Starting phenix.real_space_refine on Tue Nov 14 16:58:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/11_2023/8jiu_36328_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/11_2023/8jiu_36328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/11_2023/8jiu_36328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/11_2023/8jiu_36328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/11_2023/8jiu_36328_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jiu_36328/11_2023/8jiu_36328_updated.pdb" } resolution = 2.76 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5767 2.51 5 N 1588 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "P GLU 15": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9075 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1875 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "P" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2548 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 420 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3018 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 127 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.35, per 1000 atoms: 0.59 Number of scatterers: 9075 At special positions: 0 Unit cell: (78.183, 100.674, 171.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1663 8.00 N 1588 7.00 C 5767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.01 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.04 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.04 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DSN P 2 " Number of C-beta restraints generated: 2204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 10 sheets defined 35.7% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 10 through 37 removed outlier: 3.863A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 299 through 302 No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'P' and resid 4 through 27 Processing helix chain 'B' and resid 4 through 24 removed outlier: 4.130A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'C' and resid 8 through 21 removed outlier: 3.662A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 30 through 47 removed outlier: 3.614A pdb=" N GLU R 34 " --> pdb=" O ASP R 30 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS R 35 " --> pdb=" O PHE R 31 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS R 44 " --> pdb=" O GLY R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 90 removed outlier: 4.312A pdb=" N HIS R 89 " --> pdb=" O PRO R 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS R 90 " --> pdb=" O TRP R 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 86 through 90' Processing helix chain 'R' and resid 118 through 120 No H-bonds generated for 'chain 'R' and resid 118 through 120' Processing helix chain 'R' and resid 125 through 165 removed outlier: 3.768A pdb=" N GLY R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 200 removed outlier: 3.784A pdb=" N ILE R 176 " --> pdb=" O THR R 172 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU R 197 " --> pdb=" O VAL R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 215 Processing helix chain 'R' and resid 221 through 251 removed outlier: 3.700A pdb=" N GLY R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 270 Processing helix chain 'R' and resid 272 through 288 removed outlier: 4.371A pdb=" N MET R 276 " --> pdb=" O TRP R 272 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 301 through 303 No H-bonds generated for 'chain 'R' and resid 301 through 303' Processing helix chain 'R' and resid 305 through 307 No H-bonds generated for 'chain 'R' and resid 305 through 307' Processing helix chain 'R' and resid 309 through 335 removed outlier: 4.077A pdb=" N ASN R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA R 331 " --> pdb=" O GLN R 327 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 352 Processing helix chain 'R' and resid 355 through 357 No H-bonds generated for 'chain 'R' and resid 355 through 357' Processing helix chain 'R' and resid 361 through 364 Processing helix chain 'R' and resid 375 through 401 removed outlier: 3.763A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 416 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.409A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.842A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.720A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.647A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.267A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.850A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.435A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 336 through 339 Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.593A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.245A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1749 1.32 - 1.45: 2512 1.45 - 1.57: 4931 1.57 - 1.70: 2 1.70 - 1.82: 78 Bond restraints: 9272 Sorted by residual: bond pdb=" CA PHE R 365 " pdb=" C PHE R 365 " ideal model delta sigma weight residual 1.533 1.493 0.040 5.60e-03 3.19e+04 5.19e+01 bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.371 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C06 D6M P 101 " pdb=" C07 D6M P 101 " ideal model delta sigma weight residual 1.538 1.623 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" N ARG R 94 " pdb=" CA ARG R 94 " ideal model delta sigma weight residual 1.455 1.505 -0.050 1.23e-02 6.61e+03 1.64e+01 bond pdb=" C HIS P 1 " pdb=" N DSN P 2 " ideal model delta sigma weight residual 1.329 1.382 -0.053 1.40e-02 5.10e+03 1.45e+01 ... (remaining 9267 not shown) Histogram of bond angle deviations from ideal: 93.65 - 102.48: 36 102.48 - 111.31: 3885 111.31 - 120.15: 4631 120.15 - 128.98: 3942 128.98 - 137.81: 89 Bond angle restraints: 12583 Sorted by residual: angle pdb=" C06 D6M P 101 " pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 118.04 93.65 24.39 3.00e+00 1.11e-01 6.61e+01 angle pdb=" N LEU B 30 " pdb=" CA LEU B 30 " pdb=" C LEU B 30 " ideal model delta sigma weight residual 113.43 104.11 9.32 1.26e+00 6.30e-01 5.47e+01 angle pdb=" N LEU R 47 " pdb=" CA LEU R 47 " pdb=" C LEU R 47 " ideal model delta sigma weight residual 112.23 102.92 9.31 1.26e+00 6.30e-01 5.46e+01 angle pdb=" N VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta sigma weight residual 110.50 115.02 -4.52 6.30e-01 2.52e+00 5.15e+01 angle pdb=" N GLY R 196 " pdb=" CA GLY R 196 " pdb=" C GLY R 196 " ideal model delta sigma weight residual 112.50 104.46 8.04 1.16e+00 7.43e-01 4.81e+01 ... (remaining 12578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4706 17.30 - 34.60: 472 34.60 - 51.90: 204 51.90 - 69.20: 67 69.20 - 86.50: 15 Dihedral angle restraints: 5464 sinusoidal: 2054 harmonic: 3410 Sorted by residual: dihedral pdb=" C VAL R 280 " pdb=" N VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta harmonic sigma weight residual -122.00 -138.87 16.87 0 2.50e+00 1.60e-01 4.56e+01 dihedral pdb=" N VAL R 280 " pdb=" C VAL R 280 " pdb=" CA VAL R 280 " pdb=" CB VAL R 280 " ideal model delta harmonic sigma weight residual 123.40 138.75 -15.35 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 67 " pdb=" CB CYS R 67 " ideal model delta sinusoidal sigma weight residual -86.00 -39.94 -46.06 1 1.00e+01 1.00e-02 2.94e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1300 0.119 - 0.238: 93 0.238 - 0.357: 12 0.357 - 0.476: 3 0.476 - 0.595: 4 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA VAL R 280 " pdb=" N VAL R 280 " pdb=" C VAL R 280 " pdb=" CB VAL R 280 " both_signs ideal model delta sigma weight residual False 2.44 1.85 0.59 2.00e-01 2.50e+01 8.85e+00 chirality pdb=" CG LEU R 85 " pdb=" CB LEU R 85 " pdb=" CD1 LEU R 85 " pdb=" CD2 LEU R 85 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.82e+00 ... (remaining 1409 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 52 " -0.027 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR C 52 " 0.094 2.00e-02 2.50e+03 pdb=" O THR C 52 " -0.036 2.00e-02 2.50e+03 pdb=" N PRO C 53 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 101 " 0.018 2.00e-02 2.50e+03 3.17e-02 1.26e+01 pdb=" C04 D6M P 101 " -0.038 2.00e-02 2.50e+03 pdb=" C12 D6M P 101 " -0.031 2.00e-02 2.50e+03 pdb=" N03 D6M P 101 " 0.047 2.00e-02 2.50e+03 pdb=" O01 D6M P 101 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA DSN P 2 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C DSN P 2 " -0.058 2.00e-02 2.50e+03 pdb=" O DSN P 2 " 0.022 2.00e-02 2.50e+03 pdb=" N GLN P 3 " 0.019 2.00e-02 2.50e+03 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1590 2.75 - 3.29: 8806 3.29 - 3.83: 15474 3.83 - 4.36: 17996 4.36 - 4.90: 30063 Nonbonded interactions: 73929 Sorted by model distance: nonbonded pdb=" N GLN R 120 " pdb=" OE1 GLN R 120 " model vdw 2.217 2.520 nonbonded pdb=" O SER R 203 " pdb=" OG SER R 203 " model vdw 2.254 2.440 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.265 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.311 2.440 nonbonded pdb=" O ASP B 228 " pdb=" OG SER B 245 " model vdw 2.318 2.440 ... (remaining 73924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.890 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 28.680 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.008 0.124 9272 Z= 0.486 Angle : 1.140 24.390 12583 Z= 0.729 Chirality : 0.075 0.595 1412 Planarity : 0.006 0.080 1610 Dihedral : 18.245 86.500 3242 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 1.29 % Allowed : 6.38 % Favored : 92.33 % Rotamer: Outliers : 15.73 % Allowed : 7.54 % Favored : 76.72 % Cbeta Deviations : 0.36 % 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: -2.62 (0.23), residues: 1160 helix: -1.51 (0.24), residues: 437 sheet: -1.35 (0.35), residues: 211 loop : -1.99 (0.26), residues: 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 193 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 21 residues processed: 287 average time/residue: 1.1320 time to fit residues: 346.9364 Evaluate side-chains 166 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.5556 time to fit residues: 3.3593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN C 18 GLN R 46 ASN ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9272 Z= 0.203 Angle : 0.673 10.223 12583 Z= 0.349 Chirality : 0.042 0.299 1412 Planarity : 0.005 0.069 1610 Dihedral : 5.148 56.495 1288 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.43 % Favored : 94.22 % Rotamer: Outliers : 4.74 % Allowed : 19.83 % Favored : 75.43 % 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: -1.31 (0.24), residues: 1160 helix: 0.16 (0.26), residues: 423 sheet: -0.91 (0.34), residues: 209 loop : -1.67 (0.26), residues: 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 154 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 19 residues processed: 188 average time/residue: 1.1809 time to fit residues: 238.5061 Evaluate side-chains 160 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.1716 time to fit residues: 2.0107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN P 13 GLN B 13 GLN C 44 HIS N 120 GLN R 27 GLN R 45 HIS ** R 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9272 Z= 0.247 Angle : 0.638 8.630 12583 Z= 0.330 Chirality : 0.042 0.295 1412 Planarity : 0.004 0.060 1610 Dihedral : 4.919 52.928 1288 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.09 % Favored : 94.57 % Rotamer: Outliers : 4.20 % Allowed : 21.66 % Favored : 74.14 % 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: -0.81 (0.25), residues: 1160 helix: 0.69 (0.26), residues: 430 sheet: -0.61 (0.34), residues: 224 loop : -1.56 (0.27), residues: 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.132 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 172 average time/residue: 1.2654 time to fit residues: 232.9908 Evaluate side-chains 160 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.1440 time to fit residues: 2.4310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.5980 chunk 77 optimal weight: 40.0000 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.0070 chunk 29 optimal weight: 2.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** R 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9272 Z= 0.208 Angle : 0.648 10.723 12583 Z= 0.329 Chirality : 0.041 0.275 1412 Planarity : 0.004 0.057 1610 Dihedral : 4.824 51.568 1288 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.83 % Favored : 94.83 % Rotamer: Outliers : 4.20 % Allowed : 21.88 % Favored : 73.92 % 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: -0.44 (0.25), residues: 1160 helix: 0.94 (0.26), residues: 433 sheet: -0.31 (0.35), residues: 222 loop : -1.37 (0.27), residues: 505 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 1.195 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 21 residues processed: 177 average time/residue: 1.2084 time to fit residues: 228.7932 Evaluate side-chains 164 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 4 average time/residue: 0.1636 time to fit residues: 2.3259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 16 ASN B 88 ASN C 18 GLN N 120 GLN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 9272 Z= 0.365 Angle : 0.716 13.997 12583 Z= 0.362 Chirality : 0.044 0.252 1412 Planarity : 0.004 0.055 1610 Dihedral : 5.066 45.498 1288 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.52 % Favored : 94.22 % Rotamer: Outliers : 4.42 % Allowed : 23.17 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.46 (0.25), residues: 1160 helix: 0.91 (0.26), residues: 435 sheet: -0.33 (0.34), residues: 228 loop : -1.37 (0.27), residues: 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 1.026 Fit side-chains outliers start: 41 outliers final: 30 residues processed: 172 average time/residue: 1.2775 time to fit residues: 234.8140 Evaluate side-chains 162 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 8 average time/residue: 0.3698 time to fit residues: 4.9268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN C 18 GLN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 HIS ** R 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9272 Z= 0.204 Angle : 0.692 13.381 12583 Z= 0.346 Chirality : 0.041 0.232 1412 Planarity : 0.004 0.055 1610 Dihedral : 4.793 45.714 1288 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.66 % Favored : 95.00 % Rotamer: Outliers : 3.56 % Allowed : 26.19 % Favored : 70.26 % 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: -0.28 (0.25), residues: 1160 helix: 1.06 (0.26), residues: 445 sheet: -0.25 (0.34), residues: 227 loop : -1.30 (0.27), residues: 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 1.137 Fit side-chains outliers start: 33 outliers final: 23 residues processed: 176 average time/residue: 1.1167 time to fit residues: 211.3525 Evaluate side-chains 163 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.4523 time to fit residues: 3.0508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0770 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 0.0570 chunk 67 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9272 Z= 0.197 Angle : 0.693 12.592 12583 Z= 0.343 Chirality : 0.040 0.218 1412 Planarity : 0.004 0.055 1610 Dihedral : 4.554 44.787 1288 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.66 % Favored : 95.00 % Rotamer: Outliers : 3.66 % Allowed : 28.56 % Favored : 67.78 % 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: -0.21 (0.25), residues: 1160 helix: 1.12 (0.26), residues: 446 sheet: -0.26 (0.34), residues: 220 loop : -1.24 (0.27), residues: 494 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.105 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 169 average time/residue: 1.1350 time to fit residues: 206.3234 Evaluate side-chains 158 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.7720 time to fit residues: 4.7552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0980 chunk 65 optimal weight: 8.9990 chunk 33 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9272 Z= 0.199 Angle : 0.701 11.110 12583 Z= 0.347 Chirality : 0.041 0.208 1412 Planarity : 0.004 0.058 1610 Dihedral : 4.475 43.234 1288 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.14 % Favored : 95.60 % Rotamer: Outliers : 3.45 % Allowed : 29.31 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1160 helix: 1.18 (0.26), residues: 446 sheet: -0.17 (0.34), residues: 218 loop : -1.15 (0.27), residues: 496 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.193 Fit side-chains outliers start: 32 outliers final: 22 residues processed: 159 average time/residue: 1.1260 time to fit residues: 192.6771 Evaluate side-chains 153 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 2 average time/residue: 0.1562 time to fit residues: 1.8766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 67 optimal weight: 0.0060 chunk 108 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** R 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9272 Z= 0.211 Angle : 0.721 12.098 12583 Z= 0.356 Chirality : 0.041 0.209 1412 Planarity : 0.004 0.059 1610 Dihedral : 4.433 41.606 1288 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.14 % Favored : 95.52 % Rotamer: Outliers : 3.23 % Allowed : 29.74 % Favored : 67.03 % 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 (0.25), residues: 1160 helix: 1.16 (0.26), residues: 450 sheet: -0.10 (0.34), residues: 218 loop : -1.07 (0.28), residues: 492 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.080 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 154 average time/residue: 1.1778 time to fit residues: 194.6031 Evaluate side-chains 153 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 4 average time/residue: 0.1527 time to fit residues: 2.3197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.0870 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9272 Z= 0.211 Angle : 0.732 13.172 12583 Z= 0.363 Chirality : 0.041 0.205 1412 Planarity : 0.004 0.063 1610 Dihedral : 4.412 40.544 1288 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.14 % Favored : 95.52 % Rotamer: Outliers : 2.26 % Allowed : 30.71 % Favored : 67.03 % 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: 0.04 (0.25), residues: 1160 helix: 1.28 (0.26), residues: 444 sheet: -0.06 (0.34), residues: 219 loop : -1.06 (0.28), residues: 497 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 19 residues processed: 155 average time/residue: 1.1502 time to fit residues: 191.7780 Evaluate side-chains 152 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.0867 time to fit residues: 1.6106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.109269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.071912 restraints weight = 18186.937| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.62 r_work: 0.2936 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9272 Z= 0.211 Angle : 0.730 13.382 12583 Z= 0.359 Chirality : 0.041 0.211 1412 Planarity : 0.004 0.063 1610 Dihedral : 4.395 39.809 1288 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 3.02 % Allowed : 30.28 % Favored : 66.70 % 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: 0.07 (0.25), residues: 1160 helix: 1.19 (0.26), residues: 451 sheet: -0.03 (0.34), residues: 219 loop : -0.97 (0.28), residues: 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4167.02 seconds wall clock time: 74 minutes 24.17 seconds (4464.17 seconds total)