Starting phenix.real_space_refine on Tue May 13 23:47:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7v_36050/05_2025/8j7v_36050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7v_36050/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7v_36050/05_2025/8j7v_36050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7v_36050/05_2025/8j7v_36050.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7v_36050/05_2025/8j7v_36050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7v_36050/05_2025/8j7v_36050.cif" } resolution = 2.79 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 ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.71, per 1000 atoms: 0.61 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: 2.67 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.64 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: 3.70 Time building geometry restraints manager: 3.13 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: 0.420 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.670 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.280 ------------------------------------------------------------------------------- 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 (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: 0.39 (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 TRP 0.021 0.002 TRP F 159 HIS 0.008 0.001 HIS B 70 PHE 0.017 0.002 PHE C 36 TYR 0.029 0.002 TYR E 150 ARG 0.011 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.11197 ( 607) hydrogen bonds : angle 6.10698 ( 1779) SS BOND : bond 0.00482 ( 8) SS BOND : angle 0.93672 ( 16) covalent geometry : bond 0.00368 (11347) covalent geometry : angle 0.72515 (15445) *********************** 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 : 1.204 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: 1.3549 time to fit residues: 259.6415 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 : 1.220 ------------------------------------------------------------------------------- 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 118 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 0.0970 chunk 127 optimal weight: 7.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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 A 356 HIS C 57 ASN E 110 GLN E 204 HIS B 37 ASN B 111 ASN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 204 HIS D 142 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.215138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.168841 restraints weight = 13030.276| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.51 r_work: 0.3668 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11355 Z= 0.182 Angle : 0.603 7.092 15461 Z= 0.310 Chirality : 0.044 0.268 1774 Planarity : 0.005 0.052 1952 Dihedral : 5.371 48.942 1556 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.56 % Allowed : 23.44 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1410 helix: 1.44 (0.25), residues: 411 sheet: 0.90 (0.24), residues: 478 loop : -0.22 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.003 0.001 HIS A 356 PHE 0.019 0.002 PHE C 36 TYR 0.024 0.002 TYR C 144 ARG 0.006 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 607) hydrogen bonds : angle 4.70643 ( 1779) SS BOND : bond 0.00499 ( 8) SS BOND : angle 1.08112 ( 16) covalent geometry : bond 0.00406 (11347) covalent geometry : angle 0.60192 (15445) *********************** 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 197 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 1.143 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: 0.8196 (ttp-170) cc_final: 0.7724 (tpm170) REVERT: B 71 MET cc_start: 0.5368 (ptm) cc_final: 0.5157 (ttt) REVERT: B 91 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.4832 (pmt170) REVERT: F 43 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7259 (tptp) REVERT: D 179 MET cc_start: 0.6592 (mmm) cc_final: 0.6210 (tpt) outliers start: 44 outliers final: 17 residues processed: 181 average time/residue: 1.4138 time to fit residues: 273.7606 Evaluate side-chains 166 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 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 A residue 322 GLN 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 131 LEU Chi-restraints excluded: chain F residue 43 LYS 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 95 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 43 optimal weight: 50.0000 chunk 86 optimal weight: 50.0000 chunk 93 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.214407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.169392 restraints weight = 13183.535| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.59 r_work: 0.3659 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11355 Z= 0.177 Angle : 0.611 9.993 15461 Z= 0.308 Chirality : 0.044 0.357 1774 Planarity : 0.004 0.052 1952 Dihedral : 4.825 49.852 1535 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.88 % Allowed : 24.01 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % 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: 1.11 (0.23), residues: 1410 helix: 1.63 (0.25), residues: 413 sheet: 1.00 (0.24), residues: 477 loop : -0.16 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 167 HIS 0.003 0.001 HIS A 356 PHE 0.018 0.002 PHE C 36 TYR 0.015 0.002 TYR C 32 ARG 0.006 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 607) hydrogen bonds : angle 4.54697 ( 1779) SS BOND : bond 0.00471 ( 8) SS BOND : angle 0.96488 ( 16) covalent geometry : bond 0.00398 (11347) covalent geometry : angle 0.61011 (15445) *********************** 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 200 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8226 (ttp-170) cc_final: 0.7731 (tpm170) REVERT: B 91 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.4729 (pmt170) REVERT: F 43 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7267 (tptp) REVERT: F 57 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8546 (m) REVERT: D 179 MET cc_start: 0.6607 (mmm) cc_final: 0.6230 (tpt) outliers start: 48 outliers final: 20 residues processed: 187 average time/residue: 1.3284 time to fit residues: 266.1978 Evaluate side-chains 171 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 263 LEU 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 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 B residue 328 THR Chi-restraints excluded: chain F residue 43 LYS 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 96 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 40.0000 chunk 62 optimal weight: 0.0970 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 96 ASN C 128 GLN E 110 GLN B 70 HIS ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.215841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.171980 restraints weight = 13141.254| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.62 r_work: 0.3691 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11355 Z= 0.135 Angle : 0.593 8.700 15461 Z= 0.296 Chirality : 0.043 0.271 1774 Planarity : 0.004 0.051 1952 Dihedral : 4.676 49.145 1535 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.40 % Allowed : 24.66 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % 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: 1.24 (0.23), residues: 1410 helix: 1.79 (0.25), residues: 414 sheet: 1.07 (0.24), residues: 478 loop : -0.14 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 167 HIS 0.002 0.001 HIS B 325 PHE 0.014 0.001 PHE C 36 TYR 0.015 0.001 TYR E 150 ARG 0.006 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 607) hydrogen bonds : angle 4.42343 ( 1779) SS BOND : bond 0.00398 ( 8) SS BOND : angle 0.76039 ( 16) covalent geometry : bond 0.00306 (11347) covalent geometry : angle 0.59326 (15445) *********************** 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 195 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.184 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: 0.8200 (ttp-170) cc_final: 0.7714 (tpm170) REVERT: B 91 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.4771 (pmt170) REVERT: D 179 MET cc_start: 0.6542 (mmm) cc_final: 0.6198 (tpt) outliers start: 42 outliers final: 17 residues processed: 184 average time/residue: 1.3899 time to fit residues: 274.3355 Evaluate side-chains 165 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 277 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 E residue 192 THR 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 B residue 328 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 69 optimal weight: 50.0000 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4401 r_free = 0.4401 target = 0.215104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.170184 restraints weight = 13197.166| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.53 r_work: 0.3683 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11355 Z= 0.181 Angle : 0.626 12.102 15461 Z= 0.312 Chirality : 0.044 0.370 1774 Planarity : 0.005 0.057 1952 Dihedral : 4.806 52.046 1535 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.40 % Allowed : 25.14 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % 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: 1.26 (0.23), residues: 1410 helix: 1.86 (0.25), residues: 412 sheet: 0.95 (0.24), residues: 484 loop : -0.05 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 167 HIS 0.003 0.001 HIS C 38 PHE 0.020 0.002 PHE C 36 TYR 0.016 0.002 TYR E 150 ARG 0.007 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 607) hydrogen bonds : angle 4.40491 ( 1779) SS BOND : bond 0.00487 ( 8) SS BOND : angle 1.02115 ( 16) covalent geometry : bond 0.00409 (11347) covalent geometry : angle 0.62527 (15445) *********************** 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 194 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 1.132 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: 0.8225 (ttp-170) cc_final: 0.7719 (tpm170) REVERT: A 366 GLN cc_start: 0.8179 (mt0) cc_final: 0.7952 (mt0) REVERT: B 91 ARG cc_start: 0.6033 (OUTLIER) cc_final: 0.4770 (pmt170) REVERT: F 57 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8541 (m) REVERT: D 179 MET cc_start: 0.6622 (mmm) cc_final: 0.6272 (tpt) outliers start: 42 outliers final: 17 residues processed: 185 average time/residue: 1.3182 time to fit residues: 261.7617 Evaluate side-chains 167 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 320 SER 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 269 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 107 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 65 optimal weight: 50.0000 chunk 79 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 30 optimal weight: 0.0070 chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 overall best weight: 4.6006 ------------------------------------------------------------------------------- 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 232 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 = 0.4388 r_free = 0.4388 target = 0.213616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.167426 restraints weight = 13243.384| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.46 r_work: 0.3662 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11355 Z= 0.273 Angle : 0.676 11.227 15461 Z= 0.343 Chirality : 0.047 0.304 1774 Planarity : 0.005 0.069 1952 Dihedral : 5.119 57.600 1535 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.04 % Allowed : 24.49 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % 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: 1.14 (0.23), residues: 1410 helix: 1.82 (0.26), residues: 411 sheet: 0.82 (0.24), residues: 484 loop : -0.08 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 350 HIS 0.003 0.001 HIS B 325 PHE 0.023 0.002 PHE C 36 TYR 0.019 0.002 TYR E 150 ARG 0.007 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 607) hydrogen bonds : angle 4.50475 ( 1779) SS BOND : bond 0.00623 ( 8) SS BOND : angle 1.32321 ( 16) covalent geometry : bond 0.00624 (11347) covalent geometry : angle 0.67544 (15445) *********************** 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 198 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 1.323 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: 0.8287 (ttp-170) cc_final: 0.7779 (tpm170) REVERT: A 366 GLN cc_start: 0.8225 (mt0) cc_final: 0.7983 (mt0) REVERT: B 91 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.4568 (pmt170) REVERT: F 57 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8560 (m) REVERT: D 179 MET cc_start: 0.6670 (mmm) cc_final: 0.6319 (tpt) outliers start: 50 outliers final: 24 residues processed: 182 average time/residue: 1.3627 time to fit residues: 266.2148 Evaluate side-chains 171 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 89 LYS Chi-restraints excluded: chain A residue 320 SER 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 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 B residue 365 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 chunk 43 optimal weight: 40.0000 chunk 123 optimal weight: 0.3980 chunk 3 optimal weight: 50.0000 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 314 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.216336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173114 restraints weight = 13388.508| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.67 r_work: 0.3707 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11355 Z= 0.122 Angle : 0.610 11.703 15461 Z= 0.302 Chirality : 0.043 0.289 1774 Planarity : 0.004 0.050 1952 Dihedral : 4.737 52.219 1535 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.99 % Allowed : 26.68 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % 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: 1.36 (0.23), residues: 1410 helix: 2.02 (0.25), residues: 415 sheet: 1.01 (0.24), residues: 482 loop : -0.07 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 167 HIS 0.002 0.001 HIS B 325 PHE 0.015 0.001 PHE E 80 TYR 0.018 0.001 TYR E 150 ARG 0.008 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 607) hydrogen bonds : angle 4.31952 ( 1779) SS BOND : bond 0.00363 ( 8) SS BOND : angle 0.63588 ( 16) covalent geometry : bond 0.00274 (11347) covalent geometry : angle 0.60984 (15445) *********************** 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 189 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7694 (tpm170) REVERT: A 366 GLN cc_start: 0.8079 (mt0) cc_final: 0.7853 (mt0) REVERT: B 91 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.4602 (pmt170) REVERT: D 179 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6298 (tpt) outliers start: 37 outliers final: 17 residues processed: 179 average time/residue: 1.3769 time to fit residues: 266.3537 Evaluate side-chains 167 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS 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 192 THR 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 328 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 38 HIS 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: 50.0000 chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 46 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 114 optimal weight: 0.0870 chunk 129 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.5560 ------------------------------------------------------------------------------- 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 = 0.4413 r_free = 0.4413 target = 0.216146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.169773 restraints weight = 13171.364| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.56 r_work: 0.3686 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11355 Z= 0.145 Angle : 0.637 12.704 15461 Z= 0.316 Chirality : 0.044 0.282 1774 Planarity : 0.005 0.065 1952 Dihedral : 4.755 51.592 1535 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.99 % Allowed : 26.68 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % 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: 1.32 (0.23), residues: 1410 helix: 1.88 (0.25), residues: 414 sheet: 1.01 (0.24), residues: 482 loop : 0.01 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.002 0.001 HIS B 325 PHE 0.025 0.002 PHE B 48 TYR 0.020 0.001 TYR E 150 ARG 0.008 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 607) hydrogen bonds : angle 4.41045 ( 1779) SS BOND : bond 0.00424 ( 8) SS BOND : angle 0.83649 ( 16) covalent geometry : bond 0.00327 (11347) covalent geometry : angle 0.63670 (15445) *********************** 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 187 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8222 (ttp-170) cc_final: 0.7682 (tpm170) REVERT: A 366 GLN cc_start: 0.8095 (mt0) cc_final: 0.7872 (mt0) REVERT: B 71 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5319 (pmt) REVERT: B 91 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.4679 (pmt170) REVERT: D 179 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6294 (tpt) outliers start: 37 outliers final: 17 residues processed: 175 average time/residue: 1.3424 time to fit residues: 251.9720 Evaluate side-chains 164 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 89 LYS 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 B residue 71 MET 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 328 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 38 HIS 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 133 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 0.0050 chunk 96 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.7198 ------------------------------------------------------------------------------- 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 ** 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 = 0.215751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.168075 restraints weight = 13341.093| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.56 r_work: 0.3612 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11355 Z= 0.149 Angle : 0.653 14.028 15461 Z= 0.321 Chirality : 0.045 0.414 1774 Planarity : 0.005 0.051 1952 Dihedral : 4.749 50.632 1535 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.43 % Allowed : 27.65 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % 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: 1.37 (0.23), residues: 1410 helix: 1.98 (0.25), residues: 414 sheet: 0.98 (0.24), residues: 484 loop : 0.03 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS C 193 PHE 0.021 0.002 PHE B 48 TYR 0.019 0.001 TYR E 150 ARG 0.009 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 607) hydrogen bonds : angle 4.41416 ( 1779) SS BOND : bond 0.00432 ( 8) SS BOND : angle 0.84824 ( 16) covalent geometry : bond 0.00344 (11347) covalent geometry : angle 0.65302 (15445) *********************** 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 173 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8414 (ttp-170) cc_final: 0.7762 (tpm170) REVERT: A 366 GLN cc_start: 0.8148 (mt0) cc_final: 0.7922 (mt0) REVERT: C 140 LEU cc_start: 0.7955 (mp) cc_final: 0.7695 (mt) REVERT: B 91 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.4830 (pmt170) REVERT: F 57 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8565 (m) REVERT: D 179 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6476 (tpt) outliers start: 30 outliers final: 18 residues processed: 165 average time/residue: 1.3343 time to fit residues: 235.7925 Evaluate side-chains 166 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LYS 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 181 THR Chi-restraints excluded: chain E residue 182 LEU 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 328 THR Chi-restraints excluded: chain B residue 365 ARG 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 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 85 optimal weight: 30.0000 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4424 r_free = 0.4424 target = 0.217242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.174489 restraints weight = 13178.545| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.52 r_work: 0.3711 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11355 Z= 0.130 Angle : 0.659 14.635 15461 Z= 0.322 Chirality : 0.044 0.389 1774 Planarity : 0.004 0.050 1952 Dihedral : 4.674 48.031 1535 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.18 % Allowed : 27.81 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % 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: 1.39 (0.23), residues: 1410 helix: 2.03 (0.25), residues: 415 sheet: 1.00 (0.23), residues: 482 loop : 0.00 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS D 193 PHE 0.028 0.001 PHE B 48 TYR 0.019 0.001 TYR E 150 ARG 0.012 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 607) hydrogen bonds : angle 4.38368 ( 1779) SS BOND : bond 0.00371 ( 8) SS BOND : angle 0.68360 ( 16) covalent geometry : bond 0.00294 (11347) covalent geometry : angle 0.65849 (15445) ********************** 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 176 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8280 (ttp-170) cc_final: 0.7712 (tpm170) REVERT: A 366 GLN cc_start: 0.8022 (mt0) cc_final: 0.7782 (mt0) REVERT: B 91 ARG cc_start: 0.6119 (OUTLIER) cc_final: 0.4879 (pmt170) REVERT: D 179 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6266 (tpt) outliers start: 27 outliers final: 19 residues processed: 170 average time/residue: 1.3231 time to fit residues: 241.6126 Evaluate side-chains 163 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 249 ILE 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 141 VAL Chi-restraints excluded: chain E residue 181 THR 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 328 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 38 HIS 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 75 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 50.0000 chunk 92 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.4403 r_free = 0.4403 target = 0.215053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.169729 restraints weight = 13078.003| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.47 r_work: 0.3683 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11355 Z= 0.236 Angle : 0.709 13.762 15461 Z= 0.352 Chirality : 0.047 0.381 1774 Planarity : 0.005 0.062 1952 Dihedral : 5.033 54.777 1535 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.18 % Allowed : 28.05 % 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 (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: 1.27 (0.23), residues: 1410 helix: 1.86 (0.25), residues: 412 sheet: 0.89 (0.24), residues: 484 loop : 0.05 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 350 HIS 0.003 0.001 HIS B 325 PHE 0.025 0.002 PHE B 48 TYR 0.023 0.002 TYR E 150 ARG 0.011 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 607) hydrogen bonds : angle 4.52745 ( 1779) SS BOND : bond 0.00606 ( 8) SS BOND : angle 1.21380 ( 16) covalent geometry : bond 0.00544 (11347) covalent geometry : angle 0.70871 (15445) =============================================================================== Job complete usr+sys time: 8717.78 seconds wall clock time: 150 minutes 43.13 seconds (9043.13 seconds total)