Starting phenix.real_space_refine on Sat Nov 16 13:01:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/11_2024/8j7v_36050.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/11_2024/8j7v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/11_2024/8j7v_36050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/11_2024/8j7v_36050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/11_2024/8j7v_36050.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/11_2024/8j7v_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-5513/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: 6.73, 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: 2.68 Conformation dependent library (CDL) restraints added in 1.5 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: 1.49 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: 3.79 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: 0.410 Set stop_for_unknowns flag: 0.010 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.600 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- 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 11347 Z= 0.240 Angle : 0.725 11.901 15445 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 *********************** 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 : 1.231 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: 1.5132 time to fit residues: 289.3013 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 : 1.237 ------------------------------------------------------------------------------- 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: 30.0000 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 11347 Z= 0.266 Angle : 0.602 7.092 15445 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 *********************** 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 : 1.119 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: 0.7430 (ttp-170) cc_final: 0.6301 (tpm170) REVERT: C 91 TYR cc_start: 0.8777 (m-80) cc_final: 0.8344 (m-80) REVERT: C 179 MET cc_start: 0.7672 (tpp) cc_final: 0.7323 (tpt) REVERT: E 11 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8827 (tp) REVERT: E 72 ASP cc_start: 0.7788 (t70) cc_final: 0.7402 (t70) REVERT: E 88 ASP cc_start: 0.8421 (p0) cc_final: 0.8214 (p0) REVERT: E 107 TYR cc_start: 0.7878 (m-80) cc_final: 0.7589 (m-80) REVERT: B 91 ARG cc_start: 0.5623 (OUTLIER) cc_final: 0.4272 (pmt170) REVERT: B 125 GLU cc_start: 0.8090 (tp30) cc_final: 0.7722 (tp30) REVERT: F 43 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.6907 (tptp) REVERT: F 72 ASP cc_start: 0.8145 (t0) cc_final: 0.7894 (t70) outliers start: 44 outliers final: 17 residues processed: 181 average time/residue: 1.5174 time to fit residues: 293.5169 Evaluate side-chains 168 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 11 LEU 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 70 optimal weight: 60.0000 chunk 39 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 50.0000 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 137 optimal weight: 40.0000 chunk 113 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 43 optimal weight: 50.0000 chunk 102 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 70 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11347 Z= 0.363 Angle : 0.642 9.748 15445 Z= 0.328 Chirality : 0.046 0.338 1774 Planarity : 0.005 0.051 1952 Dihedral : 5.023 53.058 1535 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.12 % Allowed : 24.17 % Favored : 71.71 % 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: 1.01 (0.23), residues: 1410 helix: 1.54 (0.25), residues: 412 sheet: 0.90 (0.24), residues: 477 loop : -0.16 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.004 0.001 HIS A 356 PHE 0.021 0.002 PHE C 36 TYR 0.017 0.002 TYR C 32 ARG 0.006 0.001 ARG C 72 *********************** 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 204 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 1.175 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: 0.7486 (ttp-170) cc_final: 0.6319 (tpm170) REVERT: A 322 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: C 76 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8584 (p) REVERT: C 83 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6580 (tt0) REVERT: C 91 TYR cc_start: 0.8842 (m-80) cc_final: 0.8371 (m-80) REVERT: E 5 GLN cc_start: 0.7393 (mt0) cc_final: 0.6961 (mt0) REVERT: E 11 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8829 (tp) REVERT: E 72 ASP cc_start: 0.7786 (t70) cc_final: 0.7349 (t70) REVERT: E 107 TYR cc_start: 0.7953 (m-80) cc_final: 0.7691 (m-80) REVERT: B 91 ARG cc_start: 0.5615 (OUTLIER) cc_final: 0.3924 (pmt170) REVERT: F 43 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.6879 (tptp) REVERT: F 57 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8223 (m) REVERT: F 72 ASP cc_start: 0.8181 (t0) cc_final: 0.7900 (t70) outliers start: 51 outliers final: 19 residues processed: 189 average time/residue: 1.4594 time to fit residues: 295.4863 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 : 1.260 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain E residue 11 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 F residue 43 LYS Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 LYS 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 125 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 85 optimal weight: 40.0000 chunk 127 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 11347 Z= 0.424 Angle : 0.674 8.964 15445 Z= 0.344 Chirality : 0.047 0.260 1774 Planarity : 0.005 0.060 1952 Dihedral : 5.190 57.598 1535 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.85 % Allowed : 23.44 % Favored : 71.71 % 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: 0.95 (0.23), residues: 1410 helix: 1.54 (0.25), residues: 411 sheet: 0.80 (0.24), residues: 480 loop : -0.17 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 47 HIS 0.004 0.001 HIS B 325 PHE 0.024 0.002 PHE C 36 TYR 0.019 0.002 TYR C 32 ARG 0.007 0.001 ARG C 72 *********************** 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 207 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 147 time to evaluate : 1.229 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: 0.7527 (ttp-170) cc_final: 0.6324 (tpm170) REVERT: A 322 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: C 76 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8545 (p) REVERT: C 91 TYR cc_start: 0.8883 (m-80) cc_final: 0.8416 (m-80) REVERT: C 179 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7274 (tpt) REVERT: E 5 GLN cc_start: 0.7375 (mt0) cc_final: 0.6944 (mt0) REVERT: E 70 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8104 (p) REVERT: E 72 ASP cc_start: 0.7813 (t70) cc_final: 0.7314 (t70) REVERT: B 91 ARG cc_start: 0.5506 (OUTLIER) cc_final: 0.3653 (pmt170) REVERT: B 322 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7987 (mm-40) REVERT: F 43 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.6629 (tptp) REVERT: F 57 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8224 (m) REVERT: F 72 ASP cc_start: 0.8190 (t0) cc_final: 0.7902 (t70) REVERT: F 86 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6882 (mm-40) REVERT: D 18 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7276 (ttm-80) outliers start: 60 outliers final: 24 residues processed: 190 average time/residue: 1.4044 time to fit residues: 286.1255 Evaluate side-chains 178 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP 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 C residue 76 THR Chi-restraints excluded: chain C residue 179 MET 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 115 THR 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 322 GLN Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 SER 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 76 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 50.0000 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11347 Z= 0.365 Angle : 0.657 11.917 15445 Z= 0.332 Chirality : 0.046 0.351 1774 Planarity : 0.005 0.069 1952 Dihedral : 5.164 57.900 1535 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.69 % Allowed : 23.77 % 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 (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: 1.00 (0.23), residues: 1410 helix: 1.65 (0.26), residues: 411 sheet: 0.78 (0.24), residues: 480 loop : -0.15 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 47 HIS 0.003 0.001 HIS B 325 PHE 0.023 0.002 PHE C 36 TYR 0.019 0.002 TYR C 32 ARG 0.007 0.001 ARG C 72 *********************** 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 210 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 152 time to evaluate : 1.255 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: 0.7524 (ttp-170) cc_final: 0.6334 (tpm170) REVERT: A 322 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: A 366 GLN cc_start: 0.8147 (mt0) cc_final: 0.7634 (mt0) REVERT: C 76 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8546 (p) REVERT: C 91 TYR cc_start: 0.8881 (m-80) cc_final: 0.8462 (m-80) REVERT: C 173 LYS cc_start: 0.8285 (mtmm) cc_final: 0.7971 (mppt) REVERT: C 179 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7455 (tpt) REVERT: E 5 GLN cc_start: 0.7377 (mt0) cc_final: 0.6945 (mt0) REVERT: E 70 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.8112 (p) REVERT: E 72 ASP cc_start: 0.7822 (t70) cc_final: 0.7312 (t70) REVERT: B 91 ARG cc_start: 0.5497 (OUTLIER) cc_final: 0.3636 (pmt170) REVERT: B 322 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7980 (mm-40) REVERT: F 43 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.6635 (tptp) REVERT: F 57 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8227 (m) REVERT: F 72 ASP cc_start: 0.8204 (t0) cc_final: 0.7909 (t70) REVERT: D 179 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5719 (tpt) outliers start: 58 outliers final: 27 residues processed: 192 average time/residue: 1.4424 time to fit residues: 296.3055 Evaluate side-chains 186 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 179 MET 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 115 THR 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 322 GLN Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 50.0000 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 314 GLN F 73 ASN D 142 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11347 Z= 0.245 Angle : 0.620 10.614 15445 Z= 0.310 Chirality : 0.044 0.328 1774 Planarity : 0.005 0.052 1952 Dihedral : 4.979 55.380 1535 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.37 % Allowed : 24.25 % 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 (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: 1.15 (0.23), residues: 1410 helix: 1.84 (0.25), residues: 412 sheet: 0.80 (0.24), residues: 484 loop : -0.05 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.003 0.001 HIS C 38 PHE 0.019 0.002 PHE C 36 TYR 0.019 0.001 TYR E 150 ARG 0.008 0.001 ARG C 72 *********************** 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 207 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 1.471 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: 0.7499 (ttp-170) cc_final: 0.6310 (tpm170) REVERT: A 322 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: A 366 GLN cc_start: 0.8066 (mt0) cc_final: 0.7563 (mt0) REVERT: C 83 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6492 (tt0) REVERT: C 91 TYR cc_start: 0.8860 (m-80) cc_final: 0.8417 (m-80) REVERT: C 173 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7937 (mppt) REVERT: C 179 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7317 (tpt) REVERT: E 5 GLN cc_start: 0.7379 (mt0) cc_final: 0.6966 (mt0) REVERT: E 11 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8745 (tp) REVERT: E 70 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.8187 (p) REVERT: E 72 ASP cc_start: 0.7801 (t70) cc_final: 0.7306 (t70) REVERT: B 71 MET cc_start: 0.5944 (ttt) cc_final: 0.5681 (ppp) REVERT: B 91 ARG cc_start: 0.5540 (OUTLIER) cc_final: 0.3697 (pmt170) REVERT: B 322 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7952 (mm-40) REVERT: F 43 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.6715 (tptp) REVERT: F 57 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8223 (m) REVERT: F 72 ASP cc_start: 0.8187 (t0) cc_final: 0.7887 (t70) REVERT: D 18 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6966 (ttm-80) REVERT: D 179 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5758 (tpt) outliers start: 54 outliers final: 28 residues processed: 188 average time/residue: 1.4382 time to fit residues: 289.8812 Evaluate side-chains 188 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 94 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain E residue 11 LEU 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 105 MET Chi-restraints excluded: chain E residue 141 VAL 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 322 GLN Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 37 MET 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 15 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 50.0000 chunk 83 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 11347 Z= 0.339 Angle : 0.657 11.639 15445 Z= 0.331 Chirality : 0.045 0.305 1774 Planarity : 0.005 0.071 1952 Dihedral : 5.081 56.459 1535 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.45 % Allowed : 24.74 % Favored : 70.82 % 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: 1.12 (0.23), residues: 1410 helix: 1.76 (0.25), residues: 411 sheet: 0.78 (0.24), residues: 484 loop : -0.01 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.003 0.001 HIS B 325 PHE 0.022 0.002 PHE C 36 TYR 0.021 0.002 TYR E 150 ARG 0.008 0.001 ARG C 72 *********************** 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 201 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8164 (p0) REVERT: A 287 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.6319 (tpm170) REVERT: A 322 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8379 (pm20) REVERT: A 366 GLN cc_start: 0.8097 (mt0) cc_final: 0.7583 (mt0) REVERT: C 76 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8559 (p) REVERT: C 91 TYR cc_start: 0.8878 (m-80) cc_final: 0.8432 (m-80) REVERT: C 173 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7831 (mppt) REVERT: C 179 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7422 (tpt) REVERT: E 5 GLN cc_start: 0.7386 (mt0) cc_final: 0.6970 (mt0) REVERT: E 11 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8733 (tp) REVERT: E 16 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7936 (mm110) REVERT: E 70 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8167 (p) REVERT: E 72 ASP cc_start: 0.7811 (t70) cc_final: 0.7283 (t70) REVERT: E 179 LEU cc_start: 0.8120 (mm) cc_final: 0.7900 (tp) REVERT: B 71 MET cc_start: 0.5973 (ttt) cc_final: 0.5627 (ppp) REVERT: B 91 ARG cc_start: 0.5460 (OUTLIER) cc_final: 0.3639 (pmt170) REVERT: B 322 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7939 (mm-40) REVERT: F 43 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.6657 (tptp) REVERT: F 57 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8227 (m) REVERT: F 72 ASP cc_start: 0.8191 (t0) cc_final: 0.7889 (t70) REVERT: D 179 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5826 (tpt) outliers start: 55 outliers final: 29 residues processed: 183 average time/residue: 1.4301 time to fit residues: 280.8925 Evaluate side-chains 184 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 94 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain E residue 11 LEU 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 105 MET Chi-restraints excluded: chain E residue 141 VAL 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 322 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 37 MET 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 53 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 40.0000 chunk 26 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11347 Z= 0.301 Angle : 0.660 12.572 15445 Z= 0.329 Chirality : 0.045 0.297 1774 Planarity : 0.005 0.068 1952 Dihedral : 5.046 55.552 1535 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.37 % Allowed : 24.98 % Favored : 70.65 % 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: 1.74 (0.25), residues: 412 sheet: 0.78 (0.24), residues: 484 loop : -0.03 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.003 0.001 HIS C 193 PHE 0.021 0.002 PHE C 36 TYR 0.023 0.002 TYR E 150 ARG 0.007 0.001 ARG A 231 *********************** 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 199 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8141 (p0) REVERT: A 287 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.6310 (tpm170) REVERT: A 322 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: A 366 GLN cc_start: 0.8069 (mt0) cc_final: 0.7560 (mt0) REVERT: C 76 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8562 (p) REVERT: C 91 TYR cc_start: 0.8868 (m-80) cc_final: 0.8435 (m-80) REVERT: C 146 LYS cc_start: 0.8723 (mmtp) cc_final: 0.8383 (mmtm) REVERT: C 173 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7800 (mppt) REVERT: C 179 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7399 (tpt) REVERT: E 5 GLN cc_start: 0.7385 (mt0) cc_final: 0.6967 (mt0) REVERT: E 11 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8723 (tp) REVERT: E 16 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7975 (mm110) REVERT: E 70 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8175 (p) REVERT: E 72 ASP cc_start: 0.7818 (t70) cc_final: 0.7288 (t70) REVERT: B 71 MET cc_start: 0.5998 (ttt) cc_final: 0.5653 (ppp) REVERT: B 91 ARG cc_start: 0.5523 (OUTLIER) cc_final: 0.3675 (pmt170) REVERT: B 322 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7936 (mm-40) REVERT: F 43 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.6674 (tptp) REVERT: F 57 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8219 (m) REVERT: F 72 ASP cc_start: 0.8192 (t0) cc_final: 0.7887 (t70) REVERT: D 174 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7574 (p0) REVERT: D 179 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.5923 (tpt) outliers start: 54 outliers final: 29 residues processed: 183 average time/residue: 1.4106 time to fit residues: 277.6378 Evaluate side-chains 187 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 94 ASP 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 A residue 360 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain E residue 11 LEU 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 105 MET Chi-restraints excluded: chain E residue 141 VAL 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 322 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 37 MET 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 174 ASP 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 117 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 132 optimal weight: 30.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 11347 Z= 0.409 Angle : 0.709 13.872 15445 Z= 0.355 Chirality : 0.048 0.379 1774 Planarity : 0.005 0.074 1952 Dihedral : 5.216 57.491 1535 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.96 % Allowed : 25.46 % 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 (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: 1.03 (0.23), residues: 1410 helix: 1.68 (0.25), residues: 411 sheet: 0.69 (0.23), residues: 484 loop : -0.02 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.003 0.001 HIS C 193 PHE 0.024 0.002 PHE C 36 TYR 0.026 0.002 TYR E 150 ARG 0.008 0.001 ARG A 231 *********************** 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 195 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8134 (p0) REVERT: A 287 ARG cc_start: 0.7580 (ttp-170) cc_final: 0.6347 (tpm170) REVERT: A 322 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: A 366 GLN cc_start: 0.8135 (mt0) cc_final: 0.7626 (mt0) REVERT: C 76 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8533 (p) REVERT: C 91 TYR cc_start: 0.8877 (m-80) cc_final: 0.8508 (m-80) REVERT: C 146 LYS cc_start: 0.8731 (mmtp) cc_final: 0.8458 (mmtm) REVERT: C 173 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7789 (mppt) REVERT: C 179 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7396 (tpt) REVERT: E 5 GLN cc_start: 0.7391 (mt0) cc_final: 0.6952 (mt0) REVERT: E 11 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8741 (tp) REVERT: E 16 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7974 (mm110) REVERT: E 70 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.8119 (p) REVERT: E 72 ASP cc_start: 0.7825 (t70) cc_final: 0.7251 (t70) REVERT: B 71 MET cc_start: 0.6090 (ttt) cc_final: 0.5727 (ppp) REVERT: B 91 ARG cc_start: 0.5446 (OUTLIER) cc_final: 0.3592 (pmt170) REVERT: B 322 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7913 (mm-40) REVERT: F 43 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.6505 (tptp) REVERT: F 57 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8220 (m) REVERT: F 72 ASP cc_start: 0.8186 (t0) cc_final: 0.7891 (t70) REVERT: D 174 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7585 (p0) REVERT: D 179 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5896 (tpt) outliers start: 49 outliers final: 28 residues processed: 179 average time/residue: 1.4465 time to fit residues: 277.5727 Evaluate side-chains 184 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP 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 A residue 322 GLN Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain E residue 11 LEU 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 105 MET Chi-restraints excluded: chain E residue 141 VAL 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 322 GLN Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 37 MET 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 174 ASP 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 81 optimal weight: 7.9990 chunk 63 optimal weight: 30.0000 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 50.0000 chunk 88 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 11347 Z= 0.513 Angle : 0.751 13.359 15445 Z= 0.380 Chirality : 0.050 0.360 1774 Planarity : 0.006 0.073 1952 Dihedral : 5.398 59.397 1535 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.72 % Allowed : 25.71 % 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 (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: 0.85 (0.23), residues: 1410 helix: 1.51 (0.25), residues: 411 sheet: 0.58 (0.23), residues: 484 loop : -0.10 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 350 HIS 0.003 0.001 HIS B 325 PHE 0.026 0.003 PHE C 36 TYR 0.028 0.003 TYR E 150 ARG 0.009 0.001 ARG A 231 ********************** 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 195 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.8024 (t0) cc_final: 0.7531 (t0) REVERT: A 287 ARG cc_start: 0.7561 (ttp-170) cc_final: 0.6318 (tpm170) REVERT: C 76 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8503 (p) REVERT: C 91 TYR cc_start: 0.8906 (m-80) cc_final: 0.8504 (m-80) REVERT: C 173 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7765 (mppt) REVERT: C 179 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7379 (tpt) REVERT: E 5 GLN cc_start: 0.7394 (mt0) cc_final: 0.6906 (mt0) REVERT: E 11 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8721 (tp) REVERT: E 70 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8114 (p) REVERT: E 72 ASP cc_start: 0.7806 (t70) cc_final: 0.7217 (t70) REVERT: E 179 LEU cc_start: 0.8082 (mm) cc_final: 0.7877 (tp) REVERT: B 91 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.3583 (pmt170) REVERT: B 322 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7908 (mm-40) REVERT: F 43 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.6476 (tptp) REVERT: F 57 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8225 (m) REVERT: F 72 ASP cc_start: 0.8181 (t0) cc_final: 0.7900 (t70) REVERT: D 174 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7597 (p0) REVERT: D 179 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5928 (tpt) outliers start: 46 outliers final: 27 residues processed: 179 average time/residue: 1.5333 time to fit residues: 294.6127 Evaluate side-chains 184 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain E residue 11 LEU 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 105 MET Chi-restraints excluded: chain E residue 141 VAL 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 322 GLN Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain D residue 37 MET 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 174 ASP 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 34 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 50.0000 chunk 114 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.215580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.170153 restraints weight = 13085.814| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.52 r_work: 0.3735 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11347 Z= 0.217 Angle : 0.667 14.479 15445 Z= 0.328 Chirality : 0.045 0.383 1774 Planarity : 0.005 0.050 1952 Dihedral : 5.018 54.465 1535 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.75 % Allowed : 27.16 % 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 (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: 1.84 (0.25), residues: 412 sheet: 0.76 (0.23), residues: 482 loop : -0.03 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 159 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.002 PHE A 73 TYR 0.022 0.001 TYR E 150 ARG 0.012 0.001 ARG A 231 =============================================================================== Job complete usr+sys time: 4735.76 seconds wall clock time: 85 minutes 31.80 seconds (5131.80 seconds total)