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 79 ILE 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 197 ASN Chi-restraints excluded: chain N residue 214 LEU Chi-restraints excluded: chain N residue 217 THR 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 348 ARG Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 265 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 7 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 189 optimal weight: 5.9990 chunk 128 optimal weight: 30.0000 chunk 31 optimal weight: 0.4980 chunk 177 optimal weight: 30.0000 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 40.0000 chunk 145 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 ASN ** 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 = 0.174568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.138422 restraints weight = 44643.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139178 restraints weight = 77948.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139708 restraints weight = 72764.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139645 restraints weight = 51498.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141690 restraints weight = 41816.311| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21209 Z= 0.137 Angle : 0.637 13.009 29905 Z= 0.363 Chirality : 0.046 0.238 3371 Planarity : 0.004 0.047 2785 Dihedral : 27.503 168.200 5132 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.19 % Allowed : 16.57 % Favored : 81.24 % 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: -1.65 (0.20), residues: 1775 helix: 1.59 (0.22), residues: 576 sheet: -1.57 (0.35), residues: 208 loop : -2.82 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K4763 TYR 0.030 0.002 TYR H 80 PHE 0.022 0.001 PHE N 189 TRP 0.040 0.002 TRP K4769 HIS 0.004 0.001 HIS N 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (21207) covalent geometry : angle 0.63653 / 0.36 (29905) hydrogen bonds : bond 0.05229 / 3.37 ( 873) hydrogen bonds : angle 3.74354 / 2.56 ( 2190) metal coordination : bond 0.00054 / 0.04 ( 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 271 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.8892 (p) cc_final: 0.8622 (t) REVERT: A 120 MET cc_start: 0.8102 (mmm) cc_final: 0.7764 (mmp) REVERT: B 59 LYS cc_start: 0.8463 (tppp) cc_final: 0.8106 (tptt) REVERT: B 79 LYS cc_start: 0.8907 (mttt) cc_final: 0.8595 (mttm) REVERT: B 84 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6945 (tmm) REVERT: B 88 TYR cc_start: 0.7724 (m-10) cc_final: 0.7341 (m-10) REVERT: C 20 ARG cc_start: 0.7920 (ttm170) cc_final: 0.7503 (ttp80) REVERT: D 48 ASP cc_start: 0.7507 (p0) cc_final: 0.7087 (p0) REVERT: D 65 ASP cc_start: 0.8199 (t70) cc_final: 0.7878 (t0) REVERT: F 27 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7889 (mm-40) REVERT: F 96 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8328 (p) REVERT: G 84 GLN cc_start: 0.8769 (tp-100) cc_final: 0.8230 (tm-30) REVERT: N 51 TRP cc_start: 0.6396 (OUTLIER) cc_final: 0.5800 (m100) REVERT: N 74 TRP cc_start: 0.6611 (m100) cc_final: 0.6342 (m-10) REVERT: N 304 HIS cc_start: 0.7478 (t-90) cc_final: 0.7206 (t-90) REVERT: N 348 ARG cc_start: 0.0362 (OUTLIER) cc_final: -0.0001 (ptp-170) REVERT: T 313 TYR cc_start: 0.0889 (m-80) cc_final: -0.1123 (m-80) REVERT: T 336 MET cc_start: -0.1686 (mmm) cc_final: -0.1977 (mmt) REVERT: T 460 TYR cc_start: 0.4332 (m-80) cc_final: 0.3779 (m-80) outliers start: 34 outliers final: 25 residues processed: 256 average time/residue: 0.1375 time to fit residues: 54.4850 Evaluate side-chains 252 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 73 THR 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 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 214 LEU Chi-restraints excluded: chain N residue 217 THR 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 348 ARG Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 265 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 0.0050 chunk 122 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 50.0000 chunk 182 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 72 optimal weight: 40.0000 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 ASN ** 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 = 0.4307 r_free = 0.4307 target = 0.174706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137796 restraints weight = 44530.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137869 restraints weight = 72268.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138532 restraints weight = 69284.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138538 restraints weight = 46747.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.139759 restraints weight = 40235.713| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21209 Z= 0.138 Angle : 0.650 12.690 29905 Z= 0.365 Chirality : 0.046 0.324 3371 Planarity : 0.004 0.045 2785 Dihedral : 27.479 169.103 5132 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.06 % Allowed : 17.34 % Favored : 80.59 % 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: -1.53 (0.20), residues: 1775 helix: 1.71 (0.22), residues: 575 sheet: -1.55 (0.34), residues: 206 loop : -2.75 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.031 0.002 TYR H 80 PHE 0.016 0.001 PHE N 332 TRP 0.042 0.002 TRP K4769 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (21207) covalent geometry : angle 0.64964 / 0.36 (29905) hydrogen bonds : bond 0.05112 / 3.29 ( 873) hydrogen bonds : angle 3.68202 / 2.51 ( 2190) metal coordination : bond 0.00049 / 0.03 ( 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 267 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.9032 (p) cc_final: 0.8709 (t) REVERT: A 120 MET cc_start: 0.8173 (mmm) cc_final: 0.7839 (mmp) REVERT: B 59 LYS cc_start: 0.8400 (tppp) cc_final: 0.8125 (tptp) REVERT: B 79 LYS cc_start: 0.8892 (mttt) cc_final: 0.8571 (mttm) REVERT: B 84 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6965 (tmm) REVERT: B 88 TYR cc_start: 0.7712 (m-10) cc_final: 0.7306 (m-10) REVERT: C 20 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7513 (ttp80) REVERT: D 48 ASP cc_start: 0.7532 (p0) cc_final: 0.7096 (p0) REVERT: D 65 ASP cc_start: 0.8213 (t70) cc_final: 0.7896 (t0) REVERT: E 54 TYR cc_start: 0.8830 (m-80) cc_final: 0.8624 (m-80) REVERT: F 27 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7935 (mm-40) REVERT: F 96 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8293 (p) REVERT: G 84 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8282 (tm-30) REVERT: N 51 TRP cc_start: 0.6352 (OUTLIER) cc_final: 0.5693 (m100) REVERT: N 74 TRP cc_start: 0.6566 (m100) cc_final: 0.6328 (m-10) REVERT: N 304 HIS cc_start: 0.7538 (t-90) cc_final: 0.7269 (t-90) REVERT: N 348 ARG cc_start: 0.0362 (OUTLIER) cc_final: 0.0012 (ptp-170) REVERT: T 313 TYR cc_start: 0.0726 (m-80) cc_final: -0.1350 (m-10) REVERT: T 336 MET cc_start: -0.1516 (mmm) cc_final: -0.1763 (mmm) REVERT: T 460 TYR cc_start: 0.4312 (m-80) cc_final: 0.3756 (m-80) outliers start: 32 outliers final: 23 residues processed: 255 average time/residue: 0.1311 time to fit residues: 52.3810 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 : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 73 THR 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 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 124 LEU Chi-restraints excluded: chain N residue 214 LEU Chi-restraints excluded: chain N residue 217 THR 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 348 ARG Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 265 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 40.0000 chunk 10 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 158 optimal weight: 0.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4296 r_free = 0.4296 target = 0.173759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.138614 restraints weight = 44609.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.141080 restraints weight = 72966.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140313 restraints weight = 58073.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.139952 restraints weight = 51098.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140617 restraints weight = 39841.922| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21209 Z= 0.156 Angle : 0.659 12.352 29905 Z= 0.368 Chirality : 0.046 0.385 3371 Planarity : 0.004 0.046 2785 Dihedral : 27.474 169.380 5132 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 1.81 % Allowed : 17.34 % Favored : 80.85 % 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: -1.51 (0.20), residues: 1775 helix: 1.74 (0.22), residues: 574 sheet: -1.48 (0.34), residues: 215 loop : -2.76 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 317 TYR 0.035 0.002 TYR H 80 PHE 0.021 0.001 PHE N 159 TRP 0.042 0.002 TRP K4769 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (21207) covalent geometry : angle 0.65892 / 0.37 (29905) hydrogen bonds : bond 0.05341 / 3.45 ( 873) hydrogen bonds : angle 3.71649 / 2.56 ( 2190) metal coordination : bond 0.00082 / 0.06 ( 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 249 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.9039 (p) cc_final: 0.8734 (t) REVERT: A 120 MET cc_start: 0.8211 (mmm) cc_final: 0.7988 (mmp) REVERT: B 59 LYS cc_start: 0.8452 (tppp) cc_final: 0.8168 (tptt) REVERT: B 79 LYS cc_start: 0.8950 (mttt) cc_final: 0.8596 (mttm) REVERT: B 84 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7029 (tmm) REVERT: B 88 TYR cc_start: 0.7813 (m-10) cc_final: 0.7380 (m-10) REVERT: C 20 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7532 (ttp80) REVERT: D 48 ASP cc_start: 0.7647 (p0) cc_final: 0.7215 (p0) REVERT: D 65 ASP cc_start: 0.8359 (t70) cc_final: 0.8039 (t0) REVERT: F 27 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8172 (tp40) REVERT: F 96 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8298 (p) REVERT: G 84 GLN cc_start: 0.8859 (tp-100) cc_final: 0.8319 (tm-30) REVERT: H 98 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8165 (mp) REVERT: N 51 TRP cc_start: 0.6307 (OUTLIER) cc_final: 0.5632 (m100) REVERT: N 304 HIS cc_start: 0.7731 (t-90) cc_final: 0.7402 (t-90) REVERT: N 348 ARG cc_start: 0.0402 (OUTLIER) cc_final: 0.0010 (ptp-170) REVERT: O 1 MET cc_start: 0.4210 (tpp) cc_final: 0.3254 (mmp) REVERT: T 313 TYR cc_start: 0.0933 (m-80) cc_final: -0.1338 (m-10) REVERT: T 336 MET cc_start: -0.1612 (mmm) cc_final: -0.1832 (mmm) REVERT: T 460 TYR cc_start: 0.4310 (m-80) cc_final: 0.3747 (m-80) outliers start: 28 outliers final: 21 residues processed: 239 average time/residue: 0.1399 time to fit residues: 52.7163 Evaluate side-chains 241 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 73 THR 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 H residue 98 LEU Chi-restraints excluded: chain N residue 51 TRP Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 214 LEU Chi-restraints excluded: chain N residue 217 THR 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 348 ARG Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 134 CYS Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 265 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 84 optimal weight: 40.0000 chunk 103 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 189 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4287 r_free = 0.4287 target = 0.173035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138035 restraints weight = 44642.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140221 restraints weight = 77371.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139757 restraints weight = 57571.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139474 restraints weight = 49459.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140020 restraints weight = 39882.292| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3784 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= 0.176 Angle : 0.678 12.165 29905 Z= 0.377 Chirality : 0.046 0.229 3371 Planarity : 0.004 0.046 2785 Dihedral : 27.476 169.342 5132 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 1.93 % Allowed : 17.54 % Favored : 80.53 % 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: -1.56 (0.20), residues: 1775 helix: 1.63 (0.22), residues: 574 sheet: -1.53 (0.33), residues: 225 loop : -2.75 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 317 TYR 0.036 0.002 TYR H 80 PHE 0.015 0.001 PHE N 332 TRP 0.062 0.003 TRP N 74 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (21207) covalent geometry : angle 0.67772 / 0.38 (29905) hydrogen bonds : bond 0.05631 / 3.64 ( 873) hydrogen bonds : angle 3.79236 / 2.62 ( 2190) metal coordination : bond 0.00123 / 0.08 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2690.52 seconds wall clock time: 47 minutes 26.73 seconds (2846.73 seconds total)