Starting phenix.real_space_refine on Sat Aug 23 09:26:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7v_36050/08_2025/8j7v_36050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7v_36050/08_2025/8j7v_36050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j7v_36050/08_2025/8j7v_36050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7v_36050/08_2025/8j7v_36050.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j7v_36050/08_2025/8j7v_36050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7v_36050/08_2025/8j7v_36050.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.072 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 47 5.16 5 C 7093 2.51 5 N 1844 2.21 5 O 2099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11083 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2242 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 2 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "B" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2213 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 3 Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Time building chain proxies: 2.26, per 1000 atoms: 0.20 Number of scatterers: 11083 At special positions: 0 Unit cell: (103.228, 95.348, 158.388, 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 47 16.00 O 2099 8.00 N 1844 7.00 C 7093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.88 Conformation dependent library (CDL) restraints added in 268.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2682 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 26 sheets defined 32.8% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 3.508A pdb=" N PHE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 58 Processing helix chain 'A' and resid 63 through 89 removed outlier: 4.038A pdb=" N LYS A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 129 removed outlier: 4.031A pdb=" N VAL A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.840A pdb=" N ILE A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 Processing helix chain 'A' and resid 265 through 294 removed outlier: 4.460A pdb=" N ILE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.272A pdb=" N ASN A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.513A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.631A pdb=" N ILE E 64 " --> pdb=" O ALA E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.727A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.679A pdb=" N ILE B 29 " --> pdb=" O TRP B 25 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 59 Processing helix chain 'B' and resid 61 through 89 Processing helix chain 'B' and resid 101 through 132 removed outlier: 4.152A pdb=" N VAL B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 159 removed outlier: 3.917A pdb=" N LEU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 removed outlier: 4.170A pdb=" N LEU B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLY B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 294 removed outlier: 3.682A pdb=" N CYS B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.691A pdb=" N ASN B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 347 through 362 removed outlier: 3.542A pdb=" N ALA B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.626A pdb=" N ILE F 64 " --> pdb=" O ALA F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 86 through 90 removed outlier: 4.059A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 330 removed outlier: 5.781A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR A 334 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.260A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.260A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.968A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.053A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.132A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU E 45 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.344A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.344A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'B' and resid 318 through 330 removed outlier: 5.732A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.462A pdb=" N VAL F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.679A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 129 removed outlier: 6.122A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 125 through 129 removed outlier: 6.122A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.317A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.317A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AC7, first strand: chain 'D' and resid 118 through 122 removed outlier: 5.838A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 157 through 158 651 hydrogen bonds defined for protein. 1779 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: 1.45 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3463 1.34 - 1.46: 2479 1.46 - 1.58: 5337 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 11347 Sorted by residual: bond pdb=" N LYS F 213 " pdb=" CA LYS F 213 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.22e-02 6.72e+03 8.40e+00 bond pdb=" N ILE B 274 " pdb=" CA ILE B 274 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.30e-02 5.92e+03 6.25e+00 bond pdb=" N CYS E 95 " pdb=" CA CYS E 95 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 5.84e+00 bond pdb=" N ASN F 138 " pdb=" CA ASN F 138 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.70e+00 bond pdb=" N MET E 140 " pdb=" CA MET E 140 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.21e-02 6.83e+03 5.62e+00 ... (remaining 11342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 15196 2.38 - 4.76: 203 4.76 - 7.14: 35 7.14 - 9.52: 8 9.52 - 11.90: 3 Bond angle restraints: 15445 Sorted by residual: angle pdb=" CB LYS C 187 " pdb=" CG LYS C 187 " pdb=" CD LYS C 187 " ideal model delta sigma weight residual 111.30 119.18 -7.88 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CA LEU A 153 " pdb=" CB LEU A 153 " pdb=" CG LEU A 153 " ideal model delta sigma weight residual 116.30 128.20 -11.90 3.50e+00 8.16e-02 1.16e+01 angle pdb=" N MET B 257 " pdb=" CA MET B 257 " pdb=" C MET B 257 " ideal model delta sigma weight residual 112.23 108.02 4.21 1.26e+00 6.30e-01 1.12e+01 angle pdb=" N VAL D 29 " pdb=" CA VAL D 29 " pdb=" C VAL D 29 " ideal model delta sigma weight residual 111.77 108.40 3.37 1.04e+00 9.25e-01 1.05e+01 angle pdb=" CG ARG A 231 " pdb=" CD ARG A 231 " pdb=" NE ARG A 231 " ideal model delta sigma weight residual 112.00 119.08 -7.08 2.20e+00 2.07e-01 1.04e+01 ... (remaining 15440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 5786 17.15 - 34.30: 673 34.30 - 51.46: 189 51.46 - 68.61: 40 68.61 - 85.76: 20 Dihedral angle restraints: 6708 sinusoidal: 2553 harmonic: 4155 Sorted by residual: dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 198 " pdb=" CB CYS D 198 " ideal model delta sinusoidal sigma weight residual 93.00 39.00 54.00 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 198 " pdb=" CB CYS C 198 " ideal model delta sinusoidal sigma weight residual 93.00 42.51 50.49 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CA TYR F 94 " pdb=" C TYR F 94 " pdb=" N CYS F 95 " pdb=" CA CYS F 95 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 6705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1585 0.078 - 0.156: 181 0.156 - 0.234: 7 0.234 - 0.312: 0 0.312 - 0.390: 1 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CG LEU A 153 " pdb=" CB LEU A 153 " pdb=" CD1 LEU A 153 " pdb=" CD2 LEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA PHE B 72 " pdb=" N PHE B 72 " pdb=" C PHE B 72 " pdb=" CB PHE B 72 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TYR D 144 " pdb=" N TYR D 144 " pdb=" C TYR D 144 " pdb=" CB TYR D 144 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.53e-01 ... (remaining 1771 not shown) Planarity restraints: 1952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 188 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO F 189 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 188 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO E 189 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 189 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 189 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 107 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ALA B 107 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA B 107 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 108 " 0.011 2.00e-02 2.50e+03 ... (remaining 1949 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 983 2.75 - 3.28: 10877 3.28 - 3.82: 19356 3.82 - 4.36: 23130 4.36 - 4.90: 38632 Nonbonded interactions: 92978 Sorted by model distance: nonbonded pdb=" OD2 ASP D 174 " pdb=" OG1 THR D 176 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR D 186 " pdb=" OD1 ASP D 188 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP D 30 " pdb=" OG SER D 35 " model vdw 2.248 3.040 nonbonded pdb=" OD2 ASP C 174 " pdb=" OG1 THR C 176 " model vdw 2.271 3.040 nonbonded pdb=" NH2 ARG F 66 " pdb=" OD2 ASP F 89 " model vdw 2.293 3.120 ... (remaining 92973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 132 or resid 141 through 161 or resid 229 throu \ gh 259 or resid 265 through 376)) selection = (chain 'B' and (resid 22 through 132 or resid 141 through 376)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.470 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11355 Z= 0.191 Angle : 0.725 11.901 15461 Z= 0.388 Chirality : 0.047 0.390 1774 Planarity : 0.005 0.054 1952 Dihedral : 16.710 85.760 4002 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.54 % Allowed : 25.79 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.22), residues: 1410 helix: 0.75 (0.26), residues: 413 sheet: 0.71 (0.23), residues: 460 loop : -0.43 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 72 TYR 0.029 0.002 TYR E 150 PHE 0.017 0.002 PHE C 36 TRP 0.021 0.002 TRP F 159 HIS 0.008 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00368 (11347) covalent geometry : angle 0.72515 (15445) SS BOND : bond 0.00482 ( 8) SS BOND : angle 0.93672 ( 16) hydrogen bonds : bond 0.11197 ( 607) hydrogen bonds : angle 6.10698 ( 1779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.7407 (ttp-170) cc_final: 0.6383 (tpm170) REVERT: C 173 LYS cc_start: 0.8239 (mppt) cc_final: 0.7924 (pmtt) REVERT: C 179 MET cc_start: 0.7751 (tpp) cc_final: 0.7315 (tpt) REVERT: E 107 TYR cc_start: 0.7803 (m-80) cc_final: 0.7541 (m-80) REVERT: B 125 GLU cc_start: 0.7930 (tp30) cc_final: 0.7477 (tp30) REVERT: F 72 ASP cc_start: 0.7990 (t70) cc_final: 0.7695 (t70) outliers start: 19 outliers final: 14 residues processed: 179 average time/residue: 0.6182 time to fit residues: 117.8065 Evaluate side-chains 163 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 107 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 322 GLN A 356 HIS C 57 ASN C 96 ASN E 110 GLN E 204 HIS B 37 ASN B 111 ASN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B 356 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 204 HIS ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.215742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.171068 restraints weight = 13131.417| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.58 r_work: 0.3686 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11355 Z= 0.136 Angle : 0.578 7.606 15461 Z= 0.295 Chirality : 0.043 0.268 1774 Planarity : 0.004 0.053 1952 Dihedral : 5.197 46.321 1556 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.64 % Allowed : 23.20 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.23), residues: 1410 helix: 1.52 (0.26), residues: 411 sheet: 0.98 (0.24), residues: 478 loop : -0.22 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 72 TYR 0.024 0.001 TYR C 144 PHE 0.015 0.001 PHE E 80 TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00293 (11347) covalent geometry : angle 0.57750 (15445) SS BOND : bond 0.00413 ( 8) SS BOND : angle 0.85474 ( 16) hydrogen bonds : bond 0.03932 ( 607) hydrogen bonds : angle 4.65514 ( 1779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8157 (ttp-170) cc_final: 0.7695 (tpm170) REVERT: B 71 MET cc_start: 0.5314 (ptm) cc_final: 0.5100 (ttt) REVERT: B 91 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.4937 (pmt170) REVERT: D 76 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8629 (p) REVERT: D 179 MET cc_start: 0.6555 (mmm) cc_final: 0.6175 (tpt) outliers start: 45 outliers final: 13 residues processed: 184 average time/residue: 0.5832 time to fit residues: 114.6692 Evaluate side-chains 162 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 158 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 3.9990 chunk 111 optimal weight: 40.0000 chunk 106 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 117 optimal weight: 50.0000 chunk 118 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 322 GLN A 325 HIS E 110 GLN B 232 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.213308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.168136 restraints weight = 13201.042| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.55 r_work: 0.3656 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 11355 Z= 0.274 Angle : 0.665 10.118 15461 Z= 0.339 Chirality : 0.047 0.355 1774 Planarity : 0.005 0.061 1952 Dihedral : 4.790 36.278 1533 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.88 % Allowed : 23.93 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.23), residues: 1410 helix: 1.50 (0.25), residues: 412 sheet: 0.95 (0.24), residues: 476 loop : -0.16 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 72 TYR 0.018 0.002 TYR C 32 PHE 0.022 0.002 PHE C 36 TRP 0.019 0.002 TRP C 167 HIS 0.003 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00627 (11347) covalent geometry : angle 0.66448 (15445) SS BOND : bond 0.00603 ( 8) SS BOND : angle 1.28651 ( 16) hydrogen bonds : bond 0.04494 ( 607) hydrogen bonds : angle 4.66931 ( 1779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8254 (ttp-170) cc_final: 0.7772 (tpm170) REVERT: A 321 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8381 (mp) REVERT: E 5 GLN cc_start: 0.7811 (mt0) cc_final: 0.7610 (mt0) REVERT: B 91 ARG cc_start: 0.5982 (OUTLIER) cc_final: 0.4628 (pmt170) REVERT: F 57 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8556 (m) REVERT: D 179 MET cc_start: 0.6630 (mmm) cc_final: 0.6261 (tpt) outliers start: 48 outliers final: 17 residues processed: 185 average time/residue: 0.5898 time to fit residues: 116.5813 Evaluate side-chains 167 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 19 optimal weight: 0.4980 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 322 GLN C 128 GLN E 110 GLN B 70 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.215370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.168195 restraints weight = 13327.044| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.65 r_work: 0.3617 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11355 Z= 0.137 Angle : 0.608 8.693 15461 Z= 0.302 Chirality : 0.043 0.267 1774 Planarity : 0.004 0.050 1952 Dihedral : 4.522 33.542 1533 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.31 % Allowed : 25.30 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.23), residues: 1410 helix: 1.75 (0.25), residues: 412 sheet: 1.00 (0.24), residues: 479 loop : -0.14 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 72 TYR 0.017 0.001 TYR F 150 PHE 0.014 0.001 PHE C 36 TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00309 (11347) covalent geometry : angle 0.60767 (15445) SS BOND : bond 0.00395 ( 8) SS BOND : angle 0.73608 ( 16) hydrogen bonds : bond 0.03752 ( 607) hydrogen bonds : angle 4.46001 ( 1779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8325 (ttp-170) cc_final: 0.7740 (tpm170) REVERT: E 5 GLN cc_start: 0.7893 (mt0) cc_final: 0.7692 (mt0) REVERT: B 91 ARG cc_start: 0.6060 (OUTLIER) cc_final: 0.4830 (pmt170) REVERT: D 18 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7335 (ttm-80) REVERT: D 179 MET cc_start: 0.6716 (mmm) cc_final: 0.6318 (tpt) outliers start: 41 outliers final: 20 residues processed: 188 average time/residue: 0.5985 time to fit residues: 120.1978 Evaluate side-chains 168 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 12 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 139 optimal weight: 0.3980 chunk 81 optimal weight: 50.0000 chunk 78 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 322 GLN B 314 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.215896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.170818 restraints weight = 13144.474| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.45 r_work: 0.3677 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11355 Z= 0.128 Angle : 0.596 12.519 15461 Z= 0.294 Chirality : 0.043 0.341 1774 Planarity : 0.004 0.056 1952 Dihedral : 4.385 33.334 1533 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.31 % Allowed : 25.14 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.23), residues: 1410 helix: 1.93 (0.25), residues: 414 sheet: 1.08 (0.24), residues: 478 loop : -0.05 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 72 TYR 0.017 0.001 TYR E 150 PHE 0.016 0.001 PHE B 48 TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00285 (11347) covalent geometry : angle 0.59626 (15445) SS BOND : bond 0.00395 ( 8) SS BOND : angle 0.79413 ( 16) hydrogen bonds : bond 0.03579 ( 607) hydrogen bonds : angle 4.31446 ( 1779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.352 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: A 287 ARG cc_start: 0.8245 (ttp-170) cc_final: 0.7700 (tpm170) REVERT: B 91 ARG cc_start: 0.6069 (OUTLIER) cc_final: 0.4838 (pmt170) REVERT: F 1 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6665 (tt0) REVERT: D 179 MET cc_start: 0.6618 (mmm) cc_final: 0.6250 (tpt) outliers start: 41 outliers final: 18 residues processed: 183 average time/residue: 0.5532 time to fit residues: 108.3525 Evaluate side-chains 170 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain F residue 1 GLU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 322 GLN E 110 GLN B 322 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.214596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.168919 restraints weight = 13227.904| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.48 r_work: 0.3672 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11355 Z= 0.236 Angle : 0.652 10.795 15461 Z= 0.328 Chirality : 0.046 0.320 1774 Planarity : 0.005 0.063 1952 Dihedral : 4.696 35.811 1533 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.48 % Allowed : 24.90 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.23), residues: 1410 helix: 1.86 (0.26), residues: 412 sheet: 0.88 (0.24), residues: 484 loop : -0.04 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 72 TYR 0.018 0.002 TYR E 150 PHE 0.022 0.002 PHE C 36 TRP 0.030 0.002 TRP C 167 HIS 0.003 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00542 (11347) covalent geometry : angle 0.65091 (15445) SS BOND : bond 0.00561 ( 8) SS BOND : angle 1.20144 ( 16) hydrogen bonds : bond 0.04134 ( 607) hydrogen bonds : angle 4.43287 ( 1779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.7764 (tpm170) REVERT: B 91 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.4650 (pmt170) REVERT: F 57 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8545 (m) REVERT: D 179 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6447 (tpp) outliers start: 43 outliers final: 19 residues processed: 174 average time/residue: 0.6057 time to fit residues: 112.6100 Evaluate side-chains 164 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 50.0000 chunk 120 optimal weight: 0.9980 chunk 115 optimal weight: 50.0000 chunk 17 optimal weight: 40.0000 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 46 optimal weight: 30.0000 chunk 93 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 322 GLN E 110 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.215012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.169191 restraints weight = 13139.722| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.46 r_work: 0.3662 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11355 Z= 0.187 Angle : 0.641 11.784 15461 Z= 0.321 Chirality : 0.045 0.304 1774 Planarity : 0.005 0.049 1952 Dihedral : 4.666 34.948 1533 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.40 % Allowed : 26.03 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.23), residues: 1410 helix: 1.82 (0.25), residues: 412 sheet: 0.86 (0.24), residues: 484 loop : -0.00 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 72 TYR 0.020 0.002 TYR E 150 PHE 0.020 0.002 PHE C 36 TRP 0.038 0.002 TRP C 167 HIS 0.003 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00425 (11347) covalent geometry : angle 0.64021 (15445) SS BOND : bond 0.00473 ( 8) SS BOND : angle 0.98604 ( 16) hydrogen bonds : bond 0.03922 ( 607) hydrogen bonds : angle 4.42932 ( 1779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8341 (ttp-170) cc_final: 0.7789 (tpm170) REVERT: A 321 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8273 (mp) REVERT: B 91 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.4602 (pmt170) REVERT: D 179 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6498 (tpp) outliers start: 42 outliers final: 22 residues processed: 174 average time/residue: 0.5592 time to fit residues: 104.1836 Evaluate side-chains 166 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 137 optimal weight: 40.0000 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 47 optimal weight: 40.0000 chunk 102 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 322 GLN E 110 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.214944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.170783 restraints weight = 13213.600| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.51 r_work: 0.3664 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11355 Z= 0.170 Angle : 0.657 12.656 15461 Z= 0.327 Chirality : 0.045 0.314 1774 Planarity : 0.005 0.054 1952 Dihedral : 4.625 34.412 1533 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.31 % Allowed : 26.43 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.23), residues: 1410 helix: 1.82 (0.25), residues: 413 sheet: 0.88 (0.24), residues: 484 loop : -0.03 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 231 TYR 0.020 0.001 TYR E 150 PHE 0.020 0.002 PHE B 48 TRP 0.048 0.002 TRP C 167 HIS 0.003 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00389 (11347) covalent geometry : angle 0.65643 (15445) SS BOND : bond 0.00464 ( 8) SS BOND : angle 0.93915 ( 16) hydrogen bonds : bond 0.03828 ( 607) hydrogen bonds : angle 4.43609 ( 1779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.7782 (tpm170) REVERT: A 321 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8255 (mp) REVERT: A 366 GLN cc_start: 0.8177 (mt0) cc_final: 0.7893 (mt0) REVERT: B 91 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.4645 (pmt170) REVERT: F 57 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8563 (m) REVERT: D 179 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6533 (tpp) outliers start: 41 outliers final: 23 residues processed: 178 average time/residue: 0.5607 time to fit residues: 106.9505 Evaluate side-chains 169 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 16 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 322 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.214577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.168703 restraints weight = 13168.825| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.40 r_work: 0.3652 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11355 Z= 0.238 Angle : 0.706 13.940 15461 Z= 0.353 Chirality : 0.047 0.395 1774 Planarity : 0.005 0.055 1952 Dihedral : 4.828 35.993 1533 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.07 % Allowed : 26.84 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.23), residues: 1410 helix: 1.75 (0.25), residues: 411 sheet: 0.77 (0.23), residues: 484 loop : -0.01 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 231 TYR 0.022 0.002 TYR E 150 PHE 0.022 0.002 PHE C 36 TRP 0.037 0.002 TRP C 167 HIS 0.003 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00546 (11347) covalent geometry : angle 0.70548 (15445) SS BOND : bond 0.00583 ( 8) SS BOND : angle 1.24036 ( 16) hydrogen bonds : bond 0.04168 ( 607) hydrogen bonds : angle 4.50218 ( 1779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8355 (ttp-170) cc_final: 0.7785 (tpm170) REVERT: A 321 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8372 (mp) REVERT: C 59 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7790 (mm-30) REVERT: B 71 MET cc_start: 0.5638 (ppp) cc_final: 0.5190 (pmt) REVERT: B 91 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.4565 (pmt170) REVERT: F 57 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8547 (m) REVERT: D 179 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6521 (tpp) outliers start: 38 outliers final: 23 residues processed: 176 average time/residue: 0.5840 time to fit residues: 110.1793 Evaluate side-chains 171 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 106 optimal weight: 0.9990 chunk 17 optimal weight: 40.0000 chunk 44 optimal weight: 20.0000 chunk 137 optimal weight: 40.0000 chunk 20 optimal weight: 0.4980 chunk 79 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 30.0000 chunk 3 optimal weight: 50.0000 chunk 29 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 322 GLN E 110 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.214061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.170798 restraints weight = 13166.467| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.66 r_work: 0.3640 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 11355 Z= 0.263 Angle : 0.727 13.874 15461 Z= 0.364 Chirality : 0.048 0.363 1774 Planarity : 0.005 0.059 1952 Dihedral : 4.928 36.515 1533 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.75 % Allowed : 27.57 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.23), residues: 1410 helix: 1.66 (0.25), residues: 411 sheet: 0.73 (0.23), residues: 484 loop : -0.04 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 231 TYR 0.024 0.002 TYR E 150 PHE 0.027 0.002 PHE B 48 TRP 0.016 0.002 TRP F 159 HIS 0.004 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00604 (11347) covalent geometry : angle 0.72612 (15445) SS BOND : bond 0.00614 ( 8) SS BOND : angle 1.28789 ( 16) hydrogen bonds : bond 0.04284 ( 607) hydrogen bonds : angle 4.57518 ( 1779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8393 (ttp-170) cc_final: 0.7809 (tpm170) REVERT: C 59 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7786 (mm-30) REVERT: C 179 MET cc_start: 0.6617 (tpp) cc_final: 0.6392 (tpt) REVERT: B 71 MET cc_start: 0.5696 (ppp) cc_final: 0.5150 (pmt) REVERT: B 91 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.4538 (pmt170) REVERT: F 57 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8557 (m) REVERT: D 179 MET cc_start: 0.6750 (OUTLIER) cc_final: 0.6522 (tpp) outliers start: 34 outliers final: 23 residues processed: 169 average time/residue: 0.6057 time to fit residues: 109.5114 Evaluate side-chains 171 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 322 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.214933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.170214 restraints weight = 13185.519| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.41 r_work: 0.3683 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11355 Z= 0.170 Angle : 0.697 14.418 15461 Z= 0.345 Chirality : 0.045 0.375 1774 Planarity : 0.005 0.055 1952 Dihedral : 4.754 35.742 1533 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.34 % Allowed : 27.89 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.23), residues: 1410 helix: 1.81 (0.25), residues: 412 sheet: 0.81 (0.23), residues: 484 loop : -0.02 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 231 TYR 0.023 0.001 TYR E 150 PHE 0.023 0.002 PHE B 48 TRP 0.014 0.001 TRP E 47 HIS 0.003 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00389 (11347) covalent geometry : angle 0.69674 (15445) SS BOND : bond 0.00486 ( 8) SS BOND : angle 0.96523 ( 16) hydrogen bonds : bond 0.03869 ( 607) hydrogen bonds : angle 4.48046 ( 1779) =============================================================================== Job complete usr+sys time: 3771.01 seconds wall clock time: 64 minutes 58.97 seconds (3898.97 seconds total)