Starting phenix.real_space_refine on Mon Mar 11 07:37:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/03_2024/6ww2_21927.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/03_2024/6ww2_21927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/03_2024/6ww2_21927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/03_2024/6ww2_21927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/03_2024/6ww2_21927.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/03_2024/6ww2_21927.pdb" } resolution = 3.7 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= 0.001 sd= 0.039 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 32 5.16 5 C 4857 2.51 5 N 1273 2.21 5 O 1432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "K ARG 27": "NH1" <-> "NH2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 211": "NH1" <-> "NH2" Residue "R TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 232": "NH1" <-> "NH2" Residue "R PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 300": "NH1" <-> "NH2" Residue "R TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 401": "NH1" <-> "NH2" Residue "R PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 1002": "NH1" <-> "NH2" Residue "R ASP 1007": "OD1" <-> "OD2" Residue "R ARG 1113": "NH1" <-> "NH2" Residue "R GLU 444": "OE1" <-> "OE2" Residue "R PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 475": "NH1" <-> "NH2" Residue "R GLU 476": "OE1" <-> "OE2" Residue "R GLU 479": "OE1" <-> "OE2" Residue "R ARG 531": "NH1" <-> "NH2" Residue "R ARG 532": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7594 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1682 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1624 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3367 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.41, per 1000 atoms: 0.58 Number of scatterers: 7594 At special positions: 0 Unit cell: (112.112, 146.608, 98.098, 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 32 16.00 O 1432 8.00 N 1273 7.00 C 4857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 222 " - pdb=" SG CYS R 298 " distance=2.03 Simple disulfide: pdb=" SG CYS R 315 " - pdb=" SG CYS R 390 " 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=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 38.8% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.667A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.945A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.659A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 206 removed outlier: 3.703A pdb=" N GLN H 206 " --> pdb=" O LEU H 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.967A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 98 removed outlier: 3.735A pdb=" N LEU L 97 " --> pdb=" O TYR L 94 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL L 98 " --> pdb=" O TYR L 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 94 through 98' Processing helix chain 'L' and resid 185 through 189 removed outlier: 4.252A pdb=" N GLU L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 185 through 189' Processing helix chain 'R' and resid 211 through 215 removed outlier: 3.566A pdb=" N GLN R 214 " --> pdb=" O ARG R 211 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL R 215 " --> pdb=" O THR R 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 211 through 215' Processing helix chain 'R' and resid 228 through 230 No H-bonds generated for 'chain 'R' and resid 228 through 230' Processing helix chain 'R' and resid 231 through 261 removed outlier: 4.704A pdb=" N PHE R 237 " --> pdb=" O THR R 233 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE R 239 " --> pdb=" O ALA R 235 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY R 240 " --> pdb=" O THR R 236 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP R 242 " --> pdb=" O TRP R 238 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU R 245 " --> pdb=" O LEU R 241 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR R 250 " --> pdb=" O CYS R 246 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL R 254 " --> pdb=" O THR R 250 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA R 255 " --> pdb=" O SER R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 267 No H-bonds generated for 'chain 'R' and resid 265 through 267' Processing helix chain 'R' and resid 268 through 292 removed outlier: 4.188A pdb=" N ILE R 272 " --> pdb=" O GLU R 268 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE R 273 " --> pdb=" O ARG R 269 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS R 280 " --> pdb=" O ALA R 276 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE R 285 " --> pdb=" O VAL R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 297 removed outlier: 3.679A pdb=" N VAL R 296 " --> pdb=" O GLY R 292 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA R 297 " --> pdb=" O HIS R 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 292 through 297' Processing helix chain 'R' and resid 314 through 345 removed outlier: 4.028A pdb=" N VAL R 318 " --> pdb=" O LEU R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 379 removed outlier: 3.627A pdb=" N TYR R 356 " --> pdb=" O ALA R 352 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR R 359 " --> pdb=" O GLY R 355 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU R 362 " --> pdb=" O GLN R 358 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP R 365 " --> pdb=" O HIS R 361 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU R 366 " --> pdb=" O LEU R 362 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE R 367 " --> pdb=" O ALA R 363 " (cutoff:3.500A) Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 396 through 404 Processing helix chain 'R' and resid 404 through 1025 removed outlier: 3.831A pdb=" N LEU R 408 " --> pdb=" O VAL R 404 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL R 409 " --> pdb=" O LEU R 405 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU R 412 " --> pdb=" O LEU R 408 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE R 418 " --> pdb=" O VAL R 414 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN R1018 " --> pdb=" O THR R1014 " (cutoff:3.500A) Processing helix chain 'R' and resid 1029 through 1049 removed outlier: 4.204A pdb=" N LYS R1037 " --> pdb=" O ASP R1033 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA R1048 " --> pdb=" O ASP R1044 " (cutoff:3.500A) Processing helix chain 'R' and resid 1064 through 1086 removed outlier: 4.640A pdb=" N PHE R1070 " --> pdb=" O PHE R1066 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS R1082 " --> pdb=" O ASP R1078 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU R1083 " --> pdb=" O ASP R1079 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA R1084 " --> pdb=" O ALA R1080 " (cutoff:3.500A) Processing helix chain 'R' and resid 1089 through 1098 Processing helix chain 'R' and resid 1098 through 1106 removed outlier: 4.523A pdb=" N THR R1102 " --> pdb=" O GLN R1098 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR R1106 " --> pdb=" O THR R1102 " (cutoff:3.500A) Processing helix chain 'R' and resid 1106 through 479 removed outlier: 3.804A pdb=" N ARG R1113 " --> pdb=" O LYS R1109 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU R1118 " --> pdb=" O ALA R1114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU R 446 " --> pdb=" O LYS R 442 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE R 448 " --> pdb=" O GLU R 444 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG R 449 " --> pdb=" O LYS R 445 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE R 453 " --> pdb=" O ARG R 449 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR R 454 " --> pdb=" O ILE R 450 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL R 459 " --> pdb=" O LEU R 455 " (cutoff:3.500A) Proline residue: R 460 - end of helix removed outlier: 3.919A pdb=" N HIS R 473 " --> pdb=" O LEU R 469 " (cutoff:3.500A) Processing helix chain 'R' and resid 500 through 511 removed outlier: 3.805A pdb=" N LYS R 506 " --> pdb=" O VAL R 502 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR R 507 " --> pdb=" O LEU R 503 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE R 508 " --> pdb=" O MET R 504 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU R 511 " --> pdb=" O TYR R 507 " (cutoff:3.500A) Processing helix chain 'R' and resid 511 through 520 removed outlier: 4.257A pdb=" N ILE R 515 " --> pdb=" O LEU R 511 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR R 516 " --> pdb=" O VAL R 512 " (cutoff:3.500A) Processing helix chain 'R' and resid 523 through 536 removed outlier: 4.233A pdb=" N ARG R 536 " --> pdb=" O ARG R 532 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.705A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR H 53 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.068A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.068A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 165 through 168 removed outlier: 3.597A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.738A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY K 16 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER K 85 " --> pdb=" O GLY K 16 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.466A pdb=" N VAL K 12 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR K 118 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL K 117 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.927A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.189A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 146 through 147 removed outlier: 3.877A pdb=" N ALA L 195 " --> pdb=" O LYS L 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'R' and resid 381 through 383 381 hydrogen bonds defined for protein. 1065 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: 2.22 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2228 1.34 - 1.46: 2136 1.46 - 1.59: 3373 1.59 - 1.71: 0 1.71 - 1.83: 44 Bond restraints: 7781 Sorted by residual: bond pdb=" CB TRP H 102 " pdb=" CG TRP H 102 " ideal model delta sigma weight residual 1.498 1.420 0.078 3.10e-02 1.04e+03 6.30e+00 bond pdb=" C VAL R 459 " pdb=" N PRO R 460 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.12e+00 bond pdb=" CB TRP R 242 " pdb=" CG TRP R 242 " ideal model delta sigma weight residual 1.498 1.427 0.071 3.10e-02 1.04e+03 5.30e+00 bond pdb=" CB PHE H 180 " pdb=" CG PHE H 180 " ideal model delta sigma weight residual 1.502 1.454 0.048 2.30e-02 1.89e+03 4.36e+00 bond pdb=" CB VAL R 215 " pdb=" CG2 VAL R 215 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.31e+00 ... (remaining 7776 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.72: 151 105.72 - 112.81: 4086 112.81 - 119.90: 2701 119.90 - 126.98: 3534 126.98 - 134.07: 118 Bond angle restraints: 10590 Sorted by residual: angle pdb=" C GLU R 202 " pdb=" N SER R 203 " pdb=" CA SER R 203 " ideal model delta sigma weight residual 121.54 130.77 -9.23 1.91e+00 2.74e-01 2.33e+01 angle pdb=" C PHE R 196 " pdb=" N VAL R 197 " pdb=" CA VAL R 197 " ideal model delta sigma weight residual 122.13 129.76 -7.63 1.85e+00 2.92e-01 1.70e+01 angle pdb=" C MET R 261 " pdb=" N GLU R 262 " pdb=" CA GLU R 262 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C ALA R1048 " pdb=" N THR R1049 " pdb=" CA THR R1049 " ideal model delta sigma weight residual 121.70 128.66 -6.96 1.80e+00 3.09e-01 1.50e+01 angle pdb=" C SER H 217 " pdb=" N ASN H 218 " pdb=" CA ASN H 218 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 ... (remaining 10585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4139 17.84 - 35.67: 352 35.67 - 53.51: 65 53.51 - 71.35: 9 71.35 - 89.18: 7 Dihedral angle restraints: 4572 sinusoidal: 1720 harmonic: 2852 Sorted by residual: dihedral pdb=" CA PRO H 199 " pdb=" C PRO H 199 " pdb=" N SER H 200 " pdb=" CA SER H 200 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA THR R 252 " pdb=" C THR R 252 " pdb=" N THR R 253 " pdb=" CA THR R 253 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ASN R 217 " pdb=" C ASN R 217 " pdb=" N CYS R 218 " pdb=" CA CYS R 218 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 4569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 722 0.046 - 0.092: 305 0.092 - 0.137: 115 0.137 - 0.183: 35 0.183 - 0.229: 13 Chirality restraints: 1190 Sorted by residual: chirality pdb=" CB VAL R 197 " pdb=" CA VAL R 197 " pdb=" CG1 VAL R 197 " pdb=" CG2 VAL R 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CG LEU H 89 " pdb=" CB LEU H 89 " pdb=" CD1 LEU H 89 " pdb=" CD2 LEU H 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE K 98 " pdb=" CA ILE K 98 " pdb=" CG1 ILE K 98 " pdb=" CG2 ILE K 98 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1187 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 215 " -0.046 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO H 216 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO H 216 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 216 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU R 194 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.48e+00 pdb=" N PRO R 195 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO R 195 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 195 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 238 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C TRP R 238 " 0.043 2.00e-02 2.50e+03 pdb=" O TRP R 238 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE R 239 " -0.014 2.00e-02 2.50e+03 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1672 2.77 - 3.30: 7298 3.30 - 3.84: 12541 3.84 - 4.37: 13931 4.37 - 4.90: 23896 Nonbonded interactions: 59338 Sorted by model distance: nonbonded pdb=" O GLN K 3 " pdb=" OG SER K 25 " model vdw 2.240 2.440 nonbonded pdb=" O VAL R 513 " pdb=" OG1 THR R 516 " model vdw 2.258 2.440 nonbonded pdb=" O TYR L 188 " pdb=" OH TYR L 194 " model vdw 2.261 2.440 nonbonded pdb=" O SER H 142 " pdb=" OG SER H 146 " model vdw 2.272 2.440 nonbonded pdb=" OE1 GLU R 308 " pdb=" OG SER R 379 " model vdw 2.281 2.440 ... (remaining 59333 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 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: 1.390 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: 0.010 Extract box with map and model: 7.130 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.560 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.010 0.088 7781 Z= 0.636 Angle : 1.077 10.309 10590 Z= 0.590 Chirality : 0.062 0.229 1190 Planarity : 0.008 0.068 1334 Dihedral : 14.271 89.182 2723 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.31 % Favored : 89.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -2.34 (0.26), residues: 970 helix: -1.13 (0.26), residues: 312 sheet: -0.83 (0.34), residues: 238 loop : -2.25 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP H 102 HIS 0.006 0.002 HIS R 306 PHE 0.026 0.004 PHE R 325 TYR 0.036 0.003 TYR H 53 ARG 0.008 0.001 ARG L 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: R 411 TYR cc_start: 0.8736 (m-10) cc_final: 0.8286 (m-80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1895 time to fit residues: 18.5520 Evaluate side-chains 49 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.0170 chunk 88 optimal weight: 3.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7781 Z= 0.186 Angle : 0.636 6.955 10590 Z= 0.338 Chirality : 0.043 0.179 1190 Planarity : 0.005 0.057 1334 Dihedral : 5.850 25.172 1067 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.73 % Allowed : 7.08 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -1.75 (0.27), residues: 970 helix: -0.25 (0.28), residues: 320 sheet: -0.80 (0.33), residues: 240 loop : -2.09 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 333 HIS 0.006 0.001 HIS R 204 PHE 0.014 0.001 PHE R 319 TYR 0.019 0.001 TYR K 32 ARG 0.003 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: R 411 TYR cc_start: 0.8658 (m-10) cc_final: 0.8390 (m-80) outliers start: 6 outliers final: 3 residues processed: 65 average time/residue: 0.1846 time to fit residues: 17.2272 Evaluate side-chains 56 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 462 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7781 Z= 0.301 Angle : 0.653 7.134 10590 Z= 0.346 Chirality : 0.043 0.161 1190 Planarity : 0.005 0.036 1334 Dihedral : 5.637 27.573 1067 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 1.10 % Allowed : 11.72 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -1.59 (0.27), residues: 970 helix: -0.01 (0.29), residues: 320 sheet: -0.78 (0.33), residues: 247 loop : -2.05 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 333 HIS 0.003 0.001 HIS R 306 PHE 0.015 0.002 PHE H 35 TYR 0.020 0.002 TYR K 32 ARG 0.005 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 5 MET cc_start: 0.8414 (tpp) cc_final: 0.7624 (tpp) REVERT: R 411 TYR cc_start: 0.8703 (m-10) cc_final: 0.8267 (m-80) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.1604 time to fit residues: 14.9696 Evaluate side-chains 59 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 462 SER Chi-restraints excluded: chain R residue 513 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7781 Z= 0.160 Angle : 0.575 7.022 10590 Z= 0.300 Chirality : 0.041 0.154 1190 Planarity : 0.004 0.033 1334 Dihedral : 5.094 27.023 1067 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.61 % Allowed : 14.77 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -1.32 (0.27), residues: 970 helix: 0.30 (0.29), residues: 320 sheet: -0.64 (0.33), residues: 247 loop : -1.95 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 333 HIS 0.002 0.001 HIS H 178 PHE 0.013 0.001 PHE R 319 TYR 0.013 0.001 TYR H 83 ARG 0.005 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: R 411 TYR cc_start: 0.8661 (m-10) cc_final: 0.8276 (m-80) outliers start: 5 outliers final: 5 residues processed: 65 average time/residue: 0.1484 time to fit residues: 14.6551 Evaluate side-chains 60 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 462 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 0.1980 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7781 Z= 0.258 Angle : 0.617 6.903 10590 Z= 0.323 Chirality : 0.042 0.156 1190 Planarity : 0.004 0.065 1334 Dihedral : 5.138 27.806 1067 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 1.71 % Allowed : 16.36 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 (0.27), residues: 970 helix: 0.34 (0.29), residues: 320 sheet: -0.62 (0.33), residues: 249 loop : -1.93 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 333 HIS 0.003 0.001 HIS R 306 PHE 0.013 0.001 PHE R 319 TYR 0.012 0.001 TYR R 500 ARG 0.004 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 83 MET cc_start: 0.7303 (ttm) cc_final: 0.7020 (ttp) REVERT: L 5 MET cc_start: 0.8090 (tpp) cc_final: 0.7291 (tpp) REVERT: R 281 VAL cc_start: 0.9193 (t) cc_final: 0.8956 (p) REVERT: R 411 TYR cc_start: 0.8660 (m-10) cc_final: 0.8190 (m-80) outliers start: 14 outliers final: 8 residues processed: 66 average time/residue: 0.1605 time to fit residues: 16.0548 Evaluate side-chains 62 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 508 PHE Chi-restraints excluded: chain R residue 513 VAL Chi-restraints excluded: chain R residue 534 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 23 optimal weight: 8.9990 chunk 93 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7781 Z= 0.165 Angle : 0.575 6.647 10590 Z= 0.297 Chirality : 0.041 0.157 1190 Planarity : 0.004 0.053 1334 Dihedral : 4.850 26.078 1067 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.59 % Allowed : 16.73 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -1.11 (0.28), residues: 970 helix: 0.48 (0.29), residues: 321 sheet: -0.46 (0.33), residues: 248 loop : -1.91 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 333 HIS 0.003 0.001 HIS H 38 PHE 0.013 0.001 PHE R 319 TYR 0.014 0.001 TYR H 83 ARG 0.004 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 5 MET cc_start: 0.8114 (tpp) cc_final: 0.7339 (tpp) REVERT: L 163 GLU cc_start: 0.7317 (pp20) cc_final: 0.7007 (pp20) REVERT: R 411 TYR cc_start: 0.8647 (m-10) cc_final: 0.8244 (m-80) outliers start: 13 outliers final: 11 residues processed: 68 average time/residue: 0.1527 time to fit residues: 16.0977 Evaluate side-chains 66 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 508 PHE Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 534 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.0030 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7781 Z= 0.161 Angle : 0.573 6.688 10590 Z= 0.295 Chirality : 0.041 0.149 1190 Planarity : 0.004 0.047 1334 Dihedral : 4.650 24.721 1067 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.20 % Allowed : 16.61 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -0.95 (0.28), residues: 970 helix: 0.59 (0.30), residues: 315 sheet: -0.31 (0.34), residues: 240 loop : -1.78 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 333 HIS 0.003 0.001 HIS H 38 PHE 0.011 0.001 PHE R 319 TYR 0.013 0.001 TYR H 83 ARG 0.003 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: K 83 MET cc_start: 0.7014 (ttm) cc_final: 0.6813 (ttp) REVERT: L 5 MET cc_start: 0.8079 (tpp) cc_final: 0.7259 (tpp) REVERT: L 163 GLU cc_start: 0.7311 (pp20) cc_final: 0.7017 (pp20) REVERT: R 346 MET cc_start: 0.9072 (mpp) cc_final: 0.8775 (pmm) REVERT: R 411 TYR cc_start: 0.8621 (m-10) cc_final: 0.8206 (m-80) outliers start: 18 outliers final: 14 residues processed: 71 average time/residue: 0.1465 time to fit residues: 16.0453 Evaluate side-chains 71 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 462 SER Chi-restraints excluded: chain R residue 465 VAL Chi-restraints excluded: chain R residue 508 PHE Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 534 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.3980 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7781 Z= 0.310 Angle : 0.641 6.818 10590 Z= 0.335 Chirality : 0.043 0.161 1190 Planarity : 0.004 0.045 1334 Dihedral : 5.017 25.489 1067 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 1.95 % Allowed : 17.34 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -1.03 (0.28), residues: 970 helix: 0.56 (0.30), residues: 314 sheet: -0.47 (0.34), residues: 244 loop : -1.78 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 333 HIS 0.003 0.001 HIS R 306 PHE 0.014 0.002 PHE H 35 TYR 0.014 0.002 TYR K 108 ARG 0.003 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.958 Fit side-chains REVERT: L 163 GLU cc_start: 0.7425 (pp20) cc_final: 0.7088 (pp20) REVERT: R 281 VAL cc_start: 0.9097 (t) cc_final: 0.8857 (p) REVERT: R 411 TYR cc_start: 0.8674 (m-10) cc_final: 0.8169 (m-80) outliers start: 16 outliers final: 14 residues processed: 68 average time/residue: 0.1507 time to fit residues: 15.9502 Evaluate side-chains 69 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 462 SER Chi-restraints excluded: chain R residue 465 VAL Chi-restraints excluded: chain R residue 508 PHE Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 534 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7781 Z= 0.301 Angle : 0.647 6.959 10590 Z= 0.338 Chirality : 0.043 0.162 1190 Planarity : 0.004 0.042 1334 Dihedral : 5.067 25.209 1067 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.95 % Allowed : 17.46 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -1.05 (0.28), residues: 970 helix: 0.56 (0.30), residues: 314 sheet: -0.46 (0.34), residues: 245 loop : -1.83 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 333 HIS 0.005 0.001 HIS R 306 PHE 0.015 0.002 PHE R 319 TYR 0.015 0.002 TYR H 116 ARG 0.003 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: H 208 TYR cc_start: 0.7245 (m-10) cc_final: 0.6879 (m-10) REVERT: R 238 TRP cc_start: 0.8148 (OUTLIER) cc_final: 0.6612 (t-100) REVERT: R 281 VAL cc_start: 0.9095 (t) cc_final: 0.8875 (p) REVERT: R 411 TYR cc_start: 0.8662 (m-10) cc_final: 0.8187 (m-80) outliers start: 16 outliers final: 15 residues processed: 67 average time/residue: 0.1476 time to fit residues: 15.3206 Evaluate side-chains 71 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 238 TRP Chi-restraints excluded: chain R residue 390 CYS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 462 SER Chi-restraints excluded: chain R residue 465 VAL Chi-restraints excluded: chain R residue 508 PHE Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 534 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7781 Z= 0.232 Angle : 0.619 7.291 10590 Z= 0.319 Chirality : 0.042 0.158 1190 Planarity : 0.004 0.041 1334 Dihedral : 4.887 23.550 1067 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.83 % Allowed : 17.70 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -0.98 (0.28), residues: 970 helix: 0.61 (0.30), residues: 314 sheet: -0.41 (0.34), residues: 245 loop : -1.78 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 333 HIS 0.003 0.001 HIS R 306 PHE 0.014 0.001 PHE R 319 TYR 0.011 0.001 TYR R 500 ARG 0.003 0.000 ARG K 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: H 208 TYR cc_start: 0.7208 (m-10) cc_final: 0.6880 (m-10) REVERT: L 163 GLU cc_start: 0.7389 (pp20) cc_final: 0.7054 (pp20) REVERT: R 238 TRP cc_start: 0.8135 (OUTLIER) cc_final: 0.6652 (t-100) REVERT: R 281 VAL cc_start: 0.9077 (t) cc_final: 0.8838 (p) REVERT: R 411 TYR cc_start: 0.8660 (m-10) cc_final: 0.8166 (m-80) outliers start: 15 outliers final: 14 residues processed: 67 average time/residue: 0.1497 time to fit residues: 15.4326 Evaluate side-chains 68 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 236 THR Chi-restraints excluded: chain R residue 238 TRP Chi-restraints excluded: chain R residue 390 CYS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 465 VAL Chi-restraints excluded: chain R residue 508 PHE Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 534 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.074800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.060421 restraints weight = 33716.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.061475 restraints weight = 19265.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061973 restraints weight = 14258.743| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7781 Z= 0.157 Angle : 0.593 8.036 10590 Z= 0.301 Chirality : 0.041 0.147 1190 Planarity : 0.004 0.040 1334 Dihedral : 4.512 21.123 1067 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.29 % Favored : 93.61 % Rotamer: Outliers : 1.95 % Allowed : 17.70 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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: -0.78 (0.28), residues: 970 helix: 0.78 (0.30), residues: 314 sheet: -0.24 (0.34), residues: 240 loop : -1.70 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 333 HIS 0.003 0.001 HIS R 304 PHE 0.013 0.001 PHE R 319 TYR 0.013 0.001 TYR H 83 ARG 0.003 0.000 ARG K 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1487.61 seconds wall clock time: 27 minutes 52.02 seconds (1672.02 seconds total)