Starting phenix.real_space_refine on Sun Apr 7 02:39:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/04_2024/8jip_36323_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/04_2024/8jip_36323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/04_2024/8jip_36323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/04_2024/8jip_36323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/04_2024/8jip_36323_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/04_2024/8jip_36323_neut_trim_updated.pdb" } resolution = 2.85 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5961 2.51 5 N 1609 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 76": "OE1" <-> "OE2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R GLU 139": "OE1" <-> "OE2" Residue "R GLU 292": "OE1" <-> "OE2" Residue "R GLU 294": "OE1" <-> "OE2" Residue "R GLU 373": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "P GLU 12": "OE1" <-> "OE2" Residue "P GLU 17": "OE1" <-> "OE2" Residue "P GLU 27": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9362 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3109 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2016 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.51, per 1000 atoms: 0.59 Number of scatterers: 9362 At special positions: 0 Unit cell: (85.14, 100.62, 175.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1735 8.00 N 1609 7.00 C 5961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.8 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 12 sheets defined 36.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'R' and resid 32 through 50 Processing helix chain 'R' and resid 90 through 93 No H-bonds generated for 'chain 'R' and resid 90 through 93' Processing helix chain 'R' and resid 140 through 168 removed outlier: 3.505A pdb=" N THR R 149 " --> pdb=" O TYR R 145 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 203 removed outlier: 3.561A pdb=" N SER R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 199 " --> pdb=" O PHE R 195 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 221 removed outlier: 3.973A pdb=" N LEU R 218 " --> pdb=" O TRP R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 231 Processing helix chain 'R' and resid 233 through 256 removed outlier: 4.138A pdb=" N ALA R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU R 254 " --> pdb=" O TYR R 250 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 288 removed outlier: 3.735A pdb=" N TRP R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) Proline residue: R 277 - end of helix removed outlier: 3.821A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 303 through 325 removed outlier: 3.890A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 328 through 335 Processing helix chain 'R' and resid 345 through 348 No H-bonds generated for 'chain 'R' and resid 345 through 348' Processing helix chain 'R' and resid 356 through 360 Processing helix chain 'R' and resid 362 through 365 Processing helix chain 'R' and resid 378 through 401 removed outlier: 3.698A pdb=" N SER R 389 " --> pdb=" O PHE R 385 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 422 removed outlier: 3.650A pdb=" N GLU R 412 " --> pdb=" O GLU R 408 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE R 413 " --> pdb=" O VAL R 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 32 removed outlier: 3.519A pdb=" N GLN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.660A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.512A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 removed outlier: 4.492A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.580A pdb=" N ALA A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 299 through 317 removed outlier: 3.666A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 removed outlier: 3.767A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 26 removed outlier: 3.515A pdb=" N GLN P 20 " --> pdb=" O SER P 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 8 through 22 removed outlier: 3.763A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 79 through 81 removed outlier: 3.854A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 195 through 200 removed outlier: 3.685A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ALA A 220 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU A 39 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 222 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.869A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.551A pdb=" N TYR B 124 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.636A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 221 through 223 removed outlier: 4.657A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 250 through 254 removed outlier: 3.501A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 284 through 286 Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.805A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 4.182A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 93 through 97 removed outlier: 3.649A pdb=" N ALA N 97 " --> pdb=" O ASN N 35 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 71 through 73 331 hydrogen bonds defined for protein. 966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1531 1.30 - 1.43: 2611 1.43 - 1.55: 5351 1.55 - 1.68: 2 1.68 - 1.81: 77 Bond restraints: 9572 Sorted by residual: bond pdb=" C LEU R 218 " pdb=" O LEU R 218 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.22e-02 6.72e+03 3.08e+01 bond pdb=" C LEU R 89 " pdb=" N PRO R 90 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.64e+01 bond pdb=" C SER P 11 " pdb=" O SER P 11 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" CA SER P 11 " pdb=" C SER P 11 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" C ASP R 53 " pdb=" N PRO R 54 " ideal model delta sigma weight residual 1.329 1.373 -0.044 1.18e-02 7.18e+03 1.37e+01 ... (remaining 9567 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.62: 230 106.62 - 114.40: 5520 114.40 - 122.19: 5485 122.19 - 129.97: 1659 129.97 - 137.75: 89 Bond angle restraints: 12983 Sorted by residual: angle pdb=" N ARG R 64 " pdb=" CA ARG R 64 " pdb=" C ARG R 64 " ideal model delta sigma weight residual 114.31 102.32 11.99 1.29e+00 6.01e-01 8.63e+01 angle pdb=" C THR A 292 " pdb=" N PRO A 293 " pdb=" CA PRO A 293 " ideal model delta sigma weight residual 120.66 111.89 8.77 1.09e+00 8.42e-01 6.47e+01 angle pdb=" N THR R 353 " pdb=" CA THR R 353 " pdb=" C THR R 353 " ideal model delta sigma weight residual 114.04 104.13 9.91 1.24e+00 6.50e-01 6.39e+01 angle pdb=" N LEU R 379 " pdb=" CA LEU R 379 " pdb=" C LEU R 379 " ideal model delta sigma weight residual 111.07 102.56 8.51 1.07e+00 8.73e-01 6.33e+01 angle pdb=" N PRO R 73 " pdb=" CA PRO R 73 " pdb=" C PRO R 73 " ideal model delta sigma weight residual 110.80 121.96 -11.16 1.51e+00 4.39e-01 5.46e+01 ... (remaining 12978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4808 17.82 - 35.64: 572 35.64 - 53.46: 204 53.46 - 71.28: 70 71.28 - 89.11: 17 Dihedral angle restraints: 5671 sinusoidal: 2226 harmonic: 3445 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 172.23 -79.23 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual -86.00 -151.66 65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -149.84 63.84 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 5668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1288 0.101 - 0.201: 134 0.201 - 0.302: 15 0.302 - 0.403: 4 0.403 - 0.504: 1 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CA ASN R 407 " pdb=" N ASN R 407 " pdb=" C ASN R 407 " pdb=" CB ASN R 407 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" CA ASN R 63 " pdb=" N ASN R 63 " pdb=" C ASN R 63 " pdb=" CB ASN R 63 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1439 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 101 " -0.039 2.00e-02 2.50e+03 4.74e-02 2.81e+01 pdb=" C04 D6M P 101 " 0.056 2.00e-02 2.50e+03 pdb=" C12 D6M P 101 " 0.049 2.00e-02 2.50e+03 pdb=" N03 D6M P 101 " -0.064 2.00e-02 2.50e+03 pdb=" O01 D6M P 101 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 323 " 0.026 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" C ILE R 323 " -0.089 2.00e-02 2.50e+03 pdb=" O ILE R 323 " 0.033 2.00e-02 2.50e+03 pdb=" N PHE R 324 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 289 " 0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C TYR R 289 " -0.071 2.00e-02 2.50e+03 pdb=" O TYR R 289 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU R 290 " 0.024 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 596 2.71 - 3.25: 9042 3.25 - 3.80: 14845 3.80 - 4.35: 18084 4.35 - 4.90: 30186 Nonbonded interactions: 72753 Sorted by model distance: nonbonded pdb=" N GLU A 276 " pdb=" OE1 GLU A 276 " model vdw 2.156 2.520 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.216 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.229 2.440 nonbonded pdb=" O LYS N 65 " pdb=" NH1 ARG N 67 " model vdw 2.252 2.520 nonbonded pdb=" O PHE R 385 " pdb=" OG SER R 389 " model vdw 2.255 2.440 ... (remaining 72748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.450 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 29.720 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:23.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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 0.068 9572 Z= 0.410 Angle : 1.049 12.753 12983 Z= 0.699 Chirality : 0.066 0.504 1442 Planarity : 0.005 0.056 1654 Dihedral : 18.747 89.106 3425 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.62 % Favored : 92.61 % Rotamer: Outliers : 14.94 % Allowed : 9.23 % Favored : 75.83 % Cbeta Deviations : 0.09 % 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: -2.27 (0.24), residues: 1164 helix: -1.39 (0.25), residues: 422 sheet: -0.30 (0.38), residues: 190 loop : -1.99 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 39 HIS 0.005 0.001 HIS R 99 PHE 0.016 0.002 PHE R 187 TYR 0.016 0.002 TYR A 56 ARG 0.004 0.000 ARG R 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 170 time to evaluate : 1.084 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: R 107 GLU cc_start: 0.5188 (OUTLIER) cc_final: 0.4396 (pm20) REVERT: R 112 GLN cc_start: 0.1989 (OUTLIER) cc_final: 0.1314 (mt0) REVERT: A 229 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7669 (p0) REVERT: A 231 ASN cc_start: 0.9505 (t0) cc_final: 0.9303 (t0) REVERT: A 232 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8692 (mtp85) REVERT: A 359 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: P 1 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.7858 (p-80) REVERT: P 11 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.8205 (t) REVERT: P 13 TYR cc_start: 0.9042 (t80) cc_final: 0.8752 (t80) REVERT: P 21 ASP cc_start: 0.9180 (m-30) cc_final: 0.8972 (m-30) REVERT: B 44 GLN cc_start: 0.7341 (mp-120) cc_final: 0.6841 (mp-120) REVERT: B 172 GLU cc_start: 0.9190 (tp30) cc_final: 0.8825 (tp30) REVERT: B 175 GLN cc_start: 0.8456 (mp10) cc_final: 0.8089 (mp10) REVERT: B 217 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6565 (pmt) REVERT: B 220 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: B 259 GLN cc_start: 0.8264 (tp-100) cc_final: 0.8002 (tp40) REVERT: B 264 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.7397 (m-10) REVERT: B 303 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7259 (OUTLIER) REVERT: G 21 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7315 (pp-130) REVERT: N 43 LYS cc_start: 0.8857 (ptpp) cc_final: 0.8575 (pmtt) outliers start: 149 outliers final: 42 residues processed: 284 average time/residue: 1.1952 time to fit residues: 362.3128 Evaluate side-chains 165 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 112 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 43 ARG Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 47 GLN Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 412 GLU Chi-restraints excluded: chain R residue 421 ARG Chi-restraints excluded: chain R residue 423 GLU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain P residue 1 HIS Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.0040 chunk 66 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 63 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 GLN R 234 GLN R 302 ASN R 304 ASN R 338 ASN R 394 GLN R 406 ASN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9572 Z= 0.249 Angle : 0.663 9.155 12983 Z= 0.344 Chirality : 0.042 0.146 1442 Planarity : 0.004 0.043 1654 Dihedral : 10.890 77.606 1432 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 6.12 % Allowed : 18.86 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.05 (0.24), residues: 1164 helix: 0.37 (0.26), residues: 423 sheet: 0.25 (0.41), residues: 184 loop : -1.91 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 39 HIS 0.003 0.001 HIS A 324 PHE 0.037 0.002 PHE R 80 TYR 0.024 0.002 TYR R 148 ARG 0.006 0.001 ARG R 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 119 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2586 (OUTLIER) cc_final: 0.1891 (mt0) REVERT: A 52 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 53 MET cc_start: 0.9070 (mmm) cc_final: 0.8733 (mpp) REVERT: A 229 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.7999 (p0) REVERT: A 231 ASN cc_start: 0.9490 (t0) cc_final: 0.9249 (t0) REVERT: B 172 GLU cc_start: 0.9216 (tp30) cc_final: 0.8860 (tp30) REVERT: B 175 GLN cc_start: 0.8508 (mp10) cc_final: 0.8078 (mp10) REVERT: B 260 GLU cc_start: 0.7516 (pp20) cc_final: 0.7300 (pp20) REVERT: B 301 LYS cc_start: 0.7478 (mppt) cc_final: 0.7237 (mmtm) REVERT: B 303 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.6905 (m-30) REVERT: G 21 MET cc_start: 0.7400 (ppp) cc_final: 0.7101 (pp-130) REVERT: G 47 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7590 (mm-30) REVERT: N 43 LYS cc_start: 0.9030 (ptpp) cc_final: 0.8692 (pmtt) outliers start: 61 outliers final: 32 residues processed: 167 average time/residue: 1.2554 time to fit residues: 223.9962 Evaluate side-chains 138 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 103 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.0020 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 chunk 103 optimal weight: 9.9990 chunk 112 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 ASN A 238 ASN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 9572 Z= 0.174 Angle : 0.582 8.783 12983 Z= 0.296 Chirality : 0.040 0.225 1442 Planarity : 0.004 0.040 1654 Dihedral : 8.002 70.412 1358 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 3.71 % Allowed : 23.17 % Favored : 73.12 % 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: -0.53 (0.25), residues: 1164 helix: 1.03 (0.26), residues: 436 sheet: 0.58 (0.42), residues: 177 loop : -1.89 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 39 HIS 0.002 0.000 HIS P 1 PHE 0.025 0.001 PHE R 80 TYR 0.015 0.001 TYR R 148 ARG 0.010 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2665 (OUTLIER) cc_final: 0.2021 (mt0) REVERT: R 336 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7828 (ttpt) REVERT: R 372 ASP cc_start: 0.6101 (OUTLIER) cc_final: 0.5887 (p0) REVERT: A 52 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7768 (tm-30) REVERT: A 53 MET cc_start: 0.9033 (mmm) cc_final: 0.8786 (mpp) REVERT: A 229 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.7938 (p0) REVERT: A 231 ASN cc_start: 0.9499 (t0) cc_final: 0.9217 (t0) REVERT: B 172 GLU cc_start: 0.9215 (tp30) cc_final: 0.8859 (tp30) REVERT: B 175 GLN cc_start: 0.8500 (mp10) cc_final: 0.8118 (mp10) REVERT: B 260 GLU cc_start: 0.7692 (pp20) cc_final: 0.7467 (pp20) REVERT: G 21 MET cc_start: 0.7437 (ppp) cc_final: 0.7156 (pp-130) REVERT: G 42 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6868 (mt-10) outliers start: 37 outliers final: 17 residues processed: 148 average time/residue: 1.2515 time to fit residues: 198.8300 Evaluate side-chains 127 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 8.9990 chunk 77 optimal weight: 0.0970 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN R 82 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 9572 Z= 0.265 Angle : 0.606 11.337 12983 Z= 0.311 Chirality : 0.042 0.184 1442 Planarity : 0.004 0.041 1654 Dihedral : 7.220 74.690 1345 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 4.41 % Allowed : 23.27 % Favored : 72.32 % 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: -0.42 (0.25), residues: 1164 helix: 1.24 (0.26), residues: 437 sheet: 0.51 (0.41), residues: 184 loop : -1.93 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 39 HIS 0.004 0.001 HIS A 324 PHE 0.017 0.002 PHE N 108 TYR 0.019 0.001 TYR R 148 ARG 0.011 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 114 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2554 (OUTLIER) cc_final: 0.1953 (mt0) REVERT: R 224 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9005 (tm) REVERT: R 304 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7788 (m-40) REVERT: R 415 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8116 (mtmm) REVERT: A 20 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8206 (tm-30) REVERT: A 52 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 53 MET cc_start: 0.9176 (mmm) cc_final: 0.8715 (mpp) REVERT: A 229 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7888 (p0) REVERT: A 231 ASN cc_start: 0.9487 (t0) cc_final: 0.9211 (t0) REVERT: B 172 GLU cc_start: 0.9245 (tp30) cc_final: 0.8931 (tp30) REVERT: B 175 GLN cc_start: 0.8531 (mp10) cc_final: 0.8121 (mp10) REVERT: B 260 GLU cc_start: 0.7850 (pp20) cc_final: 0.7411 (pp20) REVERT: G 21 MET cc_start: 0.7511 (ppp) cc_final: 0.7193 (pp-130) REVERT: G 42 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6820 (mt-10) outliers start: 44 outliers final: 24 residues processed: 145 average time/residue: 1.2368 time to fit residues: 192.6735 Evaluate side-chains 130 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 30.0000 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 99 HIS ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 9572 Z= 0.561 Angle : 0.770 11.680 12983 Z= 0.404 Chirality : 0.049 0.290 1442 Planarity : 0.005 0.037 1654 Dihedral : 7.743 107.370 1332 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.84 % Favored : 94.07 % Rotamer: Outliers : 5.72 % Allowed : 24.27 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.24), residues: 1164 helix: 0.97 (0.25), residues: 431 sheet: -0.29 (0.38), residues: 200 loop : -2.04 (0.24), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 36 HIS 0.006 0.001 HIS B 62 PHE 0.029 0.003 PHE N 108 TYR 0.032 0.002 TYR N 80 ARG 0.008 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 104 time to evaluate : 1.117 Fit side-chains REVERT: R 415 LYS cc_start: 0.8462 (mtmm) cc_final: 0.8206 (mtmm) REVERT: A 229 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7856 (p0) REVERT: A 231 ASN cc_start: 0.9532 (t0) cc_final: 0.9264 (t0) REVERT: A 284 ARG cc_start: 0.8623 (mpp80) cc_final: 0.8362 (mpt-90) REVERT: B 175 GLN cc_start: 0.8542 (mp10) cc_final: 0.8090 (mp10) REVERT: B 298 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8062 (p0) REVERT: G 21 MET cc_start: 0.7570 (ppp) cc_final: 0.7295 (pp-130) REVERT: G 42 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6871 (mt-10) REVERT: N 5 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8091 (tp40) outliers start: 57 outliers final: 32 residues processed: 147 average time/residue: 1.0538 time to fit residues: 167.6319 Evaluate side-chains 135 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 63 ASN ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 GLN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 9572 Z= 0.204 Angle : 0.613 9.535 12983 Z= 0.314 Chirality : 0.041 0.215 1442 Planarity : 0.003 0.036 1654 Dihedral : 6.408 84.453 1323 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.44 % Favored : 96.48 % Rotamer: Outliers : 3.11 % Allowed : 27.88 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.40 (0.25), residues: 1164 helix: 1.54 (0.26), residues: 429 sheet: -0.03 (0.40), residues: 189 loop : -1.92 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 39 HIS 0.002 0.000 HIS A 324 PHE 0.016 0.001 PHE R 156 TYR 0.017 0.001 TYR R 148 ARG 0.008 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 1.145 Fit side-chains REVERT: R 112 GLN cc_start: 0.2734 (OUTLIER) cc_final: 0.0892 (pm20) REVERT: R 415 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8139 (mtmm) REVERT: A 231 ASN cc_start: 0.9496 (t0) cc_final: 0.9217 (t0) REVERT: A 284 ARG cc_start: 0.8703 (mpp80) cc_final: 0.8386 (mpt-90) REVERT: B 175 GLN cc_start: 0.8555 (mp10) cc_final: 0.8083 (mp10) REVERT: B 217 MET cc_start: 0.8037 (pmm) cc_final: 0.7808 (pmm) REVERT: B 259 GLN cc_start: 0.7937 (tp40) cc_final: 0.7667 (tm-30) REVERT: B 298 ASP cc_start: 0.8863 (m-30) cc_final: 0.8113 (p0) REVERT: G 21 MET cc_start: 0.7526 (ppp) cc_final: 0.7211 (pp-130) REVERT: N 72 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7324 (ttm170) REVERT: N 96 CYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7010 (m) outliers start: 31 outliers final: 15 residues processed: 130 average time/residue: 1.2321 time to fit residues: 171.7544 Evaluate side-chains 119 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 9572 Z= 0.193 Angle : 0.594 10.596 12983 Z= 0.302 Chirality : 0.040 0.176 1442 Planarity : 0.004 0.070 1654 Dihedral : 5.750 57.164 1319 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 3.41 % Allowed : 27.58 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.20 (0.25), residues: 1164 helix: 1.72 (0.26), residues: 430 sheet: 0.16 (0.41), residues: 189 loop : -1.87 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 39 HIS 0.002 0.000 HIS A 324 PHE 0.014 0.001 PHE R 156 TYR 0.017 0.001 TYR R 148 ARG 0.012 0.000 ARG P 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2739 (OUTLIER) cc_final: 0.0900 (pm20) REVERT: R 415 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8153 (mtmm) REVERT: A 53 MET cc_start: 0.9270 (mmm) cc_final: 0.8668 (mpp) REVERT: A 231 ASN cc_start: 0.9497 (t0) cc_final: 0.9090 (m-40) REVERT: A 284 ARG cc_start: 0.8717 (mpp80) cc_final: 0.8366 (mpt-90) REVERT: A 289 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8872 (mp0) REVERT: P 21 ASP cc_start: 0.9370 (m-30) cc_final: 0.9025 (t0) REVERT: B 9 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7774 (mp10) REVERT: B 175 GLN cc_start: 0.8553 (mp10) cc_final: 0.8097 (mp10) REVERT: B 217 MET cc_start: 0.8069 (pmm) cc_final: 0.7809 (pmm) REVERT: B 260 GLU cc_start: 0.8319 (pp20) cc_final: 0.8086 (pp20) REVERT: B 298 ASP cc_start: 0.8833 (m-30) cc_final: 0.8132 (p0) REVERT: G 21 MET cc_start: 0.7557 (ppp) cc_final: 0.7251 (pp-130) REVERT: G 47 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7710 (mm-30) REVERT: N 72 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.7287 (ttm170) REVERT: N 96 CYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6993 (m) outliers start: 34 outliers final: 19 residues processed: 134 average time/residue: 1.2027 time to fit residues: 172.9649 Evaluate side-chains 131 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 9572 Z= 0.244 Angle : 0.627 11.465 12983 Z= 0.320 Chirality : 0.041 0.169 1442 Planarity : 0.003 0.050 1654 Dihedral : 5.435 55.668 1319 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.70 % Rotamer: Outliers : 3.21 % Allowed : 28.08 % Favored : 68.71 % 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: -0.19 (0.25), residues: 1164 helix: 1.74 (0.26), residues: 432 sheet: -0.06 (0.38), residues: 206 loop : -1.82 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 243 HIS 0.003 0.001 HIS A 324 PHE 0.015 0.001 PHE N 108 TYR 0.019 0.001 TYR R 148 ARG 0.008 0.000 ARG P 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2838 (OUTLIER) cc_final: 0.1151 (OUTLIER) REVERT: R 415 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8135 (mtmm) REVERT: A 231 ASN cc_start: 0.9496 (t0) cc_final: 0.9179 (t0) REVERT: A 284 ARG cc_start: 0.8688 (mpp80) cc_final: 0.8318 (mpt-90) REVERT: A 289 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8878 (mp0) REVERT: P 21 ASP cc_start: 0.9389 (m-30) cc_final: 0.9045 (t0) REVERT: B 9 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: B 175 GLN cc_start: 0.8576 (mp10) cc_final: 0.8111 (mp10) REVERT: B 217 MET cc_start: 0.8169 (pmm) cc_final: 0.7923 (pmm) REVERT: B 260 GLU cc_start: 0.8412 (pp20) cc_final: 0.8032 (pp20) REVERT: G 21 MET cc_start: 0.7534 (ppp) cc_final: 0.7235 (pp-130) REVERT: N 96 CYS cc_start: 0.7625 (OUTLIER) cc_final: 0.6991 (m) outliers start: 32 outliers final: 22 residues processed: 136 average time/residue: 1.2093 time to fit residues: 176.7517 Evaluate side-chains 130 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0970 chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 108 optimal weight: 0.3980 chunk 66 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 9572 Z= 0.190 Angle : 0.606 11.361 12983 Z= 0.308 Chirality : 0.040 0.163 1442 Planarity : 0.003 0.052 1654 Dihedral : 5.027 56.736 1317 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 2.91 % Allowed : 28.99 % Favored : 68.10 % 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: 0.02 (0.25), residues: 1164 helix: 1.94 (0.26), residues: 432 sheet: 0.24 (0.40), residues: 189 loop : -1.77 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 110 HIS 0.002 0.000 HIS A 324 PHE 0.013 0.001 PHE R 156 TYR 0.018 0.001 TYR R 148 ARG 0.008 0.000 ARG P 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2767 (OUTLIER) cc_final: 0.1101 (OUTLIER) REVERT: R 415 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8153 (mtmm) REVERT: A 53 MET cc_start: 0.9564 (OUTLIER) cc_final: 0.8739 (mpp) REVERT: A 231 ASN cc_start: 0.9475 (t0) cc_final: 0.9075 (m-40) REVERT: A 284 ARG cc_start: 0.8696 (mpp80) cc_final: 0.8314 (mpt-90) REVERT: A 289 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8921 (mp0) REVERT: P 21 ASP cc_start: 0.9408 (m-30) cc_final: 0.9111 (t0) REVERT: B 9 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7764 (mp10) REVERT: B 175 GLN cc_start: 0.8555 (mp10) cc_final: 0.8078 (mp10) REVERT: B 217 MET cc_start: 0.8178 (pmm) cc_final: 0.7952 (pmm) REVERT: G 21 MET cc_start: 0.7528 (ppp) cc_final: 0.7233 (pp-130) REVERT: N 96 CYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7110 (m) outliers start: 29 outliers final: 18 residues processed: 133 average time/residue: 1.2211 time to fit residues: 174.1596 Evaluate side-chains 129 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 0.0060 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN R 240 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 9572 Z= 0.200 Angle : 0.624 11.776 12983 Z= 0.318 Chirality : 0.040 0.156 1442 Planarity : 0.004 0.082 1654 Dihedral : 4.702 57.023 1315 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 2.21 % Allowed : 29.59 % Favored : 68.20 % 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: 0.11 (0.25), residues: 1164 helix: 2.02 (0.26), residues: 430 sheet: 0.29 (0.40), residues: 189 loop : -1.71 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 39 HIS 0.002 0.000 HIS A 324 PHE 0.013 0.001 PHE R 156 TYR 0.017 0.001 TYR R 148 ARG 0.011 0.000 ARG R 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2643 (OUTLIER) cc_final: 0.1011 (OUTLIER) REVERT: R 415 LYS cc_start: 0.8420 (mtmm) cc_final: 0.8159 (mtmm) REVERT: A 53 MET cc_start: 0.9575 (OUTLIER) cc_final: 0.8754 (mpp) REVERT: A 231 ASN cc_start: 0.9483 (t0) cc_final: 0.9101 (m-40) REVERT: A 284 ARG cc_start: 0.8670 (mpp80) cc_final: 0.8287 (mpt-90) REVERT: A 289 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8922 (mp0) REVERT: P 21 ASP cc_start: 0.9406 (m-30) cc_final: 0.9102 (t0) REVERT: B 9 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: B 175 GLN cc_start: 0.8561 (mp10) cc_final: 0.8100 (mp10) REVERT: B 259 GLN cc_start: 0.8318 (mm-40) cc_final: 0.8112 (mm-40) REVERT: B 260 GLU cc_start: 0.8716 (pm20) cc_final: 0.8411 (pm20) REVERT: G 21 MET cc_start: 0.7468 (ppp) cc_final: 0.7173 (pp-130) REVERT: N 96 CYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7184 (m) outliers start: 22 outliers final: 16 residues processed: 128 average time/residue: 1.2771 time to fit residues: 175.3967 Evaluate side-chains 127 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.132419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.084508 restraints weight = 17424.148| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.87 r_work: 0.2975 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 9572 Z= 0.197 Angle : 0.618 11.899 12983 Z= 0.316 Chirality : 0.041 0.251 1442 Planarity : 0.004 0.068 1654 Dihedral : 4.651 56.604 1315 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.41 % Allowed : 29.09 % Favored : 68.51 % 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: 0.10 (0.25), residues: 1164 helix: 2.06 (0.26), residues: 429 sheet: 0.12 (0.39), residues: 199 loop : -1.71 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 39 HIS 0.002 0.000 HIS A 324 PHE 0.013 0.001 PHE R 156 TYR 0.018 0.001 TYR R 148 ARG 0.010 0.000 ARG R 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3929.84 seconds wall clock time: 71 minutes 27.34 seconds (4287.34 seconds total)