Starting phenix.real_space_refine on Wed Sep 25 10:08:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtj_14142/09_2024/7qtj_14142.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtj_14142/09_2024/7qtj_14142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtj_14142/09_2024/7qtj_14142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtj_14142/09_2024/7qtj_14142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtj_14142/09_2024/7qtj_14142.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtj_14142/09_2024/7qtj_14142.cif" } resolution = 4.01 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= 0.024 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 42 5.16 5 C 6285 2.51 5 N 1673 2.21 5 O 1942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9942 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "E" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1645 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1637 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.27, per 1000 atoms: 0.63 Number of scatterers: 9942 At special positions: 0 Unit cell: (82.998, 161.846, 152.163, 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 42 16.00 O 1942 8.00 N 1673 7.00 C 6285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 331 " Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 26 sheets defined 9.8% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.656A pdb=" N ASP B 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.043A pdb=" N THR B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.741A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.529A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 4.083A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.414A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.838A pdb=" N VAL A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.897A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 3.677A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.196A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 410 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.900A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.783A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.571A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.666A pdb=" N LEU B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 50 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 59 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.550A pdb=" N LYS B 98 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 132 through 136 removed outlier: 3.567A pdb=" N PHE B 134 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 153 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 151 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 156 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 143 through 144 removed outlier: 3.526A pdb=" N ASP B 156 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.624A pdb=" N SER B 165 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS B 208 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.898A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.325A pdb=" N LEU C 11 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.844A pdb=" N VAL C 133 " --> pdb=" O PHE C 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.171A pdb=" N TRP C 148 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR C 192 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 194 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS C 207 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL C 196 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 205 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.913A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.524A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.776A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 396 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 514 " --> pdb=" O TYR D 396 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AB7, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.793A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.282A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 115 through 119 removed outlier: 4.386A pdb=" N SER E 175 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR E 165 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 154 through 156 removed outlier: 4.449A pdb=" N TRP E 149 " --> pdb=" O GLN E 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.182A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AC6, first strand: chain 'F' and resid 130 through 134 removed outlier: 6.188A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 130 through 134 removed outlier: 6.188A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 161 through 164 334 hydrogen bonds defined for protein. 822 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: 3.19 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2750 1.33 - 1.45: 1966 1.45 - 1.58: 5425 1.58 - 1.70: 1 1.70 - 1.82: 47 Bond restraints: 10189 Sorted by residual: bond pdb=" CG PRO E 121 " pdb=" CD PRO E 121 " ideal model delta sigma weight residual 1.503 1.299 0.204 3.40e-02 8.65e+02 3.59e+01 bond pdb=" CA SER B 52 " pdb=" CB SER B 52 " ideal model delta sigma weight residual 1.531 1.464 0.066 1.48e-02 4.57e+03 2.00e+01 bond pdb=" N PRO E 121 " pdb=" CD PRO E 121 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" CB PRO E 121 " pdb=" CG PRO E 121 " ideal model delta sigma weight residual 1.492 1.645 -0.153 5.00e-02 4.00e+02 9.37e+00 bond pdb=" CA SER B 55 " pdb=" CB SER B 55 " ideal model delta sigma weight residual 1.532 1.488 0.044 1.48e-02 4.57e+03 8.97e+00 ... (remaining 10184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 13784 3.92 - 7.83: 66 7.83 - 11.75: 3 11.75 - 15.67: 3 15.67 - 19.59: 1 Bond angle restraints: 13857 Sorted by residual: angle pdb=" CA PRO E 121 " pdb=" N PRO E 121 " pdb=" CD PRO E 121 " ideal model delta sigma weight residual 112.00 96.57 15.43 1.40e+00 5.10e-01 1.22e+02 angle pdb=" CG ARG A 346 " pdb=" CD ARG A 346 " pdb=" NE ARG A 346 " ideal model delta sigma weight residual 112.00 92.41 19.59 2.20e+00 2.07e-01 7.93e+01 angle pdb=" N PRO E 121 " pdb=" CD PRO E 121 " pdb=" CG PRO E 121 " ideal model delta sigma weight residual 103.20 90.73 12.47 1.50e+00 4.44e-01 6.91e+01 angle pdb=" C PHE A 377 " pdb=" CA PHE A 377 " pdb=" CB PHE A 377 " ideal model delta sigma weight residual 111.85 99.84 12.01 1.47e+00 4.63e-01 6.68e+01 angle pdb=" C THR C 172 " pdb=" CA THR C 172 " pdb=" CB THR C 172 " ideal model delta sigma weight residual 114.40 106.53 7.87 1.25e+00 6.40e-01 3.97e+01 ... (remaining 13852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 5676 21.98 - 43.95: 381 43.95 - 65.93: 51 65.93 - 87.90: 22 87.90 - 109.88: 9 Dihedral angle restraints: 6139 sinusoidal: 2431 harmonic: 3708 Sorted by residual: dihedral pdb=" CB CYS B 152 " pdb=" SG CYS B 152 " pdb=" SG CYS B 208 " pdb=" CB CYS B 208 " ideal model delta sinusoidal sigma weight residual 93.00 159.95 -66.95 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" C PHE A 377 " pdb=" N PHE A 377 " pdb=" CA PHE A 377 " pdb=" CB PHE A 377 " ideal model delta harmonic sigma weight residual -122.60 -107.54 -15.06 0 2.50e+00 1.60e-01 3.63e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -131.63 45.63 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 6136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1416 0.091 - 0.181: 110 0.181 - 0.272: 9 0.272 - 0.362: 3 0.362 - 0.453: 2 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CA PHE A 377 " pdb=" N PHE A 377 " pdb=" C PHE A 377 " pdb=" CB PHE A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CA ARG A 346 " pdb=" N ARG A 346 " pdb=" C ARG A 346 " pdb=" CB ARG A 346 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA ARG B 72 " pdb=" N ARG B 72 " pdb=" C ARG B 72 " pdb=" CB ARG B 72 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 1537 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 120 " -0.100 5.00e-02 4.00e+02 1.37e-01 2.99e+01 pdb=" N PRO E 121 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 101 " -0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C HIS B 101 " 0.076 2.00e-02 2.50e+03 pdb=" O HIS B 101 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR B 102 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 51 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ILE B 51 " -0.071 2.00e-02 2.50e+03 pdb=" O ILE B 51 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 52 " 0.024 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 246 2.70 - 3.25: 9271 3.25 - 3.80: 14986 3.80 - 4.35: 19152 4.35 - 4.90: 31923 Nonbonded interactions: 75578 Sorted by model distance: nonbonded pdb=" CB ARG A 346 " pdb=" NE ARG A 346 " model vdw 2.144 2.816 nonbonded pdb=" OE1 GLN C 6 " pdb=" OG1 THR C 102 " model vdw 2.303 3.040 nonbonded pdb=" O PRO B 197 " pdb=" OG SER B 200 " model vdw 2.305 3.040 nonbonded pdb=" NH1 ARG D 403 " pdb=" O GLY D 504 " model vdw 2.310 3.120 nonbonded pdb=" OE2 GLU B 6 " pdb=" N GLY B 118 " model vdw 2.315 3.120 ... (remaining 75573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } 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: 1.940 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.600 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.004 0.204 10189 Z= 0.318 Angle : 0.727 19.587 13857 Z= 0.422 Chirality : 0.050 0.453 1540 Planarity : 0.005 0.137 1780 Dihedral : 15.202 109.878 3719 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.21 % Favored : 94.48 % Rotamer: Outliers : 1.27 % Allowed : 0.54 % Favored : 98.19 % Cbeta Deviations : 0.34 % 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: 0.17 (0.25), residues: 1268 helix: -2.11 (0.56), residues: 62 sheet: 1.33 (0.25), residues: 440 loop : -0.43 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 148 HIS 0.002 0.001 HIS C 92 PHE 0.029 0.001 PHE A 377 TYR 0.025 0.001 TYR B 102 ARG 0.005 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 ASP cc_start: 0.8876 (m-30) cc_final: 0.8606 (m-30) REVERT: A 375 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.6655 (p90) REVERT: D 375 PHE cc_start: 0.5919 (m-10) cc_final: 0.5478 (m-80) REVERT: F 10 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7425 (mm-30) outliers start: 14 outliers final: 4 residues processed: 131 average time/residue: 0.2631 time to fit residues: 47.3172 Evaluate side-chains 85 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 7.9990 chunk 95 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.0020 chunk 73 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN C 6 GLN C 138 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN E 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10189 Z= 0.164 Angle : 0.596 14.381 13857 Z= 0.300 Chirality : 0.045 0.400 1540 Planarity : 0.004 0.049 1780 Dihedral : 8.126 77.934 1497 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 0.27 % Allowed : 5.26 % Favored : 94.46 % 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: 0.18 (0.24), residues: 1268 helix: -2.20 (0.55), residues: 60 sheet: 1.29 (0.25), residues: 458 loop : -0.42 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 53 HIS 0.003 0.001 HIS B 101 PHE 0.017 0.001 PHE D 429 TYR 0.014 0.001 TYR B 102 ARG 0.004 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8585 (p0) cc_final: 0.8331 (p0) REVERT: C 145 LYS cc_start: 0.8861 (tppt) cc_final: 0.8649 (tppt) REVERT: A 389 ASP cc_start: 0.9327 (p0) cc_final: 0.8777 (p0) REVERT: A 392 PHE cc_start: 0.8283 (m-80) cc_final: 0.7899 (m-80) REVERT: D 375 PHE cc_start: 0.6017 (m-10) cc_final: 0.5614 (m-80) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.2278 time to fit residues: 39.9704 Evaluate side-chains 85 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.0770 chunk 77 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 102 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10189 Z= 0.190 Angle : 0.594 10.410 13857 Z= 0.302 Chirality : 0.045 0.280 1540 Planarity : 0.004 0.037 1780 Dihedral : 6.724 62.993 1497 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.97 % Favored : 94.79 % Rotamer: Outliers : 0.18 % Allowed : 3.63 % Favored : 96.19 % 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: 0.05 (0.24), residues: 1268 helix: -2.10 (0.61), residues: 54 sheet: 1.02 (0.24), residues: 468 loop : -0.43 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 53 HIS 0.003 0.001 HIS B 101 PHE 0.019 0.001 PHE F 29 TYR 0.014 0.001 TYR B 102 ARG 0.005 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8599 (p0) cc_final: 0.8315 (p0) REVERT: B 99 ASP cc_start: 0.8811 (t0) cc_final: 0.8449 (t0) REVERT: C 194 CYS cc_start: 0.0381 (p) cc_final: -0.0225 (p) REVERT: A 389 ASP cc_start: 0.9345 (p0) cc_final: 0.8861 (p0) REVERT: A 392 PHE cc_start: 0.8354 (m-80) cc_final: 0.7924 (m-80) outliers start: 2 outliers final: 1 residues processed: 125 average time/residue: 0.2411 time to fit residues: 41.7311 Evaluate side-chains 82 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10189 Z= 0.293 Angle : 0.663 10.056 13857 Z= 0.341 Chirality : 0.046 0.311 1540 Planarity : 0.004 0.037 1780 Dihedral : 6.314 58.695 1497 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.24), residues: 1268 helix: -2.33 (0.58), residues: 61 sheet: 0.76 (0.24), residues: 473 loop : -0.70 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 436 HIS 0.005 0.001 HIS E 199 PHE 0.020 0.002 PHE D 429 TYR 0.017 0.002 TYR C 87 ARG 0.011 0.001 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8783 (p0) cc_final: 0.8545 (p0) REVERT: B 99 ASP cc_start: 0.8854 (t0) cc_final: 0.8493 (t0) REVERT: C 14 SER cc_start: 0.8817 (p) cc_final: 0.8589 (m) REVERT: C 140 TYR cc_start: 0.7174 (t80) cc_final: 0.6617 (t80) REVERT: C 145 LYS cc_start: 0.8942 (tppt) cc_final: 0.8584 (tppt) REVERT: C 194 CYS cc_start: 0.0711 (p) cc_final: 0.0172 (p) REVERT: A 389 ASP cc_start: 0.9337 (p0) cc_final: 0.8928 (p0) REVERT: A 392 PHE cc_start: 0.8418 (m-80) cc_final: 0.7981 (m-80) REVERT: D 498 ARG cc_start: 0.5763 (ttm170) cc_final: 0.5357 (ttp-170) REVERT: D 529 LYS cc_start: 0.6966 (mmpt) cc_final: 0.6715 (tttm) REVERT: F 10 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7406 (mm-30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2542 time to fit residues: 39.8505 Evaluate side-chains 84 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 103 optimal weight: 0.0870 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10189 Z= 0.197 Angle : 0.613 10.239 13857 Z= 0.312 Chirality : 0.045 0.264 1540 Planarity : 0.004 0.036 1780 Dihedral : 5.948 57.961 1497 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -0.32 (0.24), residues: 1268 helix: -2.29 (0.58), residues: 61 sheet: 0.68 (0.24), residues: 482 loop : -0.63 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 436 HIS 0.002 0.001 HIS B 101 PHE 0.034 0.002 PHE C 71 TYR 0.015 0.001 TYR C 94 ARG 0.005 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8776 (t0) cc_final: 0.8381 (t0) REVERT: C 14 SER cc_start: 0.8799 (p) cc_final: 0.8581 (m) REVERT: C 70 GLU cc_start: 0.8629 (tt0) cc_final: 0.8098 (tm-30) REVERT: C 140 TYR cc_start: 0.7062 (t80) cc_final: 0.6441 (t80) REVERT: C 145 LYS cc_start: 0.9059 (tppt) cc_final: 0.8784 (tppt) REVERT: C 194 CYS cc_start: 0.0324 (p) cc_final: -0.0064 (p) REVERT: A 389 ASP cc_start: 0.9311 (p0) cc_final: 0.8924 (p0) REVERT: A 392 PHE cc_start: 0.8380 (m-80) cc_final: 0.7918 (m-80) REVERT: D 529 LYS cc_start: 0.7067 (mmpt) cc_final: 0.6517 (tttm) REVERT: F 10 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7395 (mm-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2658 time to fit residues: 42.1872 Evaluate side-chains 85 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10189 Z= 0.199 Angle : 0.608 9.848 13857 Z= 0.310 Chirality : 0.045 0.286 1540 Planarity : 0.004 0.035 1780 Dihedral : 5.762 57.519 1497 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.44 % Favored : 94.32 % Rotamer: Outliers : 0.09 % Allowed : 2.36 % Favored : 97.55 % 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: -0.36 (0.24), residues: 1268 helix: -2.28 (0.58), residues: 61 sheet: 0.68 (0.24), residues: 476 loop : -0.67 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 436 HIS 0.002 0.001 HIS E 199 PHE 0.030 0.002 PHE C 71 TYR 0.015 0.001 TYR E 33 ARG 0.004 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8781 (p0) cc_final: 0.8547 (p0) REVERT: B 99 ASP cc_start: 0.8820 (t0) cc_final: 0.8418 (t0) REVERT: C 14 SER cc_start: 0.8815 (p) cc_final: 0.8589 (m) REVERT: C 70 GLU cc_start: 0.8528 (tt0) cc_final: 0.8111 (tm-30) REVERT: C 140 TYR cc_start: 0.7058 (t80) cc_final: 0.6429 (t80) REVERT: C 145 LYS cc_start: 0.9087 (tppt) cc_final: 0.8776 (tppt) REVERT: C 194 CYS cc_start: 0.0321 (p) cc_final: -0.0055 (p) REVERT: A 389 ASP cc_start: 0.9317 (p0) cc_final: 0.8934 (p0) REVERT: A 392 PHE cc_start: 0.8310 (m-80) cc_final: 0.7786 (m-80) REVERT: D 498 ARG cc_start: 0.5313 (ttm170) cc_final: 0.4916 (ttp-170) REVERT: D 529 LYS cc_start: 0.7136 (mmpt) cc_final: 0.6594 (tttm) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.2325 time to fit residues: 38.2841 Evaluate side-chains 81 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 76 optimal weight: 0.2980 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN D 487 ASN E 91 GLN F 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10189 Z= 0.420 Angle : 0.773 9.413 13857 Z= 0.403 Chirality : 0.049 0.317 1540 Planarity : 0.005 0.044 1780 Dihedral : 6.506 59.323 1497 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.26 % Favored : 92.51 % Rotamer: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % 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: -0.99 (0.23), residues: 1268 helix: -2.72 (0.50), residues: 73 sheet: 0.19 (0.23), residues: 482 loop : -1.01 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 436 HIS 0.009 0.002 HIS E 199 PHE 0.034 0.003 PHE C 71 TYR 0.021 0.003 TYR C 87 ARG 0.005 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8918 (t0) cc_final: 0.8506 (t0) REVERT: C 14 SER cc_start: 0.8861 (p) cc_final: 0.8633 (m) REVERT: C 70 GLU cc_start: 0.8716 (tt0) cc_final: 0.8094 (tm-30) REVERT: C 81 GLU cc_start: 0.8575 (pp20) cc_final: 0.8350 (pm20) REVERT: C 140 TYR cc_start: 0.7317 (t80) cc_final: 0.6604 (t80) REVERT: C 145 LYS cc_start: 0.9149 (tppt) cc_final: 0.8834 (tppt) REVERT: C 194 CYS cc_start: 0.0556 (p) cc_final: 0.0270 (p) REVERT: A 389 ASP cc_start: 0.9367 (p0) cc_final: 0.9062 (p0) REVERT: A 392 PHE cc_start: 0.8284 (m-80) cc_final: 0.7765 (m-80) REVERT: A 414 GLN cc_start: 0.6887 (tm-30) cc_final: 0.6235 (tm-30) REVERT: D 498 ARG cc_start: 0.5592 (ttm170) cc_final: 0.5088 (ttp-170) REVERT: D 529 LYS cc_start: 0.7281 (mmpt) cc_final: 0.6624 (tttm) REVERT: F 10 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7401 (mm-30) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.2533 time to fit residues: 34.8628 Evaluate side-chains 78 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN D 409 GLN F 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10189 Z= 0.169 Angle : 0.645 10.770 13857 Z= 0.329 Chirality : 0.046 0.266 1540 Planarity : 0.004 0.037 1780 Dihedral : 5.899 58.470 1497 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.73 % Favored : 95.03 % Rotamer: Outliers : 0.09 % Allowed : 0.45 % Favored : 99.46 % 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: -0.65 (0.24), residues: 1268 helix: -2.53 (0.56), residues: 61 sheet: 0.48 (0.24), residues: 471 loop : -0.86 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 436 HIS 0.003 0.001 HIS B 101 PHE 0.024 0.001 PHE C 71 TYR 0.020 0.001 TYR E 33 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8777 (p0) cc_final: 0.8547 (p0) REVERT: B 99 ASP cc_start: 0.8761 (t0) cc_final: 0.8381 (t0) REVERT: B 222 ARG cc_start: 0.6881 (mmm-85) cc_final: 0.6341 (mmm-85) REVERT: C 14 SER cc_start: 0.8764 (p) cc_final: 0.8496 (m) REVERT: C 70 GLU cc_start: 0.8664 (tt0) cc_final: 0.8254 (tm-30) REVERT: C 82 ASP cc_start: 0.8724 (m-30) cc_final: 0.7875 (m-30) REVERT: C 140 TYR cc_start: 0.7230 (t80) cc_final: 0.6565 (t80) REVERT: C 145 LYS cc_start: 0.9128 (tppt) cc_final: 0.8796 (tppt) REVERT: C 194 CYS cc_start: 0.0167 (p) cc_final: -0.0169 (p) REVERT: A 389 ASP cc_start: 0.9289 (p0) cc_final: 0.8941 (p0) REVERT: A 392 PHE cc_start: 0.8283 (m-80) cc_final: 0.7745 (m-80) REVERT: D 529 LYS cc_start: 0.7228 (mmpt) cc_final: 0.6580 (tttm) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2815 time to fit residues: 49.2243 Evaluate side-chains 87 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 119 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10189 Z= 0.194 Angle : 0.626 8.982 13857 Z= 0.318 Chirality : 0.045 0.245 1540 Planarity : 0.004 0.035 1780 Dihedral : 5.699 58.751 1497 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.44 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.65 (0.24), residues: 1268 helix: -2.41 (0.57), residues: 61 sheet: 0.48 (0.24), residues: 472 loop : -0.87 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 436 HIS 0.003 0.001 HIS B 101 PHE 0.024 0.001 PHE C 71 TYR 0.014 0.001 TYR D 351 ARG 0.005 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8837 (p0) cc_final: 0.8564 (p0) REVERT: B 99 ASP cc_start: 0.8809 (t0) cc_final: 0.8414 (t0) REVERT: B 222 ARG cc_start: 0.6990 (mmm-85) cc_final: 0.6743 (mmm-85) REVERT: C 14 SER cc_start: 0.8781 (p) cc_final: 0.8533 (m) REVERT: C 70 GLU cc_start: 0.8663 (tt0) cc_final: 0.8247 (tm-30) REVERT: C 82 ASP cc_start: 0.8563 (m-30) cc_final: 0.7765 (m-30) REVERT: C 140 TYR cc_start: 0.7345 (t80) cc_final: 0.6686 (t80) REVERT: C 145 LYS cc_start: 0.9114 (tppt) cc_final: 0.8862 (tppt) REVERT: C 194 CYS cc_start: 0.0253 (p) cc_final: -0.0075 (p) REVERT: A 389 ASP cc_start: 0.9286 (p0) cc_final: 0.8937 (p0) REVERT: A 392 PHE cc_start: 0.8314 (m-80) cc_final: 0.7764 (m-80) REVERT: A 406 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9053 (mm-30) REVERT: D 529 LYS cc_start: 0.7245 (mmpt) cc_final: 0.6592 (tttm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2366 time to fit residues: 36.9685 Evaluate side-chains 88 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10189 Z= 0.375 Angle : 0.752 10.144 13857 Z= 0.389 Chirality : 0.048 0.270 1540 Planarity : 0.005 0.037 1780 Dihedral : 6.316 59.426 1497 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.33 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.08 (0.23), residues: 1268 helix: -2.64 (0.54), residues: 67 sheet: 0.17 (0.24), residues: 475 loop : -1.15 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 436 HIS 0.007 0.002 HIS E 199 PHE 0.031 0.003 PHE C 71 TYR 0.028 0.002 TYR B 94 ARG 0.005 0.001 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8911 (t0) cc_final: 0.8508 (t0) REVERT: C 70 GLU cc_start: 0.8699 (tt0) cc_final: 0.8116 (tm-30) REVERT: C 94 TYR cc_start: 0.8084 (t80) cc_final: 0.7728 (t80) REVERT: C 140 TYR cc_start: 0.7372 (t80) cc_final: 0.6690 (t80) REVERT: C 145 LYS cc_start: 0.9151 (tppt) cc_final: 0.8829 (tppt) REVERT: C 194 CYS cc_start: 0.0580 (p) cc_final: 0.0290 (p) REVERT: A 389 ASP cc_start: 0.9373 (p0) cc_final: 0.9057 (p0) REVERT: A 392 PHE cc_start: 0.8068 (m-80) cc_final: 0.7529 (m-80) REVERT: D 473 TYR cc_start: 0.8029 (t80) cc_final: 0.7712 (t80) REVERT: D 529 LYS cc_start: 0.7304 (mmpt) cc_final: 0.6641 (tttm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2436 time to fit residues: 34.8354 Evaluate side-chains 76 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 0.0020 chunk 14 optimal weight: 8.9990 chunk 27 optimal weight: 0.0770 chunk 100 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.116348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.097815 restraints weight = 35219.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.098683 restraints weight = 33947.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.099223 restraints weight = 27769.095| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10189 Z= 0.159 Angle : 0.633 8.145 13857 Z= 0.319 Chirality : 0.045 0.208 1540 Planarity : 0.004 0.036 1780 Dihedral : 5.627 55.538 1497 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -0.79 (0.24), residues: 1268 helix: -2.58 (0.53), residues: 67 sheet: 0.38 (0.24), residues: 472 loop : -0.94 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 436 HIS 0.003 0.001 HIS B 212 PHE 0.023 0.001 PHE C 71 TYR 0.015 0.001 TYR E 33 ARG 0.004 0.001 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1942.91 seconds wall clock time: 35 minutes 44.10 seconds (2144.10 seconds total)