Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 08:24:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/07_2023/7k25_22643.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/07_2023/7k25_22643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/07_2023/7k25_22643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/07_2023/7k25_22643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/07_2023/7k25_22643.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/07_2023/7k25_22643.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 1.000 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 79 5.16 5 C 8863 2.51 5 N 2352 2.21 5 O 2711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 328": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E GLU 326": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 14005 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2854 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 31, 'TRANS': 334} Chain: "B" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 31, 'TRANS': 335} Chain: "C" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2789 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 30, 'TRANS': 326} Chain: "D" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2650 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 27, 'TRANS': 312} Chain: "E" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2850 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 334} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 6.68, per 1000 atoms: 0.48 Number of scatterers: 14005 At special positions: 0 Unit cell: (167.2, 163.9, 94.6, 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 79 16.00 O 2711 8.00 N 2352 7.00 C 8863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS E 3 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS C 98 " distance=2.04 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS E 98 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.82 Conformation dependent library (CDL) restraints added in 2.0 seconds 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3272 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 32 sheets defined 11.5% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.524A pdb=" N LEU B 23 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.630A pdb=" N LEU B 79 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 304 through 315 removed outlier: 3.514A pdb=" N LEU B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 115 through 121 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.954A pdb=" N LEU C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 75 through 79 Processing helix chain 'D' and resid 115 through 121 Processing helix chain 'D' and resid 176 through 181 removed outlier: 3.547A pdb=" N ILE D 180 " --> pdb=" O THR D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 75 through 79 Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 186 through 191 Processing helix chain 'E' and resid 304 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.458A pdb=" N TYR A 289 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A 111 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS A 291 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 109 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 293 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.458A pdb=" N TYR A 289 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A 111 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS A 291 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 109 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 293 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TRP A 104 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 88 removed outlier: 6.465A pdb=" N ARG A 284 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TRP A 272 " --> pdb=" O HIS A 282 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS A 282 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.203A pdb=" N ILE A 137 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 199 Processing sheet with id=AA7, first strand: chain 'A' and resid 236 through 240 Processing sheet with id=AA8, first strand: chain 'A' and resid 236 through 240 removed outlier: 6.585A pdb=" N ARG B 284 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TRP B 272 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS B 282 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AB1, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.491A pdb=" N TYR B 289 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 111 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS B 291 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 109 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR B 293 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.491A pdb=" N TYR B 289 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 111 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS B 291 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 109 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR B 293 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 128 through 130 removed outlier: 6.309A pdb=" N ILE B 137 " --> pdb=" O PRO B 128 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 197 through 198 Processing sheet with id=AB5, first strand: chain 'B' and resid 236 through 240 Processing sheet with id=AB6, first strand: chain 'B' and resid 236 through 240 removed outlier: 4.056A pdb=" N GLY C 271 " --> pdb=" O ARG C 284 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 352 through 355 removed outlier: 4.029A pdb=" N GLY B 358 " --> pdb=" O ASP B 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 31 through 37 removed outlier: 6.509A pdb=" N TYR C 289 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR C 111 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS C 291 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL C 109 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR C 293 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 31 through 37 removed outlier: 6.509A pdb=" N TYR C 289 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR C 111 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS C 291 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL C 109 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR C 293 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP C 104 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 130 removed outlier: 6.229A pdb=" N ILE C 137 " --> pdb=" O PRO C 128 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 197 through 199 Processing sheet with id=AC3, first strand: chain 'C' and resid 236 through 240 Processing sheet with id=AC4, first strand: chain 'C' and resid 236 through 240 removed outlier: 6.677A pdb=" N ARG D 284 " --> pdb=" O MET D 270 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 31 through 37 removed outlier: 6.520A pdb=" N TYR D 289 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR D 111 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS D 291 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL D 109 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR D 293 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 31 through 37 removed outlier: 6.520A pdb=" N TYR D 289 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR D 111 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS D 291 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL D 109 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR D 293 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 128 through 130 removed outlier: 6.482A pdb=" N ILE D 137 " --> pdb=" O PRO D 128 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 197 through 200 removed outlier: 4.192A pdb=" N LEU D 156 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 236 through 240 Processing sheet with id=AD1, first strand: chain 'D' and resid 236 through 240 removed outlier: 6.697A pdb=" N ARG E 284 " --> pdb=" O MET E 270 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TRP E 272 " --> pdb=" O HIS E 282 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N HIS E 282 " --> pdb=" O TRP E 272 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 31 through 37 removed outlier: 3.729A pdb=" N SER E 108 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG E 295 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ALA E 106 " --> pdb=" O ARG E 295 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG E 297 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TRP E 104 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL E 299 " --> pdb=" O GLN E 102 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN E 102 " --> pdb=" O VAL E 299 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 128 through 130 removed outlier: 6.185A pdb=" N ILE E 137 " --> pdb=" O PRO E 128 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 197 through 199 Processing sheet with id=AD5, first strand: chain 'E' and resid 351 through 354 removed outlier: 3.934A pdb=" N THR E 351 " --> pdb=" O THR E 362 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR E 353 " --> pdb=" O THR E 360 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1224 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: 4.15 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2398 1.30 - 1.43: 3570 1.43 - 1.57: 8245 1.57 - 1.70: 0 1.70 - 1.83: 138 Bond restraints: 14351 Sorted by residual: bond pdb=" C GLY D 322 " pdb=" O GLY D 322 " ideal model delta sigma weight residual 1.232 1.169 0.064 1.43e-02 4.89e+03 1.98e+01 bond pdb=" N LEU E 96 " pdb=" CA LEU E 96 " ideal model delta sigma weight residual 1.457 1.512 -0.054 1.29e-02 6.01e+03 1.76e+01 bond pdb=" CA THR E 97 " pdb=" C THR E 97 " ideal model delta sigma weight residual 1.521 1.557 -0.036 1.28e-02 6.10e+03 8.05e+00 bond pdb=" C PRO B 213 " pdb=" N ASP B 214 " ideal model delta sigma weight residual 1.331 1.295 0.037 1.63e-02 3.76e+03 5.06e+00 bond pdb=" N THR E 97 " pdb=" CA THR E 97 " ideal model delta sigma weight residual 1.455 1.483 -0.027 1.23e-02 6.61e+03 4.92e+00 ... (remaining 14346 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.29: 466 105.29 - 112.48: 7403 112.48 - 119.66: 4699 119.66 - 126.85: 6746 126.85 - 134.03: 255 Bond angle restraints: 19569 Sorted by residual: angle pdb=" C THR E 100 " pdb=" N LEU E 101 " pdb=" CA LEU E 101 " ideal model delta sigma weight residual 122.15 132.39 -10.24 1.74e+00 3.30e-01 3.46e+01 angle pdb=" N GLY D 322 " pdb=" CA GLY D 322 " pdb=" C GLY D 322 " ideal model delta sigma weight residual 112.61 121.47 -8.86 1.60e+00 3.91e-01 3.07e+01 angle pdb=" C PRO C 213 " pdb=" N ASP C 214 " pdb=" CA ASP C 214 " ideal model delta sigma weight residual 121.20 128.16 -6.96 1.40e+00 5.10e-01 2.47e+01 angle pdb=" C CYS E 3 " pdb=" N PRO E 4 " pdb=" CA PRO E 4 " ideal model delta sigma weight residual 119.76 124.66 -4.90 1.03e+00 9.43e-01 2.26e+01 angle pdb=" CA GLY D 54 " pdb=" C GLY D 54 " pdb=" N GLN D 55 " ideal model delta sigma weight residual 118.79 113.25 5.54 1.21e+00 6.83e-01 2.09e+01 ... (remaining 19564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 7433 18.01 - 36.02: 891 36.02 - 54.03: 273 54.03 - 72.05: 56 72.05 - 90.06: 21 Dihedral angle restraints: 8674 sinusoidal: 3547 harmonic: 5127 Sorted by residual: dihedral pdb=" CB CYS D 3 " pdb=" SG CYS D 3 " pdb=" SG CYS E 98 " pdb=" CB CYS E 98 " ideal model delta sinusoidal sigma weight residual -86.00 -8.43 -77.57 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS A 98 " pdb=" SG CYS A 98 " pdb=" SG CYS E 3 " pdb=" CB CYS E 3 " ideal model delta sinusoidal sigma weight residual 93.00 154.60 -61.60 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS B 98 " pdb=" CB CYS B 98 " ideal model delta sinusoidal sigma weight residual 93.00 146.33 -53.33 1 1.00e+01 1.00e-02 3.87e+01 ... (remaining 8671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1659 0.061 - 0.122: 477 0.122 - 0.183: 42 0.183 - 0.243: 4 0.243 - 0.304: 4 Chirality restraints: 2186 Sorted by residual: chirality pdb=" CA GLN D 55 " pdb=" N GLN D 55 " pdb=" C GLN D 55 " pdb=" CB GLN D 55 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA GLN E 55 " pdb=" N GLN E 55 " pdb=" C GLN E 55 " pdb=" CB GLN E 55 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA GLN B 55 " pdb=" N GLN B 55 " pdb=" C GLN B 55 " pdb=" CB GLN B 55 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2183 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 95 " -0.026 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C ASP E 95 " 0.092 2.00e-02 2.50e+03 pdb=" O ASP E 95 " -0.035 2.00e-02 2.50e+03 pdb=" N LEU E 96 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 5 " -0.049 5.00e-02 4.00e+02 7.52e-02 9.06e+00 pdb=" N PRO E 6 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 6 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 6 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 73 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO E 74 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.039 5.00e-02 4.00e+02 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 306 2.65 - 3.21: 11802 3.21 - 3.77: 20774 3.77 - 4.34: 30341 4.34 - 4.90: 49658 Nonbonded interactions: 112881 Sorted by model distance: nonbonded pdb=" OE1 GLU B 154 " pdb=" NZ LYS B 258 " model vdw 2.084 2.520 nonbonded pdb=" O LYS C 127 " pdb=" OG1 THR C 139 " model vdw 2.139 2.440 nonbonded pdb=" O GLY A 115 " pdb=" OG SER A 118 " model vdw 2.165 2.440 nonbonded pdb=" OE1 GLN D 159 " pdb=" NZ LYS D 197 " model vdw 2.201 2.520 nonbonded pdb=" OG1 THR D 240 " pdb=" OG1 THR D 242 " model vdw 2.214 2.440 ... (remaining 112876 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' and (resid 2 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 340)) selection = (chain 'B' and (resid 2 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 340)) selection = (chain 'C' and (resid 2 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 340)) selection = (chain 'D' and (resid 2 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 340)) selection = (chain 'E' and resid 2 through 340) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.040 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 34.650 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.009 0.093 14351 Z= 0.599 Angle : 0.942 10.241 19569 Z= 0.533 Chirality : 0.055 0.304 2186 Planarity : 0.007 0.075 2552 Dihedral : 17.781 90.058 5387 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.90 % Favored : 90.65 % Rotamer Outliers : 9.18 % 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: -3.19 (0.17), residues: 1786 helix: -3.41 (0.30), residues: 114 sheet: -0.77 (0.23), residues: 411 loop : -2.66 (0.15), residues: 1261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 275 time to evaluate : 1.674 Fit side-chains outliers start: 145 outliers final: 83 residues processed: 384 average time/residue: 1.1546 time to fit residues: 487.6175 Evaluate side-chains 320 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 237 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 67 residues processed: 16 average time/residue: 0.6546 time to fit residues: 14.4899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 0.0270 chunk 45 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 160 optimal weight: 0.9980 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 ASN A 102 GLN A 126 ASN A 147 HIS ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN B 102 GLN B 123 HIS B 126 ASN B 147 HIS B 190 GLN B 282 HIS B 323 GLN B 331 GLN C 38 ASN C 88 GLN C 126 ASN C 147 HIS C 190 GLN C 282 HIS C 314 ASN C 315 ASN C 323 GLN C 331 GLN D 55 GLN D 88 GLN D 147 HIS D 301 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 126 ASN E 147 HIS E 190 GLN E 277 ASN E 282 HIS E 314 ASN E 315 ASN E 323 GLN E 331 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 14351 Z= 0.238 Angle : 0.640 8.523 19569 Z= 0.331 Chirality : 0.045 0.168 2186 Planarity : 0.006 0.058 2552 Dihedral : 5.822 27.841 1923 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.67 % Rotamer Outliers : 8.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.18), residues: 1786 helix: -1.93 (0.46), residues: 100 sheet: -0.18 (0.25), residues: 402 loop : -2.06 (0.16), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 249 time to evaluate : 1.656 Fit side-chains outliers start: 142 outliers final: 79 residues processed: 357 average time/residue: 0.9982 time to fit residues: 397.8036 Evaluate side-chains 310 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 231 time to evaluate : 1.563 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 66 residues processed: 13 average time/residue: 0.3178 time to fit residues: 7.9299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 0.0980 chunk 49 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 109 optimal weight: 0.0000 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN C 315 ASN D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 14351 Z= 0.233 Angle : 0.619 7.566 19569 Z= 0.316 Chirality : 0.045 0.163 2186 Planarity : 0.005 0.053 2552 Dihedral : 5.518 27.052 1923 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 91.99 % Rotamer Outliers : 8.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.19), residues: 1786 helix: -1.45 (0.49), residues: 100 sheet: 0.13 (0.25), residues: 400 loop : -1.81 (0.17), residues: 1286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 233 time to evaluate : 1.649 Fit side-chains outliers start: 130 outliers final: 86 residues processed: 338 average time/residue: 0.9828 time to fit residues: 372.2246 Evaluate side-chains 309 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 223 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 74 residues processed: 12 average time/residue: 0.4912 time to fit residues: 9.4543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 171 optimal weight: 0.0670 chunk 84 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN B 238 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 14351 Z= 0.289 Angle : 0.644 7.878 19569 Z= 0.328 Chirality : 0.046 0.188 2186 Planarity : 0.005 0.051 2552 Dihedral : 5.554 26.626 1923 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 91.99 % Rotamer Outliers : 8.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.19), residues: 1786 helix: -1.15 (0.51), residues: 100 sheet: 0.22 (0.26), residues: 401 loop : -1.65 (0.17), residues: 1285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 228 time to evaluate : 1.649 Fit side-chains outliers start: 135 outliers final: 94 residues processed: 332 average time/residue: 1.0114 time to fit residues: 375.8740 Evaluate side-chains 317 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 223 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 80 residues processed: 14 average time/residue: 0.4920 time to fit residues: 10.5837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 0.2980 chunk 97 optimal weight: 0.0770 chunk 2 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 145 optimal weight: 0.0470 chunk 118 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 238 GLN B 282 HIS D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 14351 Z= 0.156 Angle : 0.542 6.630 19569 Z= 0.277 Chirality : 0.042 0.148 2186 Planarity : 0.005 0.041 2552 Dihedral : 4.902 26.225 1923 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.94 % Favored : 93.00 % Rotamer Outliers : 7.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1786 helix: -0.55 (0.55), residues: 93 sheet: 0.43 (0.26), residues: 401 loop : -1.40 (0.17), residues: 1292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 240 time to evaluate : 1.766 Fit side-chains outliers start: 118 outliers final: 73 residues processed: 335 average time/residue: 1.0000 time to fit residues: 374.9662 Evaluate side-chains 301 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 228 time to evaluate : 1.715 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 68 residues processed: 5 average time/residue: 0.4587 time to fit residues: 5.2083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 89 optimal weight: 0.3980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 301 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN D 55 GLN D 315 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14351 Z= 0.206 Angle : 0.569 6.491 19569 Z= 0.290 Chirality : 0.044 0.170 2186 Planarity : 0.005 0.040 2552 Dihedral : 5.004 23.985 1923 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.50 % Favored : 92.44 % Rotamer Outliers : 6.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1786 helix: -0.38 (0.56), residues: 93 sheet: 0.47 (0.26), residues: 404 loop : -1.30 (0.17), residues: 1289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 243 time to evaluate : 1.692 Fit side-chains outliers start: 106 outliers final: 78 residues processed: 329 average time/residue: 1.0369 time to fit residues: 379.6284 Evaluate side-chains 306 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 228 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 70 residues processed: 9 average time/residue: 0.5272 time to fit residues: 7.8539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 144 optimal weight: 0.0570 chunk 95 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 106 optimal weight: 0.1980 chunk 104 optimal weight: 0.0010 chunk 78 optimal weight: 7.9990 overall best weight: 0.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 238 GLN C 315 ASN D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 14351 Z= 0.152 Angle : 0.520 5.726 19569 Z= 0.267 Chirality : 0.042 0.145 2186 Planarity : 0.005 0.046 2552 Dihedral : 4.632 24.406 1923 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.39 % Rotamer Outliers : 5.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1786 helix: -0.51 (0.55), residues: 102 sheet: 0.52 (0.26), residues: 404 loop : -1.21 (0.18), residues: 1280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 239 time to evaluate : 1.696 Fit side-chains outliers start: 89 outliers final: 67 residues processed: 318 average time/residue: 1.0393 time to fit residues: 369.3121 Evaluate side-chains 286 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 219 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 64 residues processed: 3 average time/residue: 0.4804 time to fit residues: 3.8640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.0980 chunk 68 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 116 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 238 GLN C 315 ASN D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14351 Z= 0.225 Angle : 0.575 6.591 19569 Z= 0.294 Chirality : 0.044 0.187 2186 Planarity : 0.005 0.044 2552 Dihedral : 4.909 23.737 1923 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.61 % Rotamer Outliers : 5.57 % 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: -0.97 (0.20), residues: 1786 helix: -0.31 (0.57), residues: 94 sheet: 0.55 (0.26), residues: 402 loop : -1.14 (0.18), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 230 time to evaluate : 2.769 Fit side-chains outliers start: 88 outliers final: 74 residues processed: 306 average time/residue: 1.0815 time to fit residues: 368.6519 Evaluate side-chains 297 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 223 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 69 residues processed: 5 average time/residue: 1.0412 time to fit residues: 8.0415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 158 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 124 optimal weight: 7.9990 chunk 48 optimal weight: 0.1980 chunk 143 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 104 optimal weight: 0.0970 chunk 168 optimal weight: 4.9990 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 238 GLN C 102 GLN C 315 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 14351 Z= 0.148 Angle : 0.513 5.583 19569 Z= 0.263 Chirality : 0.041 0.144 2186 Planarity : 0.004 0.044 2552 Dihedral : 4.525 24.330 1923 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.44 % Favored : 93.51 % Rotamer Outliers : 5.13 % 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 (0.20), residues: 1786 helix: -0.65 (0.52), residues: 111 sheet: 0.51 (0.26), residues: 418 loop : -1.07 (0.18), residues: 1257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 224 time to evaluate : 1.638 Fit side-chains outliers start: 81 outliers final: 66 residues processed: 298 average time/residue: 1.0392 time to fit residues: 345.2090 Evaluate side-chains 278 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 212 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 65 residues processed: 1 average time/residue: 1.0932 time to fit residues: 3.4681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.0970 chunk 79 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 238 GLN C 226 ASN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14351 Z= 0.228 Angle : 0.571 6.299 19569 Z= 0.292 Chirality : 0.044 0.181 2186 Planarity : 0.005 0.050 2552 Dihedral : 4.857 22.798 1923 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.28 % Favored : 92.67 % Rotamer Outliers : 4.68 % 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: -0.91 (0.20), residues: 1786 helix: -0.72 (0.52), residues: 110 sheet: 0.63 (0.26), residues: 402 loop : -1.08 (0.18), residues: 1274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 217 time to evaluate : 1.551 Fit side-chains outliers start: 74 outliers final: 67 residues processed: 286 average time/residue: 1.0896 time to fit residues: 347.6911 Evaluate side-chains 282 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 215 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 65 residues processed: 2 average time/residue: 0.6769 time to fit residues: 3.9454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.0370 chunk 123 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 238 GLN C 93 ASN C 226 ASN C 315 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.144110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.116469 restraints weight = 14778.759| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.54 r_work: 0.2953 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 14351 Z= 0.350 Angle : 0.658 7.158 19569 Z= 0.337 Chirality : 0.047 0.212 2186 Planarity : 0.005 0.049 2552 Dihedral : 5.362 23.585 1923 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.01 % Favored : 91.88 % Rotamer Outliers : 5.44 % 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: -0.94 (0.20), residues: 1786 helix: -0.37 (0.56), residues: 94 sheet: 0.59 (0.26), residues: 402 loop : -1.13 (0.18), residues: 1290 =============================================================================== Job complete usr+sys time: 6024.29 seconds wall clock time: 107 minutes 16.17 seconds (6436.17 seconds total)