Starting phenix.real_space_refine on Wed Feb 14 18:22:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtj_14142/02_2024/7qtj_14142.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtj_14142/02_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_14142/02_2024/7qtj_14142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtj_14142/02_2024/7qtj_14142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtj_14142/02_2024/7qtj_14142.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtj_14142/02_2024/7qtj_14142.pdb" } 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 Residue "B GLU 62": "OE1" <-> "OE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.08, per 1000 atoms: 0.61 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 - 3.50 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 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: 4.13 Conformation dependent library (CDL) restraints added in 2.0 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: 1.25 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: 3.14 Time building geometry restraints manager: 4.41 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: 90.73 - 99.43: 4 99.43 - 108.12: 452 108.12 - 116.81: 6861 116.81 - 125.50: 6370 125.50 - 134.19: 170 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 2.440 nonbonded pdb=" O PRO B 197 " pdb=" OG SER B 200 " model vdw 2.305 2.440 nonbonded pdb=" NH1 ARG D 403 " pdb=" O GLY D 504 " model vdw 2.310 2.520 nonbonded pdb=" OE2 GLU B 6 " pdb=" N GLY B 118 " model vdw 2.315 2.520 ... (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 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: 1.880 Set stop_for_unknowns flag: 0.010 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: 7.300 Check model and map are aligned: 0.190 Set scattering table: 0.090 Process input model: 31.130 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.780 ------------------------------------------------------------------------------- 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 : 1.307 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: 0.2422 time to fit residues: 43.2666 Evaluate side-chains 85 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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: 0.0170 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.0570 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 0.2980 chunk 60 optimal weight: 0.0980 chunk 73 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10189 Z= 0.138 Angle : 0.575 14.076 13857 Z= 0.287 Chirality : 0.044 0.336 1540 Planarity : 0.003 0.049 1780 Dihedral : 8.198 80.546 1497 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer: Outliers : 0.18 % Allowed : 4.26 % Favored : 95.55 % 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: 0.29 (0.25), residues: 1268 helix: -2.18 (0.54), residues: 60 sheet: 1.37 (0.25), residues: 451 loop : -0.33 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 53 HIS 0.002 0.000 HIS B 101 PHE 0.016 0.001 PHE D 429 TYR 0.014 0.001 TYR B 102 ARG 0.003 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 126 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8576 (p0) cc_final: 0.8257 (p0) REVERT: C 170 ASP cc_start: 0.7478 (p0) cc_final: 0.6484 (p0) REVERT: A 392 PHE cc_start: 0.8329 (m-80) cc_final: 0.7982 (m-80) REVERT: D 375 PHE cc_start: 0.5909 (m-10) cc_final: 0.5535 (m-80) outliers start: 2 outliers final: 0 residues processed: 126 average time/residue: 0.2385 time to fit residues: 41.6943 Evaluate side-chains 82 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.0040 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10189 Z= 0.133 Angle : 0.550 10.549 13857 Z= 0.274 Chirality : 0.044 0.236 1540 Planarity : 0.003 0.030 1780 Dihedral : 6.688 69.801 1497 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.50 % Favored : 95.27 % Rotamer: Outliers : 0.27 % Allowed : 2.90 % Favored : 96.82 % 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: 0.20 (0.25), residues: 1268 helix: -2.36 (0.53), residues: 66 sheet: 1.29 (0.24), residues: 459 loop : -0.36 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 53 HIS 0.002 0.000 HIS B 35 PHE 0.017 0.001 PHE F 29 TYR 0.013 0.001 TYR B 102 ARG 0.002 0.000 ARG F 72 *********************** 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 120 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8657 (p0) cc_final: 0.8299 (p0) REVERT: A 389 ASP cc_start: 0.9361 (p0) cc_final: 0.8732 (p0) REVERT: D 375 PHE cc_start: 0.5700 (m-10) cc_final: 0.5336 (m-80) outliers start: 3 outliers final: 3 residues processed: 119 average time/residue: 0.2332 time to fit residues: 38.4856 Evaluate side-chains 88 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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: 4.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN C 138 ASN ** 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** D 460 ASN D 487 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10189 Z= 0.249 Angle : 0.626 10.014 13857 Z= 0.319 Chirality : 0.045 0.280 1540 Planarity : 0.004 0.033 1780 Dihedral : 5.891 56.387 1497 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.52 % Favored : 94.24 % Rotamer: Outliers : 0.09 % Allowed : 5.35 % 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: -0.02 (0.24), residues: 1268 helix: -2.25 (0.59), residues: 54 sheet: 0.96 (0.24), residues: 480 loop : -0.49 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 53 HIS 0.005 0.001 HIS E 199 PHE 0.017 0.002 PHE D 429 TYR 0.016 0.002 TYR B 102 ARG 0.005 0.001 ARG D 493 *********************** 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 116 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 GLU cc_start: 0.7877 (tp30) cc_final: 0.7651 (tp30) REVERT: C 194 CYS cc_start: 0.0593 (p) cc_final: 0.0072 (p) REVERT: A 349 SER cc_start: 0.8978 (m) cc_final: 0.8770 (p) REVERT: A 389 ASP cc_start: 0.9352 (p0) cc_final: 0.8831 (p0) REVERT: A 405 ASP cc_start: 0.7882 (m-30) cc_final: 0.7660 (p0) REVERT: A 406 GLU cc_start: 0.8981 (mp0) cc_final: 0.8557 (mm-30) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.2565 time to fit residues: 40.7276 Evaluate side-chains 76 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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: 9.9990 chunk 69 optimal weight: 10.0000 chunk 1 optimal weight: 0.0670 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 84 optimal weight: 0.0370 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- 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** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10189 Z= 0.162 Angle : 0.586 10.743 13857 Z= 0.294 Chirality : 0.044 0.269 1540 Planarity : 0.004 0.032 1780 Dihedral : 5.616 59.934 1497 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.73 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -0.03 (0.24), residues: 1268 helix: -2.28 (0.57), residues: 55 sheet: 0.95 (0.24), residues: 480 loop : -0.49 (0.24), residues: 733 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 0.017 0.001 PHE D 429 TYR 0.014 0.001 TYR B 102 ARG 0.004 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 126 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 GLU cc_start: 0.7870 (tp30) cc_final: 0.7635 (tp30) REVERT: C 140 TYR cc_start: 0.6813 (t80) cc_final: 0.6571 (t80) REVERT: A 389 ASP cc_start: 0.9347 (p0) cc_final: 0.8796 (p0) REVERT: D 529 LYS cc_start: 0.6800 (mmpt) cc_final: 0.6584 (tttm) REVERT: F 2 MET cc_start: 0.6021 (mpp) cc_final: 0.5539 (mpp) REVERT: F 155 TYR cc_start: 0.7491 (p90) cc_final: 0.7189 (p90) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2482 time to fit residues: 42.7016 Evaluate side-chains 79 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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: 5.9990 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 121 optimal weight: 0.0870 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 0.0270 chunk 117 optimal weight: 0.0060 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10189 Z= 0.127 Angle : 0.561 10.009 13857 Z= 0.279 Chirality : 0.043 0.248 1540 Planarity : 0.003 0.036 1780 Dihedral : 5.279 59.729 1497 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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 (0.25), residues: 1268 helix: -2.23 (0.57), residues: 55 sheet: 1.06 (0.24), residues: 481 loop : -0.47 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.002 0.001 HIS B 101 PHE 0.015 0.001 PHE D 429 TYR 0.014 0.001 TYR D 501 ARG 0.004 0.000 ARG C 61 *********************** 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 118 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8627 (t0) cc_final: 0.8216 (t0) REVERT: C 107 GLU cc_start: 0.7817 (tp30) cc_final: 0.7613 (tp30) REVERT: C 140 TYR cc_start: 0.6824 (t80) cc_final: 0.6575 (t80) REVERT: C 194 CYS cc_start: 0.1097 (p) cc_final: 0.0141 (p) REVERT: A 389 ASP cc_start: 0.9330 (p0) cc_final: 0.8749 (p0) REVERT: D 529 LYS cc_start: 0.6802 (mmpt) cc_final: 0.6582 (tttm) REVERT: F 2 MET cc_start: 0.5749 (mpp) cc_final: 0.5243 (mpp) REVERT: F 155 TYR cc_start: 0.7340 (p90) cc_final: 0.7036 (p90) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2347 time to fit residues: 38.8282 Evaluate side-chains 78 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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: 20.0000 chunk 69 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN F 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10189 Z= 0.457 Angle : 0.776 9.951 13857 Z= 0.404 Chirality : 0.048 0.297 1540 Planarity : 0.005 0.044 1780 Dihedral : 6.074 58.561 1497 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.18 % Favored : 92.51 % Rotamer: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), residues: 1268 helix: -2.44 (0.54), residues: 67 sheet: 0.42 (0.24), residues: 481 loop : -0.89 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 353 HIS 0.010 0.002 HIS B 212 PHE 0.024 0.003 PHE B 158 TYR 0.028 0.003 TYR E 87 ARG 0.007 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 101 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.9045 (t0) cc_final: 0.8572 (t0) REVERT: C 134 CYS cc_start: 0.3847 (t) cc_final: 0.3575 (t) REVERT: A 389 ASP cc_start: 0.9421 (p0) cc_final: 0.8974 (p0) REVERT: A 405 ASP cc_start: 0.8097 (m-30) cc_final: 0.7615 (p0) REVERT: D 529 LYS cc_start: 0.6994 (mmpt) cc_final: 0.6754 (ttpp) REVERT: F 10 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7335 (mm-30) REVERT: F 155 TYR cc_start: 0.7625 (p90) cc_final: 0.7279 (p90) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.2650 time to fit residues: 36.4784 Evaluate side-chains 73 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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: 9.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10189 Z= 0.161 Angle : 0.616 11.158 13857 Z= 0.312 Chirality : 0.044 0.300 1540 Planarity : 0.004 0.034 1780 Dihedral : 5.606 57.543 1497 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -0.33 (0.24), residues: 1268 helix: -2.27 (0.59), residues: 55 sheet: 0.73 (0.25), residues: 464 loop : -0.67 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS B 212 PHE 0.034 0.002 PHE C 71 TYR 0.013 0.001 TYR F 95 ARG 0.005 0.000 ARG D 355 *********************** 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 119 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8849 (t0) cc_final: 0.8377 (t0) REVERT: C 70 GLU cc_start: 0.8810 (tt0) cc_final: 0.8378 (tm-30) REVERT: C 194 CYS cc_start: 0.0726 (p) cc_final: 0.0116 (p) REVERT: A 389 ASP cc_start: 0.9436 (p0) cc_final: 0.9060 (p0) REVERT: D 529 LYS cc_start: 0.6945 (mmpt) cc_final: 0.6744 (tttm) REVERT: F 2 MET cc_start: 0.6504 (mpp) cc_final: 0.6051 (mpp) REVERT: F 155 TYR cc_start: 0.7583 (p90) cc_final: 0.7135 (p90) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2493 time to fit residues: 40.7941 Evaluate side-chains 80 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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: 5.9990 chunk 116 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 0.0040 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 74 optimal weight: 30.0000 chunk 119 optimal weight: 5.9990 overall best weight: 4.2000 ------------------------------------------------------------------------------- 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** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10189 Z= 0.399 Angle : 0.765 10.121 13857 Z= 0.396 Chirality : 0.048 0.283 1540 Planarity : 0.005 0.040 1780 Dihedral : 6.188 59.426 1497 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.97 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -0.97 (0.24), residues: 1268 helix: -2.56 (0.54), residues: 67 sheet: 0.22 (0.24), residues: 477 loop : -1.04 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP F 50 HIS 0.008 0.002 HIS B 212 PHE 0.045 0.003 PHE C 71 TYR 0.028 0.003 TYR C 94 ARG 0.007 0.001 ARG D 498 *********************** 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 99 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.9070 (t0) cc_final: 0.8607 (t0) REVERT: C 70 GLU cc_start: 0.8728 (tt0) cc_final: 0.8247 (tm-30) REVERT: C 194 CYS cc_start: 0.0926 (p) cc_final: 0.0213 (p) REVERT: A 389 ASP cc_start: 0.9458 (p0) cc_final: 0.9158 (p0) REVERT: D 415 THR cc_start: 0.7807 (t) cc_final: 0.7475 (t) REVERT: D 467 ASP cc_start: 0.6945 (p0) cc_final: 0.6684 (p0) REVERT: D 473 TYR cc_start: 0.8044 (t80) cc_final: 0.7827 (t80) REVERT: D 529 LYS cc_start: 0.7186 (mmpt) cc_final: 0.6815 (tttm) REVERT: F 10 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7387 (mm-30) REVERT: F 155 TYR cc_start: 0.7786 (p90) cc_final: 0.7374 (p90) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2466 time to fit residues: 34.2360 Evaluate side-chains 76 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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: 7.9990 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.0070 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.3604 ------------------------------------------------------------------------------- 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** ** E 91 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: 0.7557 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10189 Z= 0.250 Angle : 0.665 9.294 13857 Z= 0.340 Chirality : 0.045 0.252 1540 Planarity : 0.004 0.040 1780 Dihedral : 5.990 58.683 1497 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.68 % Favored : 94.09 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % 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: -0.93 (0.24), residues: 1268 helix: -2.46 (0.57), residues: 61 sheet: 0.23 (0.24), residues: 480 loop : -1.04 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 50 HIS 0.002 0.001 HIS E 199 PHE 0.034 0.002 PHE C 71 TYR 0.017 0.002 TYR B 102 ARG 0.004 0.000 ARG A 346 ********************** 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 108 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8912 (t0) cc_final: 0.8379 (t0) REVERT: C 70 GLU cc_start: 0.8603 (tt0) cc_final: 0.8267 (tm-30) REVERT: C 194 CYS cc_start: 0.0928 (p) cc_final: 0.0244 (p) REVERT: A 389 ASP cc_start: 0.9448 (p0) cc_final: 0.9132 (p0) REVERT: D 375 PHE cc_start: 0.4963 (m-80) cc_final: 0.4659 (m-80) REVERT: D 415 THR cc_start: 0.7802 (t) cc_final: 0.7477 (t) REVERT: D 529 LYS cc_start: 0.7183 (mmpt) cc_final: 0.6809 (tttm) REVERT: F 2 MET cc_start: 0.6335 (mpp) cc_final: 0.5826 (mpp) REVERT: F 155 TYR cc_start: 0.7791 (p90) cc_final: 0.7299 (p90) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.2469 time to fit residues: 36.7558 Evaluate side-chains 76 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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: 4.9990 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.112000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.094463 restraints weight = 35791.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.095341 restraints weight = 43908.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.095880 restraints weight = 36915.421| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10189 Z= 0.401 Angle : 0.777 11.440 13857 Z= 0.401 Chirality : 0.048 0.261 1540 Planarity : 0.005 0.043 1780 Dihedral : 6.433 59.980 1497 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.12 % Favored : 91.64 % Rotamer: Outliers : 0.09 % Allowed : 0.54 % Favored : 99.36 % 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: -1.35 (0.23), residues: 1268 helix: -2.63 (0.55), residues: 67 sheet: -0.10 (0.24), residues: 483 loop : -1.29 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP F 50 HIS 0.007 0.002 HIS E 199 PHE 0.039 0.002 PHE C 71 TYR 0.030 0.002 TYR C 94 ARG 0.006 0.001 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1968.66 seconds wall clock time: 37 minutes 17.45 seconds (2237.45 seconds total)