Starting phenix.real_space_refine on Fri Mar 15 08:32:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsx_30849/03_2024/7dsx_30849_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsx_30849/03_2024/7dsx_30849.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsx_30849/03_2024/7dsx_30849_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsx_30849/03_2024/7dsx_30849_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsx_30849/03_2024/7dsx_30849_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsx_30849/03_2024/7dsx_30849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsx_30849/03_2024/7dsx_30849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsx_30849/03_2024/7dsx_30849_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsx_30849/03_2024/7dsx_30849_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.087 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 44 5.16 5 C 7306 2.51 5 N 1804 2.21 5 O 1952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 16": "OE1" <-> "OE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A GLU 570": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11106 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1450 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4038 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 16, 'TRANS': 492} Chain: "C" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1450 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4038 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 16, 'TRANS': 492} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'HG0': 1, 'PGT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGT:plan-1': 3, 'PGT:plan-2': 3} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'HG0': 1, 'PGT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGT:plan-1': 3, 'PGT:plan-2': 3} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 6.09, per 1000 atoms: 0.55 Number of scatterers: 11106 At special positions: 0 Unit cell: (146.64, 73.84, 98.8, 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 44 16.00 O 1952 8.00 N 1804 7.00 C 7306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.67 Conformation dependent library (CDL) restraints added in 2.2 seconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 0 sheets defined 58.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 23.35 Creating SS restraints... Processing helix chain 'D' and resid 15 through 21 Processing helix chain 'D' and resid 25 through 39 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 63 through 70 Processing helix chain 'D' and resid 80 through 90 removed outlier: 4.289A pdb=" N HIS D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 111 through 122 removed outlier: 4.169A pdb=" N ALA D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 149 through 163 Processing helix chain 'D' and resid 174 through 180 removed outlier: 3.588A pdb=" N LYS D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 188 No H-bonds generated for 'chain 'D' and resid 185 through 188' Processing helix chain 'B' and resid 100 through 121 removed outlier: 3.570A pdb=" N ILE B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 128 No H-bonds generated for 'chain 'B' and resid 125 through 128' Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 166 through 175 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 197 No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 200 through 213 Processing helix chain 'B' and resid 223 through 234 removed outlier: 3.907A pdb=" N PHE B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 253 through 270 removed outlier: 4.116A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ALA B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 311 removed outlier: 3.553A pdb=" N GLY B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 333 removed outlier: 4.017A pdb=" N GLU B 330 " --> pdb=" O ARG B 327 " (cutoff:3.500A) Proline residue: B 331 - end of helix No H-bonds generated for 'chain 'B' and resid 327 through 333' Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.749A pdb=" N ILE B 357 " --> pdb=" O ILE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 367 No H-bonds generated for 'chain 'B' and resid 364 through 367' Processing helix chain 'B' and resid 374 through 400 removed outlier: 3.937A pdb=" N MET B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 438 removed outlier: 3.842A pdb=" N ALA B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 454 Processing helix chain 'B' and resid 460 through 463 No H-bonds generated for 'chain 'B' and resid 460 through 463' Processing helix chain 'B' and resid 478 through 493 removed outlier: 4.073A pdb=" N THR B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 506 Proline residue: B 501 - end of helix removed outlier: 3.821A pdb=" N ASP B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 538 removed outlier: 3.752A pdb=" N ASP B 536 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 556 Processing helix chain 'B' and resid 572 through 590 Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 63 through 70 Processing helix chain 'C' and resid 80 through 90 removed outlier: 4.289A pdb=" N HIS C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 111 through 122 removed outlier: 4.168A pdb=" N ALA C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 149 through 163 Processing helix chain 'C' and resid 174 through 180 removed outlier: 3.588A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 188 No H-bonds generated for 'chain 'C' and resid 185 through 188' Processing helix chain 'A' and resid 100 through 121 removed outlier: 3.570A pdb=" N ILE A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 128 No H-bonds generated for 'chain 'A' and resid 125 through 128' Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 194 through 197 No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.906A pdb=" N PHE A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 253 through 270 removed outlier: 4.115A pdb=" N ASP A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ALA A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 311 removed outlier: 3.553A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 removed outlier: 4.017A pdb=" N GLU A 330 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Proline residue: A 331 - end of helix No H-bonds generated for 'chain 'A' and resid 327 through 333' Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.750A pdb=" N ILE A 357 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 367 No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 374 through 400 removed outlier: 3.937A pdb=" N MET A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 438 removed outlier: 3.842A pdb=" N ALA A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 454 Processing helix chain 'A' and resid 460 through 463 No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 478 through 493 removed outlier: 4.073A pdb=" N THR A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 Proline residue: A 501 - end of helix removed outlier: 3.821A pdb=" N ASP A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 538 removed outlier: 3.753A pdb=" N ASP A 536 " --> pdb=" O THR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 556 Processing helix chain 'A' and resid 572 through 590 484 hydrogen bonds defined for protein. 1452 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: 2.86 Time building geometry restraints manager: 5.04 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: 1776 1.31 - 1.44: 3030 1.44 - 1.57: 6478 1.57 - 1.69: 0 1.69 - 1.82: 74 Bond restraints: 11358 Sorted by residual: bond pdb=" C12 HG0 B1003 " pdb=" N2 HG0 B1003 " ideal model delta sigma weight residual 1.452 1.245 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C12 HG0 A 604 " pdb=" N3 HG0 A 604 " ideal model delta sigma weight residual 1.450 1.243 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C12 HG0 B1003 " pdb=" N3 HG0 B1003 " ideal model delta sigma weight residual 1.450 1.243 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C12 HG0 A 604 " pdb=" N2 HG0 A 604 " ideal model delta sigma weight residual 1.452 1.245 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C12 HG0 B1003 " pdb=" N1 HG0 B1003 " ideal model delta sigma weight residual 1.260 1.438 -0.178 2.00e-02 2.50e+03 7.90e+01 ... (remaining 11353 not shown) Histogram of bond angle deviations from ideal: 94.45 - 102.39: 47 102.39 - 110.33: 2777 110.33 - 118.27: 5929 118.27 - 126.21: 6451 126.21 - 134.15: 156 Bond angle restraints: 15360 Sorted by residual: angle pdb=" C PHE D 119 " pdb=" CA PHE D 119 " pdb=" CB PHE D 119 " ideal model delta sigma weight residual 110.67 127.47 -16.80 1.92e+00 2.71e-01 7.66e+01 angle pdb=" C PHE C 119 " pdb=" CA PHE C 119 " pdb=" CB PHE C 119 " ideal model delta sigma weight residual 110.67 127.46 -16.79 1.92e+00 2.71e-01 7.65e+01 angle pdb=" N LEU B 163 " pdb=" CA LEU B 163 " pdb=" C LEU B 163 " ideal model delta sigma weight residual 113.23 124.01 -10.78 1.24e+00 6.50e-01 7.56e+01 angle pdb=" N LEU A 163 " pdb=" CA LEU A 163 " pdb=" C LEU A 163 " ideal model delta sigma weight residual 113.23 124.00 -10.77 1.24e+00 6.50e-01 7.55e+01 angle pdb=" N GLU A 346 " pdb=" CA GLU A 346 " pdb=" C GLU A 346 " ideal model delta sigma weight residual 113.50 104.31 9.19 1.23e+00 6.61e-01 5.59e+01 ... (remaining 15355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 5926 17.05 - 34.09: 558 34.09 - 51.14: 146 51.14 - 68.18: 24 68.18 - 85.23: 16 Dihedral angle restraints: 6670 sinusoidal: 2674 harmonic: 3996 Sorted by residual: dihedral pdb=" C PHE D 119 " pdb=" N PHE D 119 " pdb=" CA PHE D 119 " pdb=" CB PHE D 119 " ideal model delta harmonic sigma weight residual -122.60 -146.60 24.00 0 2.50e+00 1.60e-01 9.22e+01 dihedral pdb=" C PHE C 119 " pdb=" N PHE C 119 " pdb=" CA PHE C 119 " pdb=" CB PHE C 119 " ideal model delta harmonic sigma weight residual -122.60 -146.58 23.98 0 2.50e+00 1.60e-01 9.20e+01 dihedral pdb=" N PHE D 119 " pdb=" C PHE D 119 " pdb=" CA PHE D 119 " pdb=" CB PHE D 119 " ideal model delta harmonic sigma weight residual 122.80 140.70 -17.90 0 2.50e+00 1.60e-01 5.13e+01 ... (remaining 6667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 1736 0.168 - 0.336: 18 0.336 - 0.505: 4 0.505 - 0.673: 0 0.673 - 0.841: 2 Chirality restraints: 1760 Sorted by residual: chirality pdb=" CA PHE D 119 " pdb=" N PHE D 119 " pdb=" C PHE D 119 " pdb=" CB PHE D 119 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA PHE C 119 " pdb=" N PHE C 119 " pdb=" C PHE C 119 " pdb=" CB PHE C 119 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" CA VAL A 160 " pdb=" N VAL A 160 " pdb=" C VAL A 160 " pdb=" CB VAL A 160 " both_signs ideal model delta sigma weight residual False 2.44 2.84 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 1757 not shown) Planarity restraints: 1912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 182 " -0.023 2.00e-02 2.50e+03 1.88e-02 6.19e+00 pdb=" CG PHE B 182 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 182 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 182 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 182 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 182 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 182 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 182 " 0.023 2.00e-02 2.50e+03 1.88e-02 6.18e+00 pdb=" CG PHE A 182 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 182 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 182 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 182 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 182 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 182 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 101 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 102 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.030 5.00e-02 4.00e+02 ... (remaining 1909 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2196 2.76 - 3.29: 11349 3.29 - 3.83: 18042 3.83 - 4.36: 21580 4.36 - 4.90: 35966 Nonbonded interactions: 89133 Sorted by model distance: nonbonded pdb=" OG1 THR A 197 " pdb=" OD1 ASN A 266 " model vdw 2.221 2.440 nonbonded pdb=" OG1 THR B 197 " pdb=" OD1 ASN B 266 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR B 433 " pdb=" OE1 GLN B 449 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR A 433 " pdb=" OE1 GLN A 449 " model vdw 2.231 2.440 nonbonded pdb=" NZ LYS B 116 " pdb=" OG SER B 388 " model vdw 2.265 2.520 ... (remaining 89128 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 85 through 593 or resid 602)) selection = (chain 'B' and (resid 85 through 593 or resid 1002)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 4.060 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 32.370 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.010 0.207 11358 Z= 0.640 Angle : 1.093 16.804 15360 Z= 0.621 Chirality : 0.067 0.841 1760 Planarity : 0.005 0.054 1912 Dihedral : 14.916 85.225 4094 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.34 % Allowed : 0.84 % Favored : 98.83 % Cbeta Deviations : 0.31 % 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: -2.95 (0.21), residues: 1380 helix: -1.60 (0.15), residues: 952 sheet: None (None), residues: 0 loop : -2.46 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 434 HIS 0.009 0.002 HIS A 523 PHE 0.043 0.003 PHE A 182 TYR 0.022 0.002 TYR A 209 ARG 0.005 0.001 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 261 time to evaluate : 1.115 Fit side-chains REVERT: C 132 ARG cc_start: 0.7326 (mtp180) cc_final: 0.6927 (mtp180) REVERT: A 131 GLU cc_start: 0.8055 (pp20) cc_final: 0.7586 (pp20) REVERT: A 318 PHE cc_start: 0.8591 (t80) cc_final: 0.8379 (t80) outliers start: 4 outliers final: 1 residues processed: 263 average time/residue: 0.2647 time to fit residues: 93.9404 Evaluate side-chains 186 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 HIS ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS A 523 HIS ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11358 Z= 0.208 Angle : 0.631 8.364 15360 Z= 0.324 Chirality : 0.043 0.177 1760 Planarity : 0.004 0.042 1912 Dihedral : 7.733 81.891 1551 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.17 % Allowed : 10.82 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.22), residues: 1380 helix: -0.64 (0.17), residues: 916 sheet: None (None), residues: 0 loop : -2.53 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 386 HIS 0.005 0.001 HIS B 523 PHE 0.023 0.002 PHE A 182 TYR 0.016 0.001 TYR B 577 ARG 0.008 0.001 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 1.276 Fit side-chains REVERT: B 115 MET cc_start: 0.7744 (mmm) cc_final: 0.7499 (mmm) REVERT: B 312 TYR cc_start: 0.7227 (m-10) cc_final: 0.6721 (m-10) REVERT: B 327 ARG cc_start: 0.7843 (mmt-90) cc_final: 0.7583 (mmp80) REVERT: B 493 PHE cc_start: 0.8358 (m-10) cc_final: 0.7972 (m-80) REVERT: A 131 GLU cc_start: 0.7591 (pp20) cc_final: 0.6963 (pp20) REVERT: A 296 LEU cc_start: 0.7259 (mt) cc_final: 0.7007 (mt) REVERT: A 327 ARG cc_start: 0.7683 (mmt-90) cc_final: 0.7480 (mmp80) REVERT: A 493 PHE cc_start: 0.8460 (m-10) cc_final: 0.8012 (m-80) REVERT: A 552 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7548 (mtm-85) outliers start: 14 outliers final: 11 residues processed: 206 average time/residue: 0.2297 time to fit residues: 67.6613 Evaluate side-chains 186 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 175 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 20.0000 chunk 38 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS B 578 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11358 Z= 0.271 Angle : 0.621 6.835 15360 Z= 0.319 Chirality : 0.044 0.153 1760 Planarity : 0.004 0.041 1912 Dihedral : 7.661 83.577 1550 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.52 % Allowed : 12.75 % Favored : 83.72 % 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: -1.63 (0.23), residues: 1380 helix: -0.44 (0.17), residues: 932 sheet: None (None), residues: 0 loop : -2.32 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 386 HIS 0.006 0.001 HIS A 376 PHE 0.021 0.002 PHE C 119 TYR 0.020 0.001 TYR B 209 ARG 0.006 0.001 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 215 time to evaluate : 1.218 Fit side-chains REVERT: D 189 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.6642 (tmm) REVERT: B 115 MET cc_start: 0.7855 (mmm) cc_final: 0.7561 (mmm) REVERT: B 312 TYR cc_start: 0.7288 (m-10) cc_final: 0.6714 (m-10) REVERT: B 327 ARG cc_start: 0.7847 (mmt-90) cc_final: 0.7614 (mmp80) REVERT: B 435 PHE cc_start: 0.7915 (t80) cc_final: 0.7637 (t80) REVERT: C 189 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.6577 (tmm) REVERT: A 296 LEU cc_start: 0.7301 (mt) cc_final: 0.7022 (mt) REVERT: A 493 PHE cc_start: 0.8459 (m-10) cc_final: 0.8030 (m-80) REVERT: A 497 MET cc_start: 0.6931 (ptm) cc_final: 0.6498 (ppp) REVERT: A 528 ASP cc_start: 0.7804 (t70) cc_final: 0.7571 (t0) REVERT: A 548 ASP cc_start: 0.7393 (t70) cc_final: 0.7060 (t70) REVERT: A 552 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.7547 (mtm-85) outliers start: 42 outliers final: 27 residues processed: 235 average time/residue: 0.2306 time to fit residues: 78.1829 Evaluate side-chains 225 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 537 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.4980 chunk 93 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN B 578 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11358 Z= 0.198 Angle : 0.567 7.199 15360 Z= 0.291 Chirality : 0.042 0.148 1760 Planarity : 0.004 0.037 1912 Dihedral : 7.413 85.872 1550 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.10 % Allowed : 16.36 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.23), residues: 1380 helix: -0.08 (0.17), residues: 920 sheet: None (None), residues: 0 loop : -2.18 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 386 HIS 0.004 0.001 HIS A 376 PHE 0.015 0.001 PHE A 119 TYR 0.016 0.001 TYR B 209 ARG 0.008 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 1.218 Fit side-chains REVERT: D 189 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.6529 (tmm) REVERT: B 312 TYR cc_start: 0.7124 (m-10) cc_final: 0.6548 (m-10) REVERT: B 435 PHE cc_start: 0.7853 (t80) cc_final: 0.7603 (t80) REVERT: B 493 PHE cc_start: 0.8347 (m-10) cc_final: 0.7936 (m-80) REVERT: C 189 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.6167 (tmm) REVERT: A 141 LEU cc_start: 0.8265 (tp) cc_final: 0.7987 (tp) REVERT: A 312 TYR cc_start: 0.7148 (m-10) cc_final: 0.6525 (m-10) REVERT: A 493 PHE cc_start: 0.8384 (m-10) cc_final: 0.8012 (m-80) REVERT: A 497 MET cc_start: 0.6756 (ptm) cc_final: 0.6223 (ppp) REVERT: A 552 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.7506 (mtm-85) outliers start: 37 outliers final: 23 residues processed: 215 average time/residue: 0.2340 time to fit residues: 71.5671 Evaluate side-chains 202 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 537 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11358 Z= 0.212 Angle : 0.568 7.084 15360 Z= 0.294 Chirality : 0.042 0.142 1760 Planarity : 0.004 0.041 1912 Dihedral : 7.406 84.735 1550 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.94 % Allowed : 17.03 % Favored : 79.03 % 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: -1.10 (0.23), residues: 1380 helix: -0.03 (0.17), residues: 928 sheet: None (None), residues: 0 loop : -2.11 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 386 HIS 0.004 0.001 HIS A 376 PHE 0.014 0.001 PHE C 119 TYR 0.016 0.001 TYR B 577 ARG 0.009 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 201 time to evaluate : 1.177 Fit side-chains REVERT: D 189 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.6430 (tmm) REVERT: B 134 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7744 (mp) REVERT: B 312 TYR cc_start: 0.7093 (m-10) cc_final: 0.6500 (m-10) REVERT: B 435 PHE cc_start: 0.7876 (t80) cc_final: 0.7607 (t80) REVERT: B 493 PHE cc_start: 0.8402 (m-10) cc_final: 0.7995 (m-80) REVERT: C 189 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.5724 (tmm) REVERT: A 134 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7652 (mp) REVERT: A 141 LEU cc_start: 0.8220 (tp) cc_final: 0.7936 (tp) REVERT: A 312 TYR cc_start: 0.7162 (m-10) cc_final: 0.6534 (m-10) REVERT: A 493 PHE cc_start: 0.8389 (m-10) cc_final: 0.8000 (m-80) REVERT: A 497 MET cc_start: 0.6841 (ptm) cc_final: 0.6320 (ppp) REVERT: A 548 ASP cc_start: 0.7291 (t70) cc_final: 0.6932 (t70) REVERT: A 552 ARG cc_start: 0.7564 (ttp-170) cc_final: 0.7354 (mtm-85) outliers start: 47 outliers final: 32 residues processed: 223 average time/residue: 0.2299 time to fit residues: 73.9913 Evaluate side-chains 223 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 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 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11358 Z= 0.270 Angle : 0.596 6.874 15360 Z= 0.307 Chirality : 0.043 0.164 1760 Planarity : 0.004 0.039 1912 Dihedral : 7.621 81.904 1550 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.11 % Allowed : 18.46 % Favored : 77.43 % 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: -1.18 (0.23), residues: 1380 helix: -0.11 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -2.08 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 386 HIS 0.004 0.001 HIS A 376 PHE 0.015 0.001 PHE C 119 TYR 0.017 0.001 TYR B 577 ARG 0.007 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 1.178 Fit side-chains REVERT: D 189 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.6451 (tmm) REVERT: B 134 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7775 (mp) REVERT: B 312 TYR cc_start: 0.7204 (m-10) cc_final: 0.6595 (m-10) REVERT: B 435 PHE cc_start: 0.7957 (t80) cc_final: 0.7668 (t80) REVERT: B 493 PHE cc_start: 0.8422 (m-10) cc_final: 0.7995 (m-80) REVERT: C 189 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.5774 (tmm) REVERT: A 134 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7686 (mp) REVERT: A 141 LEU cc_start: 0.8243 (tp) cc_final: 0.7961 (tp) REVERT: A 312 TYR cc_start: 0.7249 (m-10) cc_final: 0.6603 (m-10) REVERT: A 493 PHE cc_start: 0.8413 (m-10) cc_final: 0.8020 (m-80) REVERT: A 497 MET cc_start: 0.6820 (ptm) cc_final: 0.6277 (ppp) REVERT: A 552 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7531 (mtm-85) outliers start: 49 outliers final: 35 residues processed: 216 average time/residue: 0.2279 time to fit residues: 70.2783 Evaluate side-chains 215 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS B 584 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11358 Z= 0.290 Angle : 0.626 8.854 15360 Z= 0.321 Chirality : 0.044 0.169 1760 Planarity : 0.004 0.038 1912 Dihedral : 7.751 79.881 1550 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.53 % Allowed : 18.96 % Favored : 76.51 % 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: -1.25 (0.23), residues: 1380 helix: -0.22 (0.17), residues: 934 sheet: None (None), residues: 0 loop : -1.99 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 386 HIS 0.004 0.001 HIS B 408 PHE 0.015 0.002 PHE C 119 TYR 0.017 0.001 TYR B 577 ARG 0.005 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 190 time to evaluate : 1.330 Fit side-chains REVERT: D 189 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.6471 (tmm) REVERT: B 89 PHE cc_start: 0.6137 (OUTLIER) cc_final: 0.5836 (m-10) REVERT: B 134 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7772 (mp) REVERT: B 312 TYR cc_start: 0.7226 (m-10) cc_final: 0.6618 (m-10) REVERT: B 327 ARG cc_start: 0.7609 (mmt-90) cc_final: 0.7330 (mmp80) REVERT: B 435 PHE cc_start: 0.7960 (t80) cc_final: 0.7667 (t80) REVERT: B 493 PHE cc_start: 0.8423 (m-10) cc_final: 0.7996 (m-80) REVERT: C 189 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.5735 (tmm) REVERT: A 89 PHE cc_start: 0.6170 (OUTLIER) cc_final: 0.5947 (m-80) REVERT: A 134 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7690 (mp) REVERT: A 141 LEU cc_start: 0.8298 (tp) cc_final: 0.8041 (tp) REVERT: A 312 TYR cc_start: 0.7260 (m-10) cc_final: 0.6619 (m-10) REVERT: A 493 PHE cc_start: 0.8374 (m-10) cc_final: 0.7909 (m-80) REVERT: A 497 MET cc_start: 0.6764 (ptm) cc_final: 0.6219 (ppp) REVERT: A 552 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7528 (mtm-85) outliers start: 54 outliers final: 41 residues processed: 216 average time/residue: 0.2347 time to fit residues: 71.5509 Evaluate side-chains 228 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 487 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.0010 chunk 83 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS B 584 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 584 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11358 Z= 0.183 Angle : 0.576 8.529 15360 Z= 0.298 Chirality : 0.041 0.157 1760 Planarity : 0.004 0.040 1912 Dihedral : 7.494 81.534 1550 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.69 % Allowed : 19.71 % Favored : 76.59 % 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: -0.95 (0.23), residues: 1380 helix: 0.04 (0.17), residues: 928 sheet: None (None), residues: 0 loop : -1.94 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 386 HIS 0.003 0.000 HIS A 376 PHE 0.013 0.001 PHE C 83 TYR 0.015 0.001 TYR B 577 ARG 0.005 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 188 time to evaluate : 1.306 Fit side-chains REVERT: D 77 GLN cc_start: 0.6917 (mp10) cc_final: 0.6532 (mm110) REVERT: D 189 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.6196 (tmm) REVERT: B 134 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7721 (mp) REVERT: B 312 TYR cc_start: 0.6991 (m-10) cc_final: 0.6470 (m-10) REVERT: B 327 ARG cc_start: 0.7483 (mmt-90) cc_final: 0.7255 (mmp80) REVERT: B 435 PHE cc_start: 0.7915 (t80) cc_final: 0.7635 (t80) REVERT: B 493 PHE cc_start: 0.8355 (m-10) cc_final: 0.7965 (m-80) REVERT: C 189 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.5531 (tmm) REVERT: A 134 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7671 (mp) REVERT: A 141 LEU cc_start: 0.8228 (tp) cc_final: 0.7974 (tp) REVERT: A 312 TYR cc_start: 0.7070 (m-10) cc_final: 0.6477 (m-10) REVERT: A 493 PHE cc_start: 0.8309 (m-10) cc_final: 0.7929 (m-80) REVERT: A 497 MET cc_start: 0.6842 (ptm) cc_final: 0.6242 (ppp) outliers start: 44 outliers final: 34 residues processed: 211 average time/residue: 0.2298 time to fit residues: 69.4360 Evaluate side-chains 213 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 487 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 0.0970 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 HIS ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11358 Z= 0.166 Angle : 0.549 7.566 15360 Z= 0.285 Chirality : 0.040 0.168 1760 Planarity : 0.004 0.039 1912 Dihedral : 7.186 81.249 1550 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.44 % Allowed : 20.05 % Favored : 76.51 % 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: -0.69 (0.23), residues: 1380 helix: 0.25 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -1.87 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 386 HIS 0.003 0.000 HIS A 376 PHE 0.011 0.001 PHE B 382 TYR 0.018 0.001 TYR A 577 ARG 0.005 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 1.155 Fit side-chains REVERT: D 189 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.5631 (tmm) REVERT: B 134 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7671 (mp) REVERT: B 312 TYR cc_start: 0.6838 (m-10) cc_final: 0.6352 (m-10) REVERT: B 435 PHE cc_start: 0.7890 (t80) cc_final: 0.7618 (t80) REVERT: B 493 PHE cc_start: 0.8356 (m-10) cc_final: 0.8040 (m-80) REVERT: B 497 MET cc_start: 0.7093 (ptm) cc_final: 0.6839 (ppp) REVERT: C 189 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.5552 (tmm) REVERT: A 134 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7628 (mp) REVERT: A 141 LEU cc_start: 0.8271 (tp) cc_final: 0.8010 (tp) REVERT: A 312 TYR cc_start: 0.6887 (m-10) cc_final: 0.6361 (m-10) REVERT: A 349 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7727 (m-70) REVERT: A 432 LEU cc_start: 0.7972 (mt) cc_final: 0.7724 (mt) REVERT: A 493 PHE cc_start: 0.8317 (m-10) cc_final: 0.7936 (m-80) REVERT: A 497 MET cc_start: 0.6869 (ptm) cc_final: 0.6242 (ppp) outliers start: 41 outliers final: 30 residues processed: 205 average time/residue: 0.2208 time to fit residues: 65.3070 Evaluate side-chains 211 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 487 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 0.0050 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 0.0770 chunk 85 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.5954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 HIS ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11358 Z= 0.171 Angle : 0.559 7.391 15360 Z= 0.289 Chirality : 0.041 0.180 1760 Planarity : 0.004 0.039 1912 Dihedral : 6.995 80.851 1550 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.02 % Allowed : 20.64 % Favored : 76.34 % 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: -0.58 (0.23), residues: 1380 helix: 0.34 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -1.84 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 386 HIS 0.010 0.001 HIS A 349 PHE 0.011 0.001 PHE B 382 TYR 0.016 0.001 TYR A 577 ARG 0.005 0.000 ARG D 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.271 Fit side-chains REVERT: D 189 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.5578 (tmm) REVERT: B 134 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7675 (mp) REVERT: B 283 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: B 312 TYR cc_start: 0.6835 (m-10) cc_final: 0.6234 (m-10) REVERT: B 435 PHE cc_start: 0.7911 (t80) cc_final: 0.7624 (t80) REVERT: B 493 PHE cc_start: 0.8338 (m-10) cc_final: 0.8020 (m-80) REVERT: B 497 MET cc_start: 0.7034 (ptm) cc_final: 0.6796 (ppp) REVERT: C 189 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.5538 (tmm) REVERT: A 134 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7621 (mp) REVERT: A 141 LEU cc_start: 0.8219 (tp) cc_final: 0.7991 (tp) REVERT: A 264 LEU cc_start: 0.8179 (tp) cc_final: 0.7820 (mp) REVERT: A 312 TYR cc_start: 0.6859 (m-10) cc_final: 0.6328 (m-10) REVERT: A 349 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7423 (m-70) REVERT: A 432 LEU cc_start: 0.7949 (mt) cc_final: 0.7689 (mt) REVERT: A 493 PHE cc_start: 0.8324 (m-10) cc_final: 0.7947 (m-80) REVERT: A 497 MET cc_start: 0.6827 (ptm) cc_final: 0.6217 (ppp) outliers start: 36 outliers final: 30 residues processed: 207 average time/residue: 0.2209 time to fit residues: 66.6292 Evaluate side-chains 222 residues out of total 1214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 487 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 0.0040 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.200632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.166905 restraints weight = 13299.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.170546 restraints weight = 7447.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.172899 restraints weight = 5230.862| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11358 Z= 0.190 Angle : 0.563 7.891 15360 Z= 0.291 Chirality : 0.041 0.186 1760 Planarity : 0.004 0.038 1912 Dihedral : 6.901 79.281 1550 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.85 % Allowed : 21.22 % Favored : 75.92 % 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: -0.55 (0.23), residues: 1380 helix: 0.36 (0.17), residues: 928 sheet: None (None), residues: 0 loop : -1.83 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 386 HIS 0.005 0.000 HIS A 349 PHE 0.011 0.001 PHE A 382 TYR 0.016 0.001 TYR A 577 ARG 0.005 0.000 ARG D 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2320.75 seconds wall clock time: 44 minutes 25.20 seconds (2665.20 seconds total)