Starting phenix.real_space_refine on Wed Feb 14 03:59:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2024/7eja_31157_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2024/7eja_31157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2024/7eja_31157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2024/7eja_31157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2024/7eja_31157_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eja_31157/02_2024/7eja_31157_updated.pdb" } resolution = 3.6 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= -0.007 sd= 0.192 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 58 5.16 5 C 5487 2.51 5 N 1458 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "R ARG 202": "NH1" <-> "NH2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R ARG 240": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R ARG 383": "NH1" <-> "NH2" Residue "R ARG 450": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8584 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1632 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 198} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2541 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2193 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1785 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CZX': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 5.19, per 1000 atoms: 0.60 Number of scatterers: 8584 At special positions: 0 Unit cell: (88.4, 120.7, 124.95, 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 58 16.00 O 1581 8.00 N 1458 7.00 C 5487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 13 sheets defined 32.1% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.912A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 209 through 217 removed outlier: 4.272A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N CYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE A 216 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLU A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.566A pdb=" N ASP A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 330 through 349 Processing helix chain 'B' and resid 8 through 24 removed outlier: 3.591A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.802A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 46 removed outlier: 4.601A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 73 Processing helix chain 'R' and resid 82 through 107 removed outlier: 3.571A pdb=" N PHE R 86 " --> pdb=" O GLN R 83 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL R 97 " --> pdb=" O ASP R 94 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL R 101 " --> pdb=" O ALA R 98 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE R 102 " --> pdb=" O THR R 99 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 121 through 150 Processing helix chain 'R' and resid 153 through 159 removed outlier: 4.988A pdb=" N LEU R 158 " --> pdb=" O ILE R 154 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS R 159 " --> pdb=" O GLU R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 181 Processing helix chain 'R' and resid 209 through 241 removed outlier: 3.683A pdb=" N ILE R 213 " --> pdb=" O LYS R 209 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER R 214 " --> pdb=" O TRP R 210 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ALA R 222 " --> pdb=" O GLY R 218 " (cutoff:3.500A) Proline residue: R 223 - end of helix Processing helix chain 'R' and resid 377 through 410 removed outlier: 3.698A pdb=" N ASN R 382 " --> pdb=" O ARG R 378 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE R 398 " --> pdb=" O VAL R 394 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL R 399 " --> pdb=" O ILE R 395 " (cutoff:3.500A) Proline residue: R 404 - end of helix Processing helix chain 'R' and resid 421 through 442 removed outlier: 3.950A pdb=" N ASN R 437 " --> pdb=" O SER R 434 " (cutoff:3.500A) Proline residue: R 438 - end of helix Processing helix chain 'R' and resid 446 through 456 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 264 through 269 removed outlier: 4.030A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 34 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 201 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.931A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.513A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.956A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 201 removed outlier: 3.661A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 250 through 253 Processing sheet with id= G, first strand: chain 'B' and resid 296 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.590A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.804A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 92 through 99 removed outlier: 6.315A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 134 through 136 removed outlier: 6.949A pdb=" N LYS H 232 " --> pdb=" O VAL H 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'H' and resid 143 through 148 removed outlier: 3.952A pdb=" N PHE H 200 " --> pdb=" O CYS H 147 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 214 through 219 345 hydrogen bonds defined for protein. 840 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: 2.21 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1385 1.31 - 1.44: 2457 1.44 - 1.56: 4847 1.56 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8768 Sorted by residual: bond pdb=" N ILE R 123 " pdb=" CA ILE R 123 " ideal model delta sigma weight residual 1.461 1.396 0.065 1.17e-02 7.31e+03 3.07e+01 bond pdb=" N ASN A 346 " pdb=" CA ASN A 346 " ideal model delta sigma weight residual 1.459 1.400 0.060 1.20e-02 6.94e+03 2.47e+01 bond pdb=" CA TYR R 156 " pdb=" C TYR R 156 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.29e-02 6.01e+03 2.45e+01 bond pdb=" CA ASN A 346 " pdb=" C ASN A 346 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.26e-02 6.30e+03 2.30e+01 bond pdb=" N PRO R 438 " pdb=" CD PRO R 438 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.22e+01 ... (remaining 8763 not shown) Histogram of bond angle deviations from ideal: 99.74 - 107.23: 241 107.23 - 114.71: 5135 114.71 - 122.19: 4958 122.19 - 129.67: 1483 129.67 - 137.16: 64 Bond angle restraints: 11881 Sorted by residual: angle pdb=" N ARG R 378 " pdb=" CA ARG R 378 " pdb=" C ARG R 378 " ideal model delta sigma weight residual 111.28 121.19 -9.91 1.09e+00 8.42e-01 8.27e+01 angle pdb=" N LYS A 211 " pdb=" CA LYS A 211 " pdb=" C LYS A 211 " ideal model delta sigma weight residual 111.14 119.75 -8.61 1.08e+00 8.57e-01 6.36e+01 angle pdb=" N HIS A 214 " pdb=" CA HIS A 214 " pdb=" C HIS A 214 " ideal model delta sigma weight residual 111.28 119.83 -8.55 1.09e+00 8.42e-01 6.16e+01 angle pdb=" N LYS R 159 " pdb=" CA LYS R 159 " pdb=" C LYS R 159 " ideal model delta sigma weight residual 113.15 122.41 -9.26 1.19e+00 7.06e-01 6.06e+01 angle pdb=" N CYS R 121 " pdb=" CA CYS R 121 " pdb=" C CYS R 121 " ideal model delta sigma weight residual 112.90 103.56 9.34 1.31e+00 5.83e-01 5.08e+01 ... (remaining 11876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.99: 5081 33.99 - 67.98: 90 67.98 - 101.97: 9 101.97 - 135.95: 0 135.95 - 169.94: 2 Dihedral angle restraints: 5182 sinusoidal: 2004 harmonic: 3178 Sorted by residual: dihedral pdb=" N ILE R 123 " pdb=" C ILE R 123 " pdb=" CA ILE R 123 " pdb=" CB ILE R 123 " ideal model delta harmonic sigma weight residual 123.40 109.48 13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" C PHE A 216 " pdb=" N PHE A 216 " pdb=" CA PHE A 216 " pdb=" CB PHE A 216 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" CA ILE G 25 " pdb=" C ILE G 25 " pdb=" N ASP G 26 " pdb=" CA ASP G 26 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 5179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1292 0.110 - 0.219: 39 0.219 - 0.329: 12 0.329 - 0.438: 4 0.438 - 0.548: 2 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA PHE A 216 " pdb=" N PHE A 216 " pdb=" C PHE A 216 " pdb=" CB PHE A 216 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" CA GLU A 217 " pdb=" N GLU A 217 " pdb=" C GLU A 217 " pdb=" CB GLU A 217 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA LYS R 159 " pdb=" N LYS R 159 " pdb=" C LYS R 159 " pdb=" CB LYS R 159 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 1346 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 161 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO R 162 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 162 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 162 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 183 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C THR A 183 " -0.034 2.00e-02 2.50e+03 pdb=" O THR A 183 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 184 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 282 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A 283 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.026 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 4 2.21 - 2.88: 3396 2.88 - 3.55: 12495 3.55 - 4.23: 18707 4.23 - 4.90: 31496 Nonbonded interactions: 66098 Sorted by model distance: nonbonded pdb=" CE2 PHE H 32 " pdb=" NH2 ARG H 98 " model vdw 1.533 3.420 nonbonded pdb=" OE1 GLN R 83 " pdb=" NH2 ARG R 160 " model vdw 1.893 2.520 nonbonded pdb=" CZ PHE H 32 " pdb=" NH2 ARG H 98 " model vdw 2.085 3.420 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.175 2.440 nonbonded pdb=" OG SER H 192 " pdb=" OG1 THR H 203 " model vdw 2.215 2.440 ... (remaining 66093 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 4.070 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.150 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.005 0.066 8768 Z= 0.292 Angle : 0.850 14.408 11881 Z= 0.537 Chirality : 0.059 0.548 1349 Planarity : 0.004 0.055 1496 Dihedral : 13.816 169.942 3121 Min Nonbonded Distance : 1.533 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.11 % Allowed : 0.75 % Favored : 99.14 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.43 (0.26), residues: 1075 helix: 1.20 (0.28), residues: 341 sheet: -0.37 (0.33), residues: 263 loop : -1.32 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS A 189 PHE 0.022 0.001 PHE R 398 TYR 0.013 0.001 TYR R 156 ARG 0.005 0.000 ARG R 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8705 (mmm-85) REVERT: B 36 ASN cc_start: 0.8672 (m-40) cc_final: 0.8362 (p0) REVERT: B 255 LEU cc_start: 0.9382 (pt) cc_final: 0.9117 (mm) REVERT: B 261 LEU cc_start: 0.9371 (mt) cc_final: 0.9168 (mt) REVERT: B 280 LYS cc_start: 0.9349 (tptp) cc_final: 0.9026 (tptp) REVERT: B 292 PHE cc_start: 0.7801 (m-10) cc_final: 0.7482 (m-10) REVERT: G 21 MET cc_start: 0.8107 (mmp) cc_final: 0.7295 (mtm) REVERT: G 32 LYS cc_start: 0.9511 (ptpp) cc_final: 0.9293 (ptmm) REVERT: G 42 GLU cc_start: 0.8135 (tp30) cc_final: 0.7530 (mt-10) REVERT: G 58 GLU cc_start: 0.8998 (mp0) cc_final: 0.8428 (mp0) REVERT: R 53 CYS cc_start: 0.9179 (m) cc_final: 0.8880 (p) REVERT: R 57 LEU cc_start: 0.9416 (tp) cc_final: 0.9184 (tp) REVERT: R 109 GLU cc_start: 0.8887 (tp30) cc_final: 0.8314 (tm-30) REVERT: R 450 ARG cc_start: 0.9489 (mtm110) cc_final: 0.9216 (mtm-85) REVERT: H 46 GLU cc_start: 0.8579 (pt0) cc_final: 0.8189 (pm20) REVERT: H 90 ASP cc_start: 0.8059 (m-30) cc_final: 0.7532 (m-30) REVERT: H 137 VAL cc_start: 0.7359 (m) cc_final: 0.7129 (m) REVERT: H 180 MET cc_start: 0.8772 (ppp) cc_final: 0.8273 (ppp) REVERT: H 210 GLU cc_start: 0.8971 (mp0) cc_final: 0.8577 (mp0) REVERT: H 211 ASP cc_start: 0.7848 (m-30) cc_final: 0.7330 (m-30) REVERT: H 218 MET cc_start: 0.8712 (tmm) cc_final: 0.8146 (tmm) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.2315 time to fit residues: 70.1040 Evaluate side-chains 152 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 40.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8768 Z= 0.211 Angle : 0.692 10.321 11881 Z= 0.361 Chirality : 0.044 0.175 1349 Planarity : 0.005 0.053 1496 Dihedral : 8.077 163.439 1193 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.94 % Allowed : 13.12 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.51 (0.26), residues: 1075 helix: 0.93 (0.27), residues: 343 sheet: -0.26 (0.33), residues: 275 loop : -1.33 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.009 0.001 HIS A 196 PHE 0.028 0.001 PHE R 387 TYR 0.024 0.001 TYR R 156 ARG 0.007 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8953 (mmm160) cc_final: 0.8728 (mmm-85) REVERT: A 354 TYR cc_start: 0.8556 (p90) cc_final: 0.8262 (p90) REVERT: B 36 ASN cc_start: 0.8645 (m-40) cc_final: 0.8328 (p0) REVERT: B 292 PHE cc_start: 0.7907 (m-10) cc_final: 0.7567 (m-10) REVERT: G 17 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8497 (pm20) REVERT: G 21 MET cc_start: 0.8157 (mmp) cc_final: 0.7393 (mtm) REVERT: G 32 LYS cc_start: 0.9410 (ptpp) cc_final: 0.9201 (ptmm) REVERT: G 38 MET cc_start: 0.6492 (ptp) cc_final: 0.6058 (ptt) REVERT: G 42 GLU cc_start: 0.8118 (tp30) cc_final: 0.7602 (mt-10) REVERT: G 58 GLU cc_start: 0.9020 (mp0) cc_final: 0.8413 (mp0) REVERT: R 109 GLU cc_start: 0.8860 (tp30) cc_final: 0.8225 (tm-30) REVERT: R 450 ARG cc_start: 0.9493 (mtm110) cc_final: 0.9234 (mtm-85) REVERT: H 34 MET cc_start: 0.8533 (tpp) cc_final: 0.8283 (tpp) REVERT: H 180 MET cc_start: 0.8777 (ppp) cc_final: 0.8239 (ppp) REVERT: H 218 MET cc_start: 0.8653 (tmm) cc_final: 0.8353 (tmm) outliers start: 18 outliers final: 13 residues processed: 180 average time/residue: 0.2198 time to fit residues: 53.5516 Evaluate side-chains 162 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain H residue 182 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 27 optimal weight: 0.4980 chunk 98 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 152 GLN R 433 ASN H 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8768 Z= 0.317 Angle : 0.706 11.251 11881 Z= 0.370 Chirality : 0.044 0.153 1349 Planarity : 0.005 0.052 1496 Dihedral : 8.101 160.863 1193 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.23 % Allowed : 16.67 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.77 (0.26), residues: 1075 helix: 0.74 (0.27), residues: 337 sheet: -0.35 (0.32), residues: 269 loop : -1.52 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.007 0.001 HIS B 183 PHE 0.017 0.002 PHE A 260 TYR 0.024 0.002 TYR R 409 ARG 0.007 0.001 ARG R 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.9016 (mmm160) cc_final: 0.8793 (mmm-85) REVERT: A 320 TYR cc_start: 0.8608 (m-80) cc_final: 0.7490 (m-10) REVERT: A 354 TYR cc_start: 0.8745 (p90) cc_final: 0.8303 (p90) REVERT: B 12 GLU cc_start: 0.9294 (pt0) cc_final: 0.8971 (pm20) REVERT: B 17 GLN cc_start: 0.7416 (tm-30) cc_final: 0.7059 (pp30) REVERT: B 36 ASN cc_start: 0.8646 (m-40) cc_final: 0.8408 (p0) REVERT: B 292 PHE cc_start: 0.8278 (m-10) cc_final: 0.7932 (m-10) REVERT: G 38 MET cc_start: 0.6534 (ptp) cc_final: 0.6181 (ptt) REVERT: G 42 GLU cc_start: 0.8136 (tp30) cc_final: 0.7615 (mt-10) REVERT: G 58 GLU cc_start: 0.9055 (mp0) cc_final: 0.8448 (mp0) REVERT: R 109 GLU cc_start: 0.8903 (tp30) cc_final: 0.8294 (tm-30) REVERT: R 204 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8801 (tm-30) REVERT: R 450 ARG cc_start: 0.9520 (mtm110) cc_final: 0.9285 (mtm-85) REVERT: H 180 MET cc_start: 0.8816 (ppp) cc_final: 0.8256 (ppp) REVERT: H 218 MET cc_start: 0.8694 (tmm) cc_final: 0.8405 (tmm) outliers start: 30 outliers final: 23 residues processed: 172 average time/residue: 0.2142 time to fit residues: 49.9373 Evaluate side-chains 161 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain H residue 182 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 104 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8768 Z= 0.226 Angle : 0.682 11.422 11881 Z= 0.348 Chirality : 0.043 0.165 1349 Planarity : 0.004 0.047 1496 Dihedral : 8.039 161.880 1193 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.55 % Allowed : 18.28 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.69 (0.26), residues: 1075 helix: 0.84 (0.28), residues: 333 sheet: -0.23 (0.33), residues: 261 loop : -1.51 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.007 0.001 HIS A 196 PHE 0.021 0.001 PHE R 387 TYR 0.025 0.001 TYR R 409 ARG 0.004 0.000 ARG H 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8611 (tm-30) REVERT: A 228 LEU cc_start: 0.3797 (OUTLIER) cc_final: 0.3553 (pp) REVERT: A 313 ARG cc_start: 0.9019 (mmm160) cc_final: 0.8807 (mmm-85) REVERT: A 354 TYR cc_start: 0.8737 (p90) cc_final: 0.8411 (p90) REVERT: B 12 GLU cc_start: 0.9299 (pt0) cc_final: 0.8980 (pm20) REVERT: B 17 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7181 (pp30) REVERT: B 36 ASN cc_start: 0.8629 (m-40) cc_final: 0.8308 (p0) REVERT: B 292 PHE cc_start: 0.8237 (m-10) cc_final: 0.7877 (m-10) REVERT: G 21 MET cc_start: 0.8514 (mmm) cc_final: 0.7467 (mtm) REVERT: G 38 MET cc_start: 0.6549 (ptp) cc_final: 0.6273 (ptt) REVERT: G 42 GLU cc_start: 0.8097 (tp30) cc_final: 0.7580 (mt-10) REVERT: G 58 GLU cc_start: 0.9083 (mp0) cc_final: 0.8473 (mp0) REVERT: R 79 LEU cc_start: 0.9148 (tp) cc_final: 0.8896 (tp) REVERT: R 109 GLU cc_start: 0.8828 (tp30) cc_final: 0.8247 (tm-30) REVERT: R 450 ARG cc_start: 0.9525 (mtm110) cc_final: 0.9296 (mtm-85) REVERT: H 218 MET cc_start: 0.8687 (tmm) cc_final: 0.8434 (tmm) outliers start: 33 outliers final: 24 residues processed: 175 average time/residue: 0.2130 time to fit residues: 50.7850 Evaluate side-chains 165 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 20.0000 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8768 Z= 0.255 Angle : 0.693 10.783 11881 Z= 0.356 Chirality : 0.043 0.192 1349 Planarity : 0.004 0.048 1496 Dihedral : 8.005 159.772 1193 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.87 % Allowed : 19.78 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.84 (0.26), residues: 1075 helix: 0.67 (0.28), residues: 336 sheet: -0.32 (0.33), residues: 263 loop : -1.57 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.006 0.001 HIS A 196 PHE 0.019 0.001 PHE R 387 TYR 0.014 0.002 TYR H 215 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.3945 (OUTLIER) cc_final: 0.3700 (pp) REVERT: A 354 TYR cc_start: 0.8760 (p90) cc_final: 0.8409 (p90) REVERT: B 12 GLU cc_start: 0.9294 (pt0) cc_final: 0.8961 (pm20) REVERT: B 36 ASN cc_start: 0.8622 (m-40) cc_final: 0.8305 (p0) REVERT: B 241 PHE cc_start: 0.7555 (p90) cc_final: 0.7238 (p90) REVERT: B 292 PHE cc_start: 0.8349 (m-10) cc_final: 0.7948 (m-10) REVERT: G 21 MET cc_start: 0.8648 (mmm) cc_final: 0.7705 (mtm) REVERT: G 38 MET cc_start: 0.6603 (ptp) cc_final: 0.6323 (ptt) REVERT: G 42 GLU cc_start: 0.8089 (tp30) cc_final: 0.7577 (mt-10) REVERT: G 58 GLU cc_start: 0.9081 (mp0) cc_final: 0.8419 (mp0) REVERT: R 79 LEU cc_start: 0.9170 (tp) cc_final: 0.8912 (tp) REVERT: R 109 GLU cc_start: 0.8818 (tp30) cc_final: 0.8256 (tm-30) REVERT: R 450 ARG cc_start: 0.9526 (mtm110) cc_final: 0.9298 (mtm180) REVERT: H 34 MET cc_start: 0.8547 (tpp) cc_final: 0.8317 (tpp) REVERT: H 83 MET cc_start: 0.7784 (mmm) cc_final: 0.7563 (mmp) REVERT: H 218 MET cc_start: 0.8703 (tmm) cc_final: 0.8472 (tmm) outliers start: 36 outliers final: 29 residues processed: 171 average time/residue: 0.2096 time to fit residues: 48.9227 Evaluate side-chains 166 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8768 Z= 0.297 Angle : 0.712 10.840 11881 Z= 0.366 Chirality : 0.044 0.141 1349 Planarity : 0.004 0.047 1496 Dihedral : 7.974 156.504 1193 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.98 % Allowed : 20.97 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1075 helix: 0.63 (0.28), residues: 336 sheet: -0.55 (0.32), residues: 270 loop : -1.59 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.007 0.001 HIS B 225 PHE 0.025 0.002 PHE R 387 TYR 0.012 0.002 TYR R 156 ARG 0.004 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8775 (p90) cc_final: 0.8486 (p90) REVERT: B 12 GLU cc_start: 0.9285 (pt0) cc_final: 0.8953 (pm20) REVERT: B 36 ASN cc_start: 0.8594 (m-40) cc_final: 0.8297 (p0) REVERT: B 241 PHE cc_start: 0.7594 (p90) cc_final: 0.7349 (p90) REVERT: B 283 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7292 (ttt180) REVERT: B 292 PHE cc_start: 0.8477 (m-10) cc_final: 0.8179 (m-80) REVERT: G 21 MET cc_start: 0.8641 (mmm) cc_final: 0.7728 (mtm) REVERT: G 38 MET cc_start: 0.6490 (ptp) cc_final: 0.6226 (ptt) REVERT: G 42 GLU cc_start: 0.8098 (tp30) cc_final: 0.7594 (mt-10) REVERT: G 58 GLU cc_start: 0.9118 (mp0) cc_final: 0.8477 (mp0) REVERT: R 79 LEU cc_start: 0.9173 (tp) cc_final: 0.8932 (tp) REVERT: R 109 GLU cc_start: 0.8816 (tp30) cc_final: 0.8278 (tm-30) REVERT: R 450 ARG cc_start: 0.9519 (mtm110) cc_final: 0.9292 (mtm180) REVERT: H 83 MET cc_start: 0.7932 (mmm) cc_final: 0.7716 (mmp) REVERT: H 210 GLU cc_start: 0.8834 (mp0) cc_final: 0.8604 (pm20) outliers start: 37 outliers final: 32 residues processed: 166 average time/residue: 0.2057 time to fit residues: 46.7541 Evaluate side-chains 174 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 439 VAL Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8768 Z= 0.184 Angle : 0.703 16.867 11881 Z= 0.349 Chirality : 0.043 0.185 1349 Planarity : 0.004 0.049 1496 Dihedral : 7.770 154.161 1193 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.66 % Allowed : 21.72 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.82 (0.26), residues: 1075 helix: 0.72 (0.29), residues: 334 sheet: -0.29 (0.34), residues: 245 loop : -1.57 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.005 0.001 HIS B 225 PHE 0.019 0.001 PHE R 387 TYR 0.014 0.001 TYR H 163 ARG 0.003 0.000 ARG R 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8750 (p90) cc_final: 0.8425 (p90) REVERT: B 12 GLU cc_start: 0.9291 (pt0) cc_final: 0.8957 (pm20) REVERT: B 36 ASN cc_start: 0.8581 (m-40) cc_final: 0.8246 (p0) REVERT: B 156 GLN cc_start: 0.8902 (mt0) cc_final: 0.8540 (mp10) REVERT: B 241 PHE cc_start: 0.7584 (p90) cc_final: 0.7343 (p90) REVERT: B 292 PHE cc_start: 0.8301 (m-10) cc_final: 0.7994 (m-10) REVERT: G 21 MET cc_start: 0.8633 (mmm) cc_final: 0.7736 (mtm) REVERT: G 38 MET cc_start: 0.6419 (ptp) cc_final: 0.6182 (ptt) REVERT: G 42 GLU cc_start: 0.8052 (tp30) cc_final: 0.7567 (mt-10) REVERT: G 58 GLU cc_start: 0.9103 (mp0) cc_final: 0.8468 (mp0) REVERT: R 79 LEU cc_start: 0.9180 (tp) cc_final: 0.8884 (tp) REVERT: R 109 GLU cc_start: 0.8773 (tp30) cc_final: 0.8293 (tm-30) REVERT: R 446 HIS cc_start: 0.9120 (OUTLIER) cc_final: 0.8734 (t70) REVERT: R 448 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8752 (t80) REVERT: H 34 MET cc_start: 0.8541 (tpp) cc_final: 0.8314 (tpp) REVERT: H 83 MET cc_start: 0.7904 (mmm) cc_final: 0.7629 (mmp) outliers start: 34 outliers final: 27 residues processed: 181 average time/residue: 0.1996 time to fit residues: 49.8012 Evaluate side-chains 172 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 439 VAL Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 448 PHE Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8768 Z= 0.228 Angle : 0.726 15.221 11881 Z= 0.363 Chirality : 0.043 0.178 1349 Planarity : 0.004 0.049 1496 Dihedral : 7.667 149.989 1193 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.44 % Allowed : 23.01 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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: -0.84 (0.26), residues: 1075 helix: 0.69 (0.28), residues: 334 sheet: -0.43 (0.33), residues: 264 loop : -1.51 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.007 0.001 HIS B 225 PHE 0.034 0.001 PHE R 387 TYR 0.019 0.001 TYR H 223 ARG 0.005 0.000 ARG R 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8738 (p90) cc_final: 0.8479 (p90) REVERT: B 12 GLU cc_start: 0.9291 (pt0) cc_final: 0.8959 (pm20) REVERT: B 36 ASN cc_start: 0.8576 (m-40) cc_final: 0.8263 (p0) REVERT: B 78 LYS cc_start: 0.9596 (mmmm) cc_final: 0.9145 (mmmm) REVERT: B 241 PHE cc_start: 0.7571 (p90) cc_final: 0.7356 (p90) REVERT: B 283 ARG cc_start: 0.7628 (ttt180) cc_final: 0.7355 (ttt180) REVERT: B 292 PHE cc_start: 0.8414 (m-10) cc_final: 0.8161 (m-80) REVERT: G 21 MET cc_start: 0.8641 (mmm) cc_final: 0.7781 (mtm) REVERT: G 42 GLU cc_start: 0.8067 (tp30) cc_final: 0.7768 (mt-10) REVERT: G 58 GLU cc_start: 0.9105 (mp0) cc_final: 0.8469 (mp0) REVERT: R 79 LEU cc_start: 0.9191 (tp) cc_final: 0.8912 (tp) REVERT: R 109 GLU cc_start: 0.8763 (tp30) cc_final: 0.8253 (tm-30) REVERT: R 446 HIS cc_start: 0.9114 (OUTLIER) cc_final: 0.8678 (t70) REVERT: H 34 MET cc_start: 0.8515 (tpp) cc_final: 0.8284 (tpp) REVERT: H 83 MET cc_start: 0.7935 (mmm) cc_final: 0.7611 (mmp) REVERT: H 190 ARG cc_start: 0.5638 (OUTLIER) cc_final: 0.5421 (ptm160) outliers start: 32 outliers final: 27 residues processed: 170 average time/residue: 0.2126 time to fit residues: 49.6446 Evaluate side-chains 173 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 439 VAL Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 0.0000 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8768 Z= 0.188 Angle : 0.742 14.560 11881 Z= 0.365 Chirality : 0.043 0.169 1349 Planarity : 0.004 0.050 1496 Dihedral : 7.505 146.123 1193 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.23 % Allowed : 23.12 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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 (0.26), residues: 1075 helix: 0.66 (0.29), residues: 334 sheet: -0.36 (0.33), residues: 264 loop : -1.49 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.005 0.001 HIS B 225 PHE 0.032 0.001 PHE R 387 TYR 0.012 0.001 TYR R 156 ARG 0.005 0.000 ARG R 450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 GLU cc_start: 0.9291 (pt0) cc_final: 0.8956 (pm20) REVERT: B 36 ASN cc_start: 0.8543 (m-40) cc_final: 0.8288 (p0) REVERT: B 283 ARG cc_start: 0.7514 (ttt180) cc_final: 0.7213 (ttt180) REVERT: B 292 PHE cc_start: 0.8328 (m-10) cc_final: 0.8084 (m-10) REVERT: G 21 MET cc_start: 0.8656 (mmm) cc_final: 0.7802 (mtm) REVERT: G 38 MET cc_start: 0.6606 (ptt) cc_final: 0.5696 (ptt) REVERT: G 42 GLU cc_start: 0.8327 (tp30) cc_final: 0.7721 (mt-10) REVERT: G 58 GLU cc_start: 0.9095 (mp0) cc_final: 0.8465 (mp0) REVERT: R 79 LEU cc_start: 0.9102 (tp) cc_final: 0.8886 (tp) REVERT: R 109 GLU cc_start: 0.8736 (tp30) cc_final: 0.8259 (tm-30) REVERT: R 428 TRP cc_start: 0.8594 (m100) cc_final: 0.8368 (m100) REVERT: R 446 HIS cc_start: 0.9089 (OUTLIER) cc_final: 0.8691 (t70) REVERT: H 34 MET cc_start: 0.8504 (tpp) cc_final: 0.8258 (tpp) REVERT: H 190 ARG cc_start: 0.5551 (OUTLIER) cc_final: 0.5331 (ptm160) outliers start: 30 outliers final: 25 residues processed: 166 average time/residue: 0.2217 time to fit residues: 49.9393 Evaluate side-chains 169 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 439 VAL Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 190 ARG Chi-restraints excluded: chain H residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 99 optimal weight: 30.0000 chunk 85 optimal weight: 50.0000 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8768 Z= 0.288 Angle : 0.782 13.836 11881 Z= 0.390 Chirality : 0.044 0.198 1349 Planarity : 0.004 0.049 1496 Dihedral : 7.530 143.557 1193 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.86 % Rotamer: Outliers : 3.01 % Allowed : 23.55 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1075 helix: 0.51 (0.28), residues: 334 sheet: -0.49 (0.33), residues: 265 loop : -1.51 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS B 225 PHE 0.033 0.002 PHE R 387 TYR 0.013 0.002 TYR R 156 ARG 0.005 0.000 ARG R 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 GLU cc_start: 0.9278 (pt0) cc_final: 0.8948 (pm20) REVERT: B 36 ASN cc_start: 0.8581 (m-40) cc_final: 0.8333 (p0) REVERT: B 283 ARG cc_start: 0.7680 (ttt180) cc_final: 0.7356 (ttt180) REVERT: B 292 PHE cc_start: 0.8490 (m-10) cc_final: 0.8133 (m-80) REVERT: G 21 MET cc_start: 0.8670 (mmm) cc_final: 0.7859 (mtm) REVERT: G 38 MET cc_start: 0.6406 (ptt) cc_final: 0.5423 (ptt) REVERT: G 42 GLU cc_start: 0.8343 (tp30) cc_final: 0.7730 (mt-10) REVERT: G 58 GLU cc_start: 0.9101 (mp0) cc_final: 0.8483 (mp0) REVERT: R 79 LEU cc_start: 0.9124 (tp) cc_final: 0.8908 (tp) REVERT: R 109 GLU cc_start: 0.8761 (tp30) cc_final: 0.8220 (tm-30) REVERT: H 34 MET cc_start: 0.8518 (tpp) cc_final: 0.8271 (tpp) REVERT: H 190 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.5338 (ptm160) outliers start: 28 outliers final: 26 residues processed: 157 average time/residue: 0.2168 time to fit residues: 46.3737 Evaluate side-chains 165 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 140 CYS Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 382 ASN Chi-restraints excluded: chain R residue 439 VAL Chi-restraints excluded: chain R residue 446 HIS Chi-restraints excluded: chain R residue 454 LYS Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.092036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.068177 restraints weight = 31647.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070225 restraints weight = 17510.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071612 restraints weight = 12043.471| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8768 Z= 0.195 Angle : 0.751 13.659 11881 Z= 0.371 Chirality : 0.043 0.164 1349 Planarity : 0.004 0.050 1496 Dihedral : 7.442 142.448 1193 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 2.80 % Allowed : 23.87 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 1.14 % 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 (0.26), residues: 1075 helix: 0.56 (0.29), residues: 334 sheet: -0.55 (0.33), residues: 269 loop : -1.48 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.005 0.001 HIS B 225 PHE 0.031 0.001 PHE R 387 TYR 0.012 0.001 TYR R 156 ARG 0.004 0.000 ARG R 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1887.64 seconds wall clock time: 35 minutes 9.50 seconds (2109.50 seconds total)