Starting phenix.real_space_refine on Wed Mar 20 21:24:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiw_0693/03_2024/6kiw_0693.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiw_0693/03_2024/6kiw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiw_0693/03_2024/6kiw_0693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiw_0693/03_2024/6kiw_0693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiw_0693/03_2024/6kiw_0693.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiw_0693/03_2024/6kiw_0693.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "K ARG 4779": "NH1" <-> "NH2" Residue "K ARG 4789": "NH1" <-> "NH2" Residue "K ARG 4864": "NH1" <-> "NH2" Residue "N ARG 76": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N ARG 190": "NH1" <-> "NH2" Residue "N ARG 228": "NH1" <-> "NH2" Residue "N ARG 272": "NH1" <-> "NH2" Residue "T TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 11.26, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 9.25 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 8.11 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: 8.78 Time building geometry restraints manager: 9.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4683 1.33 - 1.45: 5751 1.45 - 1.57: 10114 1.57 - 1.70: 576 1.70 - 1.82: 83 Bond restraints: 21207 Sorted by residual: bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.47e+00 bond pdb=" C LYS F 31 " pdb=" N PRO F 32 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.23e-02 6.61e+03 3.26e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.07e+00 bond pdb=" C HIS N 67 " pdb=" N PRO N 68 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 bond pdb=" CA LEU T 392 " pdb=" CB LEU T 392 " ideal model delta sigma weight residual 1.526 1.554 -0.028 1.76e-02 3.23e+03 2.45e+00 ... (remaining 21202 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.48: 1573 105.48 - 113.13: 11909 113.13 - 120.78: 9689 120.78 - 128.43: 6332 128.43 - 136.08: 402 Bond angle restraints: 29905 Sorted by residual: angle pdb=" N VAL K4824 " pdb=" CA VAL K4824 " pdb=" C VAL K4824 " ideal model delta sigma weight residual 112.17 104.37 7.80 9.50e-01 1.11e+00 6.75e+01 angle pdb=" C ASP B 24 " pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 121.54 132.68 -11.14 1.91e+00 2.74e-01 3.40e+01 angle pdb=" C ARG A 49 " pdb=" N GLU A 50 " pdb=" CA GLU A 50 " ideal model delta sigma weight residual 121.54 132.63 -11.09 1.91e+00 2.74e-01 3.37e+01 angle pdb=" C ARG E 49 " pdb=" N GLU E 50 " pdb=" CA GLU E 50 " ideal model delta sigma weight residual 121.54 132.62 -11.08 1.91e+00 2.74e-01 3.37e+01 angle pdb=" C GLU N 327 " pdb=" N ASN N 328 " pdb=" CA ASN N 328 " ideal model delta sigma weight residual 121.54 131.12 -9.58 1.91e+00 2.74e-01 2.51e+01 ... (remaining 29900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 10527 34.75 - 69.51: 1426 69.51 - 104.26: 21 104.26 - 139.02: 2 139.02 - 173.77: 2 Dihedral angle restraints: 11978 sinusoidal: 6738 harmonic: 5240 Sorted by residual: dihedral pdb=" CA GLU N 327 " pdb=" C GLU N 327 " pdb=" N ASN N 328 " pdb=" CA ASN N 328 " ideal model delta harmonic sigma weight residual 180.00 145.72 34.28 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA ALA N 333 " pdb=" C ALA N 333 " pdb=" N PRO N 334 " pdb=" CA PRO N 334 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA TYR N 115 " pdb=" C TYR N 115 " pdb=" N HIS N 116 " pdb=" CA HIS N 116 " ideal model delta harmonic sigma weight residual 180.00 150.56 29.44 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 11975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2267 0.046 - 0.091: 802 0.091 - 0.137: 255 0.137 - 0.182: 40 0.182 - 0.228: 7 Chirality restraints: 3371 Sorted by residual: chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA GLU E 59 " pdb=" N GLU E 59 " pdb=" C GLU E 59 " pdb=" CB GLU E 59 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3368 not shown) Planarity restraints: 2785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 50 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLU E 50 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU E 50 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE E 51 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 50 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C GLU A 50 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 50 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 51 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER R 223 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO R 224 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO R 224 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 224 " -0.037 5.00e-02 4.00e+02 ... (remaining 2782 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1397 2.73 - 3.27: 17332 3.27 - 3.81: 35509 3.81 - 4.36: 41871 4.36 - 4.90: 64146 Nonbonded interactions: 160255 Sorted by model distance: nonbonded pdb=" OG SER K4850 " pdb="ZN ZN K5001 " model vdw 2.182 2.230 nonbonded pdb=" O PHE T 464 " pdb=" OH TYR T 468 " model vdw 2.252 2.440 nonbonded pdb=" OG SER R 129 " pdb=" OD2 ASP R 150 " model vdw 2.257 2.440 nonbonded pdb=" OG SER R 175 " pdb=" OG SER R 189 " model vdw 2.269 2.440 nonbonded pdb=" OG SER R 223 " pdb=" OD1 ASN R 225 " model vdw 2.273 2.440 ... (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 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 5.330 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 64.560 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21207 Z= 0.352 Angle : 0.887 14.126 29905 Z= 0.509 Chirality : 0.051 0.228 3371 Planarity : 0.007 0.067 2785 Dihedral : 22.755 173.773 8600 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (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 TRP 0.026 0.002 TRP R 286 HIS 0.008 0.002 HIS B 75 PHE 0.016 0.002 PHE N 189 TYR 0.040 0.003 TYR H 37 ARG 0.007 0.001 ARG T 343 *********************** 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 fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8680 (tt0) cc_final: 0.8349 (tt0) REVERT: B 27 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7769 (tm-30) REVERT: B 77 LYS cc_start: 0.9049 (tppt) cc_final: 0.8778 (mtmt) REVERT: B 79 LYS cc_start: 0.9008 (mttt) cc_final: 0.8667 (mttm) REVERT: B 88 TYR cc_start: 0.8010 (m-10) cc_final: 0.7747 (m-10) REVERT: C 38 ASN cc_start: 0.8392 (m110) cc_final: 0.8163 (p0) REVERT: C 90 ASP cc_start: 0.8954 (t0) cc_final: 0.8666 (t0) REVERT: C 100 VAL cc_start: 0.9486 (t) cc_final: 0.9266 (p) REVERT: D 33 SER cc_start: 0.9108 (t) cc_final: 0.8842 (m) REVERT: D 51 ILE cc_start: 0.9192 (tt) cc_final: 0.8973 (tt) REVERT: D 65 ASP cc_start: 0.8689 (t0) cc_final: 0.8029 (t0) REVERT: D 116 THR cc_start: 0.8651 (m) cc_final: 0.8356 (p) REVERT: F 82 THR cc_start: 0.9362 (p) cc_final: 0.9124 (m) REVERT: F 84 MET cc_start: 0.7780 (mmm) cc_final: 0.7094 (mmm) REVERT: G 18 SER cc_start: 0.9278 (m) cc_final: 0.8956 (t) REVERT: G 84 GLN cc_start: 0.9016 (tp40) cc_final: 0.8774 (tp40) REVERT: G 101 THR cc_start: 0.9451 (m) cc_final: 0.9149 (p) REVERT: G 110 ASN cc_start: 0.8377 (t160) cc_final: 0.8136 (p0) REVERT: H 82 LYS cc_start: 0.9135 (mttt) cc_final: 0.8635 (mttm) REVERT: K 4886 TYR cc_start: 0.6052 (m-10) cc_final: 0.5767 (m-80) REVERT: N 50 ILE cc_start: 0.8020 (mt) cc_final: 0.7717 (pt) REVERT: N 209 LYS cc_start: 0.8676 (tmtp) cc_final: 0.8399 (tttt) REVERT: R 149 PHE cc_start: 0.4278 (m-10) cc_final: 0.3567 (m-10) REVERT: R 155 ILE cc_start: 0.5056 (mt) cc_final: 0.4780 (mt) REVERT: R 173 PRO cc_start: 0.5486 (Cg_exo) cc_final: 0.5184 (Cg_endo) REVERT: T 313 TYR cc_start: 0.0721 (m-80) cc_final: -0.0487 (m-80) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.4283 time to fit residues: 256.9986 Evaluate side-chains 242 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 159 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 184 optimal weight: 40.0000 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 55 GLN E 68 GLN G 110 ASN H 46 HIS K4794 HIS K4811 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 GLN T 456 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 21207 Z= 0.273 Angle : 0.693 11.235 29905 Z= 0.391 Chirality : 0.042 0.162 3371 Planarity : 0.005 0.090 2785 Dihedral : 27.876 173.240 5132 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.58 % Allowed : 9.80 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.18), residues: 1775 helix: 0.14 (0.21), residues: 573 sheet: -1.82 (0.36), residues: 187 loop : -3.18 (0.17), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 51 HIS 0.011 0.001 HIS K4833 PHE 0.023 0.002 PHE N 206 TYR 0.041 0.002 TYR T 475 ARG 0.006 0.001 ARG N 103 *********************** 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 319 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 279 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8116 (mmm) cc_final: 0.7823 (mmm) REVERT: B 27 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 77 LYS cc_start: 0.9109 (tppt) cc_final: 0.8764 (ttmt) REVERT: B 79 LYS cc_start: 0.9099 (mttt) cc_final: 0.8700 (mttm) REVERT: B 88 TYR cc_start: 0.8013 (m-10) cc_final: 0.7705 (m-10) REVERT: C 20 ARG cc_start: 0.8523 (ttm170) cc_final: 0.7922 (ttp80) REVERT: C 38 ASN cc_start: 0.8423 (m110) cc_final: 0.8202 (p0) REVERT: C 61 GLU cc_start: 0.8686 (tp30) cc_final: 0.8323 (tp30) REVERT: C 92 GLU cc_start: 0.7336 (pm20) cc_final: 0.7066 (pm20) REVERT: C 100 VAL cc_start: 0.9399 (t) cc_final: 0.9138 (p) REVERT: D 33 SER cc_start: 0.9168 (t) cc_final: 0.8901 (m) REVERT: D 48 ASP cc_start: 0.7575 (p0) cc_final: 0.7366 (p0) REVERT: D 65 ASP cc_start: 0.8662 (t0) cc_final: 0.8065 (t0) REVERT: D 88 SER cc_start: 0.9219 (p) cc_final: 0.8991 (m) REVERT: E 51 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9158 (tt) REVERT: E 59 GLU cc_start: 0.8233 (pm20) cc_final: 0.7984 (pm20) REVERT: E 73 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8132 (tm-30) REVERT: E 74 ILE cc_start: 0.8763 (pt) cc_final: 0.7748 (pt) REVERT: E 79 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7969 (mtpt) REVERT: F 27 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8218 (mm-40) REVERT: F 82 THR cc_start: 0.9408 (p) cc_final: 0.9134 (m) REVERT: F 84 MET cc_start: 0.7689 (mmm) cc_final: 0.6940 (mmm) REVERT: G 84 GLN cc_start: 0.8974 (tp40) cc_final: 0.8437 (tp40) REVERT: G 101 THR cc_start: 0.9481 (m) cc_final: 0.9049 (p) REVERT: G 110 ASN cc_start: 0.8464 (t0) cc_final: 0.8195 (p0) REVERT: K 4886 TYR cc_start: 0.6239 (m-10) cc_final: 0.6020 (m-80) REVERT: N 134 MET cc_start: 0.7298 (tmm) cc_final: 0.7076 (tmm) REVERT: N 159 PHE cc_start: 0.5823 (m-80) cc_final: 0.5446 (m-10) REVERT: N 209 LYS cc_start: 0.8798 (tmtp) cc_final: 0.8484 (tttt) REVERT: O 1 MET cc_start: 0.3539 (OUTLIER) cc_final: 0.3322 (mtt) REVERT: R 173 PRO cc_start: 0.5638 (Cg_exo) cc_final: 0.5372 (Cg_endo) REVERT: T 313 TYR cc_start: 0.1279 (m-80) cc_final: -0.0657 (m-80) REVERT: T 460 TYR cc_start: 0.4077 (m-80) cc_final: 0.3445 (m-80) outliers start: 40 outliers final: 25 residues processed: 300 average time/residue: 0.3221 time to fit residues: 146.4963 Evaluate side-chains 271 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 243 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 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 K residue 4807 ASN Chi-restraints excluded: chain N residue 192 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 343 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 chunk 184 optimal weight: 40.0000 chunk 199 optimal weight: 30.0000 chunk 164 optimal weight: 0.0070 chunk 183 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 108 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN E 39 HIS H 92 GLN ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21207 Z= 0.241 Angle : 0.649 14.474 29905 Z= 0.366 Chirality : 0.041 0.180 3371 Planarity : 0.005 0.055 2785 Dihedral : 27.626 172.180 5132 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.03 % Allowed : 11.54 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.19), residues: 1775 helix: 0.88 (0.22), residues: 575 sheet: -2.08 (0.31), residues: 242 loop : -3.05 (0.17), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 51 HIS 0.006 0.001 HIS K4833 PHE 0.028 0.002 PHE N 206 TYR 0.022 0.002 TYR H 80 ARG 0.005 0.001 ARG N 162 *********************** 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 305 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 258 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8831 (m-80) cc_final: 0.8252 (m-80) REVERT: B 27 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7725 (tm-30) REVERT: B 79 LYS cc_start: 0.9062 (mttt) cc_final: 0.8682 (mttm) REVERT: B 85 ASP cc_start: 0.8891 (m-30) cc_final: 0.8601 (m-30) REVERT: C 20 ARG cc_start: 0.8509 (ttm170) cc_final: 0.7942 (ttp80) REVERT: C 61 GLU cc_start: 0.8676 (tp30) cc_final: 0.8338 (tp30) REVERT: C 90 ASP cc_start: 0.8649 (t0) cc_final: 0.8066 (t0) REVERT: D 33 SER cc_start: 0.9173 (t) cc_final: 0.8888 (m) REVERT: D 48 ASP cc_start: 0.7767 (p0) cc_final: 0.7247 (p0) REVERT: D 65 ASP cc_start: 0.8650 (t0) cc_final: 0.8142 (t0) REVERT: D 73 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8255 (mm-30) REVERT: F 27 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8259 (mm-40) REVERT: F 84 MET cc_start: 0.7642 (mmm) cc_final: 0.7301 (mmm) REVERT: G 84 GLN cc_start: 0.8983 (tp40) cc_final: 0.8597 (tp40) REVERT: G 101 THR cc_start: 0.9463 (m) cc_final: 0.8899 (p) REVERT: H 68 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7257 (mm-30) REVERT: K 4786 TYR cc_start: 0.5258 (m-10) cc_final: 0.5013 (m-10) REVERT: K 4820 GLN cc_start: 0.5978 (mp10) cc_final: 0.5751 (tp40) REVERT: K 4886 TYR cc_start: 0.6244 (m-10) cc_final: 0.6029 (m-80) REVERT: N 134 MET cc_start: 0.7660 (tmm) cc_final: 0.7237 (tmm) REVERT: N 199 THR cc_start: 0.8557 (t) cc_final: 0.8254 (t) REVERT: N 209 LYS cc_start: 0.8689 (tmtp) cc_final: 0.8409 (tttt) REVERT: N 255 LYS cc_start: 0.4743 (tptt) cc_final: 0.4473 (tptt) REVERT: N 332 PHE cc_start: 0.5061 (OUTLIER) cc_final: 0.4549 (t80) REVERT: O 1 MET cc_start: 0.3572 (ttm) cc_final: 0.3248 (mtt) REVERT: T 313 TYR cc_start: 0.1173 (m-80) cc_final: -0.0795 (m-80) REVERT: T 460 TYR cc_start: 0.4198 (m-80) cc_final: 0.3628 (m-80) outliers start: 47 outliers final: 30 residues processed: 285 average time/residue: 0.3205 time to fit residues: 141.1978 Evaluate side-chains 273 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 4798 ILE Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 192 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 332 PHE Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain T residue 328 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 20 optimal weight: 0.4980 chunk 88 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 chunk 185 optimal weight: 8.9990 chunk 196 optimal weight: 40.0000 chunk 96 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 52 optimal weight: 0.0370 overall best weight: 2.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 31 HIS C 38 ASN G 84 GLN G 110 ASN ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21207 Z= 0.244 Angle : 0.641 13.982 29905 Z= 0.360 Chirality : 0.041 0.180 3371 Planarity : 0.004 0.051 2785 Dihedral : 27.454 172.273 5132 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.68 % Allowed : 11.73 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.19), residues: 1775 helix: 1.12 (0.22), residues: 581 sheet: -1.85 (0.33), residues: 228 loop : -2.98 (0.17), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 114 HIS 0.005 0.001 HIS B 75 PHE 0.022 0.001 PHE N 206 TYR 0.024 0.002 TYR H 80 ARG 0.006 0.000 ARG G 99 *********************** 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 305 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 248 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8142 (mmm) cc_final: 0.7770 (mmm) REVERT: B 27 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7697 (tm-30) REVERT: B 79 LYS cc_start: 0.9061 (mttt) cc_final: 0.8687 (mttm) REVERT: B 88 TYR cc_start: 0.7951 (m-10) cc_final: 0.7652 (m-10) REVERT: C 20 ARG cc_start: 0.8534 (ttm170) cc_final: 0.7987 (ttp80) REVERT: C 24 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8277 (mm-40) REVERT: C 61 GLU cc_start: 0.8688 (tp30) cc_final: 0.8321 (tp30) REVERT: C 90 ASP cc_start: 0.8644 (t0) cc_final: 0.8121 (t0) REVERT: D 33 SER cc_start: 0.9199 (t) cc_final: 0.8977 (m) REVERT: D 48 ASP cc_start: 0.7942 (p0) cc_final: 0.7360 (p0) REVERT: D 65 ASP cc_start: 0.8659 (t0) cc_final: 0.8275 (t0) REVERT: D 73 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8155 (mm-30) REVERT: E 73 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8285 (tm-30) REVERT: E 74 ILE cc_start: 0.8474 (pt) cc_final: 0.7844 (pt) REVERT: F 27 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8239 (mm-40) REVERT: F 84 MET cc_start: 0.7702 (mmm) cc_final: 0.7419 (mmt) REVERT: G 84 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8581 (tp40) REVERT: G 99 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7885 (mmt90) REVERT: G 101 THR cc_start: 0.9446 (m) cc_final: 0.8820 (p) REVERT: H 36 ILE cc_start: 0.8561 (pt) cc_final: 0.8302 (mt) REVERT: K 4786 TYR cc_start: 0.5458 (m-10) cc_final: 0.5021 (m-10) REVERT: K 4886 TYR cc_start: 0.6230 (m-10) cc_final: 0.5963 (m-80) REVERT: N 51 TRP cc_start: 0.6056 (OUTLIER) cc_final: 0.5851 (m100) REVERT: N 134 MET cc_start: 0.7652 (tmm) cc_final: 0.7325 (tmm) REVERT: N 209 LYS cc_start: 0.8695 (tmtp) cc_final: 0.8417 (tttt) REVERT: N 255 LYS cc_start: 0.4607 (tptt) cc_final: 0.4403 (tptt) REVERT: N 332 PHE cc_start: 0.5236 (OUTLIER) cc_final: 0.4215 (t80) REVERT: R 234 LEU cc_start: 0.6571 (mt) cc_final: 0.6334 (mp) REVERT: T 313 TYR cc_start: 0.1133 (m-80) cc_final: -0.0884 (m-80) REVERT: T 460 TYR cc_start: 0.4208 (m-80) cc_final: 0.3658 (m-80) outliers start: 57 outliers final: 36 residues processed: 287 average time/residue: 0.3304 time to fit residues: 148.3695 Evaluate side-chains 275 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 237 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 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 82 THR 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 51 TRP Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 192 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 326 VAL Chi-restraints excluded: chain N residue 332 PHE Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 146 optimal weight: 0.0970 chunk 80 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN N 328 ASN ** R 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21207 Z= 0.264 Angle : 0.644 13.289 29905 Z= 0.361 Chirality : 0.041 0.158 3371 Planarity : 0.004 0.050 2785 Dihedral : 27.339 172.210 5132 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.55 % Allowed : 12.38 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.19), residues: 1775 helix: 1.19 (0.22), residues: 578 sheet: -1.88 (0.32), residues: 236 loop : -2.86 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 114 HIS 0.007 0.001 HIS B 75 PHE 0.017 0.001 PHE N 189 TYR 0.031 0.002 TYR H 80 ARG 0.003 0.000 ARG H 30 *********************** 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 301 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 246 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: A 120 MET cc_start: 0.8151 (mmm) cc_final: 0.7711 (mmm) REVERT: B 27 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 79 LYS cc_start: 0.9065 (mttt) cc_final: 0.8668 (mttm) REVERT: B 84 MET cc_start: 0.7811 (mmm) cc_final: 0.7528 (mmm) REVERT: B 88 TYR cc_start: 0.7977 (m-10) cc_final: 0.7666 (m-10) REVERT: C 20 ARG cc_start: 0.8500 (ttm170) cc_final: 0.7965 (ttp80) REVERT: C 61 GLU cc_start: 0.8684 (tp30) cc_final: 0.8327 (tp30) REVERT: C 90 ASP cc_start: 0.8694 (t0) cc_final: 0.8377 (t0) REVERT: D 33 SER cc_start: 0.9249 (t) cc_final: 0.8938 (m) REVERT: D 37 TYR cc_start: 0.8835 (m-10) cc_final: 0.8628 (m-10) REVERT: D 48 ASP cc_start: 0.8020 (p0) cc_final: 0.7405 (p0) REVERT: D 65 ASP cc_start: 0.8674 (t0) cc_final: 0.8293 (t0) REVERT: F 27 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8473 (mm-40) REVERT: F 63 GLU cc_start: 0.8476 (tt0) cc_final: 0.8228 (tt0) REVERT: G 84 GLN cc_start: 0.8961 (tp-100) cc_final: 0.8529 (tt0) REVERT: G 99 ARG cc_start: 0.8167 (mmm160) cc_final: 0.7854 (mmt90) REVERT: H 56 MET cc_start: 0.8999 (tpp) cc_final: 0.8799 (tpp) REVERT: K 4886 TYR cc_start: 0.6241 (m-10) cc_final: 0.5973 (m-80) REVERT: N 134 MET cc_start: 0.7730 (tmm) cc_final: 0.7198 (tmm) REVERT: N 206 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.6814 (m-10) REVERT: N 209 LYS cc_start: 0.8653 (tmtp) cc_final: 0.8410 (tttt) REVERT: N 255 LYS cc_start: 0.4601 (tptt) cc_final: 0.4364 (tptt) REVERT: N 273 GLN cc_start: 0.7874 (mp10) cc_final: 0.7383 (mp10) REVERT: N 332 PHE cc_start: 0.5407 (OUTLIER) cc_final: 0.4392 (t80) REVERT: R 234 LEU cc_start: 0.6626 (mt) cc_final: 0.6370 (mp) REVERT: T 313 TYR cc_start: 0.1073 (m-80) cc_final: -0.0965 (m-80) REVERT: T 460 TYR cc_start: 0.4230 (m-80) cc_final: 0.3704 (m-80) outliers start: 55 outliers final: 37 residues processed: 281 average time/residue: 0.3067 time to fit residues: 135.8336 Evaluate side-chains 272 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 232 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 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 82 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain 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 86 THR Chi-restraints excluded: chain N residue 192 THR Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 226 ASP Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 328 ASN Chi-restraints excluded: chain N residue 332 PHE Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 230 LEU 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 66 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 196 optimal weight: 50.0000 chunk 163 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 ASN ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21207 Z= 0.200 Angle : 0.609 12.923 29905 Z= 0.343 Chirality : 0.040 0.167 3371 Planarity : 0.004 0.046 2785 Dihedral : 27.165 172.409 5132 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.03 % Allowed : 13.80 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.20), residues: 1775 helix: 1.50 (0.22), residues: 582 sheet: -1.65 (0.34), residues: 221 loop : -2.78 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K4769 HIS 0.005 0.001 HIS B 75 PHE 0.011 0.001 PHE A 84 TYR 0.031 0.001 TYR H 80 ARG 0.007 0.000 ARG H 30 *********************** 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 292 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 245 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: A 93 GLN cc_start: 0.8685 (tt0) cc_final: 0.8323 (tt0) REVERT: A 120 MET cc_start: 0.8113 (mmm) cc_final: 0.7650 (mmm) REVERT: B 27 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 79 LYS cc_start: 0.9030 (mttt) cc_final: 0.8646 (mttm) REVERT: B 88 TYR cc_start: 0.7862 (m-10) cc_final: 0.7626 (m-10) REVERT: C 20 ARG cc_start: 0.8484 (ttm170) cc_final: 0.7940 (ttp80) REVERT: C 61 GLU cc_start: 0.8666 (tp30) cc_final: 0.8312 (tp30) REVERT: C 90 ASP cc_start: 0.8652 (t0) cc_final: 0.8352 (t0) REVERT: C 92 GLU cc_start: 0.7385 (pm20) cc_final: 0.7141 (pm20) REVERT: D 33 SER cc_start: 0.9198 (t) cc_final: 0.8978 (m) REVERT: D 48 ASP cc_start: 0.8094 (p0) cc_final: 0.7505 (p0) REVERT: D 65 ASP cc_start: 0.8628 (t0) cc_final: 0.8329 (t0) REVERT: D 68 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7740 (mm-30) REVERT: E 74 ILE cc_start: 0.8672 (mt) cc_final: 0.8378 (mt) REVERT: F 27 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8455 (mm-40) REVERT: F 63 GLU cc_start: 0.8473 (tt0) cc_final: 0.8171 (tt0) REVERT: F 96 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8140 (p) REVERT: G 84 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8469 (tt0) REVERT: G 99 ARG cc_start: 0.8159 (mmm160) cc_final: 0.7915 (mmt90) REVERT: H 56 MET cc_start: 0.8895 (tpp) cc_final: 0.8691 (tpp) REVERT: K 4886 TYR cc_start: 0.6234 (m-10) cc_final: 0.5938 (m-80) REVERT: N 134 MET cc_start: 0.7641 (tmm) cc_final: 0.7274 (tmm) REVERT: N 209 LYS cc_start: 0.8646 (tmtp) cc_final: 0.8403 (tttt) REVERT: N 332 PHE cc_start: 0.5655 (OUTLIER) cc_final: 0.4272 (t80) REVERT: R 234 LEU cc_start: 0.6749 (mt) cc_final: 0.6543 (mp) REVERT: T 313 TYR cc_start: 0.0969 (m-80) cc_final: -0.1030 (m-80) REVERT: T 460 TYR cc_start: 0.4357 (m-80) cc_final: 0.3827 (m-80) outliers start: 47 outliers final: 35 residues processed: 274 average time/residue: 0.3018 time to fit residues: 128.9974 Evaluate side-chains 273 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 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 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 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 K residue 4846 TYR Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 192 THR Chi-restraints excluded: chain N residue 197 ASN Chi-restraints excluded: chain N residue 226 ASP Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 332 PHE Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 40.0000 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 109 optimal weight: 30.0000 chunk 195 optimal weight: 30.0000 chunk 122 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 21207 Z= 0.470 Angle : 0.776 12.293 29905 Z= 0.427 Chirality : 0.046 0.212 3371 Planarity : 0.005 0.047 2785 Dihedral : 27.438 171.338 5132 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 3.80 % Allowed : 14.12 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.19), residues: 1775 helix: 0.87 (0.21), residues: 572 sheet: -1.58 (0.32), residues: 225 loop : -2.91 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP R 114 HIS 0.011 0.001 HIS B 75 PHE 0.022 0.002 PHE N 159 TYR 0.038 0.003 TYR H 80 ARG 0.005 0.001 ARG H 30 *********************** 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 298 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 239 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8196 (mmm) cc_final: 0.7888 (mmm) REVERT: B 79 LYS cc_start: 0.9114 (mttt) cc_final: 0.8682 (mttm) REVERT: B 88 TYR cc_start: 0.8002 (m-10) cc_final: 0.7736 (m-10) REVERT: B 92 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8235 (ttp-170) REVERT: C 20 ARG cc_start: 0.8528 (ttm170) cc_final: 0.8022 (ttp80) REVERT: C 61 GLU cc_start: 0.8758 (tp30) cc_final: 0.8356 (tp30) REVERT: D 33 SER cc_start: 0.9336 (t) cc_final: 0.9070 (m) REVERT: D 48 ASP cc_start: 0.8180 (p0) cc_final: 0.7505 (p0) REVERT: D 65 ASP cc_start: 0.8768 (t0) cc_final: 0.8206 (t0) REVERT: D 68 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7780 (mm-30) REVERT: F 27 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8467 (mm-40) REVERT: F 63 GLU cc_start: 0.8435 (tt0) cc_final: 0.8138 (tt0) REVERT: F 96 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8350 (p) REVERT: G 84 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8307 (tm-30) REVERT: G 99 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7983 (mmt90) REVERT: H 98 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8251 (mp) REVERT: K 4886 TYR cc_start: 0.6466 (m-10) cc_final: 0.6230 (m-80) REVERT: N 134 MET cc_start: 0.7714 (tmm) cc_final: 0.7356 (tmm) REVERT: N 209 LYS cc_start: 0.8628 (tmtp) cc_final: 0.8407 (tttt) REVERT: N 304 HIS cc_start: 0.7709 (t-90) cc_final: 0.7295 (t-90) REVERT: N 332 PHE cc_start: 0.5795 (OUTLIER) cc_final: 0.4692 (t80) REVERT: T 313 TYR cc_start: 0.1220 (m-80) cc_final: -0.0920 (m-10) REVERT: T 336 MET cc_start: -0.1904 (mmm) cc_final: -0.2142 (mmm) REVERT: T 460 TYR cc_start: 0.4264 (m-80) cc_final: 0.3716 (m-80) outliers start: 59 outliers final: 42 residues processed: 278 average time/residue: 0.3156 time to fit residues: 134.7476 Evaluate side-chains 274 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 228 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 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 25 ASN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 87 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 86 THR Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 192 THR Chi-restraints excluded: chain N residue 197 ASN Chi-restraints excluded: chain N residue 214 LEU Chi-restraints excluded: chain N residue 226 ASP Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 290 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 332 PHE Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21207 Z= 0.211 Angle : 0.636 12.540 29905 Z= 0.356 Chirality : 0.041 0.177 3371 Planarity : 0.004 0.043 2785 Dihedral : 27.195 171.507 5132 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.90 % Allowed : 15.93 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.20), residues: 1775 helix: 1.43 (0.22), residues: 577 sheet: -1.40 (0.34), residues: 211 loop : -2.77 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K4769 HIS 0.005 0.001 HIS B 75 PHE 0.017 0.001 PHE R 39 TYR 0.024 0.002 TYR H 80 ARG 0.005 0.000 ARG H 30 *********************** 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 282 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 237 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8231 (tp40) REVERT: A 120 MET cc_start: 0.8134 (mmm) cc_final: 0.7831 (mmm) REVERT: B 27 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7568 (tm-30) REVERT: B 79 LYS cc_start: 0.9040 (mttt) cc_final: 0.8639 (mttm) REVERT: C 20 ARG cc_start: 0.8491 (ttm170) cc_final: 0.7975 (ttp80) REVERT: C 61 GLU cc_start: 0.8663 (tp30) cc_final: 0.8313 (tp30) REVERT: C 90 ASP cc_start: 0.8671 (t0) cc_final: 0.8094 (t0) REVERT: C 92 GLU cc_start: 0.7456 (pm20) cc_final: 0.7138 (pm20) REVERT: D 33 SER cc_start: 0.9227 (t) cc_final: 0.8954 (m) REVERT: D 48 ASP cc_start: 0.8251 (p0) cc_final: 0.7697 (p0) REVERT: D 56 MET cc_start: 0.8174 (tpp) cc_final: 0.7930 (tpp) REVERT: D 65 ASP cc_start: 0.8617 (t0) cc_final: 0.8290 (t0) REVERT: D 68 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7777 (mm-30) REVERT: F 27 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8500 (mm-40) REVERT: F 63 GLU cc_start: 0.8459 (tt0) cc_final: 0.8194 (tt0) REVERT: F 96 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8143 (p) REVERT: G 84 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8203 (tm-30) REVERT: G 101 THR cc_start: 0.9420 (m) cc_final: 0.8783 (p) REVERT: H 98 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7835 (mp) REVERT: K 4886 TYR cc_start: 0.6358 (m-10) cc_final: 0.6055 (m-80) REVERT: N 134 MET cc_start: 0.7837 (tmm) cc_final: 0.7553 (tmm) REVERT: N 304 HIS cc_start: 0.7465 (t-90) cc_final: 0.7123 (t-90) REVERT: N 332 PHE cc_start: 0.5642 (OUTLIER) cc_final: 0.4434 (t80) REVERT: N 348 ARG cc_start: 0.0610 (OUTLIER) cc_final: 0.0286 (ptp-170) REVERT: T 313 TYR cc_start: 0.1200 (m-80) cc_final: -0.1037 (m-10) REVERT: T 460 TYR cc_start: 0.4354 (m-80) cc_final: 0.3799 (m-80) outliers start: 45 outliers final: 33 residues processed: 265 average time/residue: 0.3161 time to fit residues: 129.5728 Evaluate side-chains 260 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 222 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 4807 ASN Chi-restraints excluded: chain K residue 4846 TYR Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 192 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 326 VAL Chi-restraints excluded: chain N residue 332 PHE Chi-restraints excluded: chain N residue 343 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 230 LEU Chi-restraints excluded: chain T residue 500 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 109 optimal weight: 0.0570 chunk 79 optimal weight: 10.0000 chunk 143 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 164 optimal weight: 0.0470 chunk 172 optimal weight: 5.9990 chunk 181 optimal weight: 0.0870 chunk 119 optimal weight: 6.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K4848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21207 Z= 0.160 Angle : 0.603 12.477 29905 Z= 0.339 Chirality : 0.039 0.206 3371 Planarity : 0.004 0.044 2785 Dihedral : 26.995 173.157 5132 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.45 % Allowed : 16.25 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1775 helix: 1.89 (0.22), residues: 581 sheet: -1.50 (0.32), residues: 240 loop : -2.59 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP K4769 HIS 0.003 0.001 HIS A 113 PHE 0.026 0.001 PHE R 137 TYR 0.021 0.001 TYR H 80 ARG 0.005 0.000 ARG H 30 *********************** 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 276 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 238 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8027 (mmm) cc_final: 0.7517 (mmm) REVERT: B 43 VAL cc_start: 0.9026 (t) cc_final: 0.8768 (p) REVERT: B 72 TYR cc_start: 0.9061 (m-80) cc_final: 0.8020 (m-80) REVERT: B 79 LYS cc_start: 0.8984 (mttt) cc_final: 0.8621 (mttm) REVERT: C 20 ARG cc_start: 0.8468 (ttm170) cc_final: 0.7968 (ttp80) REVERT: C 61 GLU cc_start: 0.8634 (tp30) cc_final: 0.8334 (tp30) REVERT: C 90 ASP cc_start: 0.8673 (t0) cc_final: 0.8366 (t0) REVERT: C 92 GLU cc_start: 0.7496 (pm20) cc_final: 0.7265 (pm20) REVERT: D 33 SER cc_start: 0.9132 (t) cc_final: 0.8840 (m) REVERT: D 48 ASP cc_start: 0.8220 (p0) cc_final: 0.7720 (p0) REVERT: D 65 ASP cc_start: 0.8591 (t0) cc_final: 0.8277 (t0) REVERT: D 68 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7708 (mm-30) REVERT: F 27 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8444 (tp40) REVERT: F 96 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.7997 (p) REVERT: G 24 GLN cc_start: 0.7741 (mp10) cc_final: 0.7479 (mp10) REVERT: G 74 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8559 (ttmt) REVERT: G 84 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8132 (tm-30) REVERT: H 98 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7881 (mp) REVERT: K 4886 TYR cc_start: 0.6309 (m-10) cc_final: 0.6025 (m-80) REVERT: N 134 MET cc_start: 0.7803 (tmm) cc_final: 0.7557 (tmm) REVERT: N 304 HIS cc_start: 0.7337 (t-90) cc_final: 0.6937 (t-90) REVERT: N 348 ARG cc_start: 0.0686 (OUTLIER) cc_final: 0.0380 (ptp-170) REVERT: O 1 MET cc_start: 0.4225 (mmt) cc_final: 0.3192 (mmt) REVERT: R 149 PHE cc_start: 0.4143 (m-80) cc_final: 0.3773 (m-80) REVERT: R 173 PRO cc_start: 0.6044 (Cg_exo) cc_final: 0.5836 (Cg_endo) REVERT: T 313 TYR cc_start: 0.0811 (m-80) cc_final: -0.1416 (m-10) REVERT: T 460 TYR cc_start: 0.4342 (m-80) cc_final: 0.3846 (m-80) outliers start: 38 outliers final: 27 residues processed: 264 average time/residue: 0.3048 time to fit residues: 124.0327 Evaluate side-chains 249 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 4807 ASN Chi-restraints excluded: chain K residue 4829 MET Chi-restraints excluded: chain K residue 4846 TYR Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 192 THR Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 343 VAL Chi-restraints excluded: chain N residue 348 ARG Chi-restraints excluded: chain R residue 114 TRP Chi-restraints excluded: chain R residue 131 TYR Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN H 81 ASN ** K4848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21207 Z= 0.376 Angle : 0.717 11.983 29905 Z= 0.394 Chirality : 0.044 0.186 3371 Planarity : 0.005 0.045 2785 Dihedral : 27.218 171.158 5132 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.39 % Allowed : 17.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.20), residues: 1775 helix: 1.43 (0.21), residues: 572 sheet: -1.50 (0.32), residues: 232 loop : -2.64 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP K4769 HIS 0.009 0.001 HIS B 75 PHE 0.025 0.002 PHE R 137 TYR 0.060 0.002 TYR B 88 ARG 0.004 0.001 ARG H 30 ********************** 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 259 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 222 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8623 (tt0) cc_final: 0.8189 (tp40) REVERT: A 73 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: A 120 MET cc_start: 0.8216 (mmm) cc_final: 0.7893 (mmm) REVERT: B 59 LYS cc_start: 0.7840 (tttt) cc_final: 0.7617 (tppt) REVERT: B 79 LYS cc_start: 0.9073 (mttt) cc_final: 0.8657 (mttm) REVERT: B 92 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8143 (ttp-170) REVERT: C 20 ARG cc_start: 0.8508 (ttm170) cc_final: 0.8007 (ttp80) REVERT: C 61 GLU cc_start: 0.8726 (tp30) cc_final: 0.8323 (tp30) REVERT: C 90 ASP cc_start: 0.8668 (t0) cc_final: 0.8312 (t0) REVERT: D 33 SER cc_start: 0.9256 (t) cc_final: 0.8956 (m) REVERT: D 48 ASP cc_start: 0.8214 (p0) cc_final: 0.7611 (p0) REVERT: D 65 ASP cc_start: 0.8680 (t0) cc_final: 0.8291 (t0) REVERT: D 68 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7775 (mm-30) REVERT: E 42 ARG cc_start: 0.8936 (ttm-80) cc_final: 0.8500 (ttm-80) REVERT: F 27 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8516 (mm-40) REVERT: F 63 GLU cc_start: 0.8492 (tt0) cc_final: 0.8272 (tt0) REVERT: F 96 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8218 (p) REVERT: G 84 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8296 (tm-30) REVERT: H 98 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8155 (mp) REVERT: K 4886 TYR cc_start: 0.6352 (m-10) cc_final: 0.6085 (m-10) REVERT: N 134 MET cc_start: 0.7872 (tmm) cc_final: 0.7562 (tmm) REVERT: N 304 HIS cc_start: 0.7491 (t-90) cc_final: 0.7149 (t-90) REVERT: N 348 ARG cc_start: 0.0724 (OUTLIER) cc_final: 0.0452 (ptp-170) REVERT: R 149 PHE cc_start: 0.4042 (m-80) cc_final: 0.3795 (m-80) REVERT: T 313 TYR cc_start: 0.1104 (m-80) cc_final: -0.1156 (m-10) REVERT: T 460 TYR cc_start: 0.4528 (m-80) cc_final: 0.3908 (m-80) outliers start: 37 outliers final: 26 residues processed: 248 average time/residue: 0.3146 time to fit residues: 120.6383 Evaluate side-chains 251 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 119 ILE 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 85 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 4807 ASN Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 192 THR Chi-restraints excluded: chain N residue 197 ASN Chi-restraints excluded: chain N residue 226 ASP 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 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 230 LEU Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 30.0000 chunk 49 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** K4848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.174993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.137631 restraints weight = 44502.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136362 restraints weight = 77355.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137110 restraints weight = 70355.225| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21207 Z= 0.169 Angle : 0.614 12.444 29905 Z= 0.343 Chirality : 0.040 0.206 3371 Planarity : 0.004 0.043 2785 Dihedral : 26.997 171.409 5132 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.13 % Allowed : 17.21 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.20), residues: 1775 helix: 1.84 (0.22), residues: 581 sheet: -1.28 (0.33), residues: 232 loop : -2.59 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP K4769 HIS 0.003 0.001 HIS D 79 PHE 0.030 0.001 PHE R 222 TYR 0.026 0.002 TYR H 80 ARG 0.005 0.000 ARG D 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.36 seconds wall clock time: 66 minutes 21.17 seconds (3981.17 seconds total)