Starting phenix.real_space_refine on Tue Jul 29 07:34:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7v_36050/07_2025/8j7v_36050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7v_36050/07_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_36050/07_2025/8j7v_36050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7v_36050/07_2025/8j7v_36050.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7v_36050/07_2025/8j7v_36050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7v_36050/07_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-5711/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: 7.00, per 1000 atoms: 0.63 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: 2.80 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: 1.50 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: 3.67 Time building geometry restraints manager: 3.33 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: 0.400 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.560 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.230 ------------------------------------------------------------------------------- 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 : 1.230 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: 1.4608 time to fit residues: 279.0034 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 : 1.209 ------------------------------------------------------------------------------- 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 = 0.168840 restraints weight = 13030.287| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.51 r_work: 0.3674 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 1.084 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: 0.8166 (ttp-170) cc_final: 0.7708 (tpm170) REVERT: B 71 MET cc_start: 0.5327 (ptm) cc_final: 0.5123 (ttt) REVERT: B 91 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.4820 (pmt170) REVERT: D 179 MET cc_start: 0.6556 (mmm) cc_final: 0.6180 (tpt) outliers start: 44 outliers final: 17 residues processed: 181 average time/residue: 1.3744 time to fit residues: 266.4743 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 : 1.289 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 115 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.215263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.170483 restraints weight = 13179.519| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.55 r_work: 0.3690 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11355 Z= 0.139 Angle : 0.593 10.456 15461 Z= 0.298 Chirality : 0.043 0.375 1774 Planarity : 0.004 0.052 1952 Dihedral : 4.697 47.781 1535 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.64 % Allowed : 24.17 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.23), residues: 1410 helix: 1.71 (0.25), residues: 412 sheet: 1.04 (0.24), residues: 478 loop : -0.17 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 167 HIS 0.002 0.001 HIS B 325 PHE 0.014 0.001 PHE C 36 TYR 0.014 0.001 TYR C 144 ARG 0.006 0.000 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 607) hydrogen bonds : angle 4.51595 ( 1779) SS BOND : bond 0.00408 ( 8) SS BOND : angle 0.80643 ( 16) covalent geometry : bond 0.00306 (11347) covalent geometry : angle 0.59320 (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 197 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8168 (ttp-170) cc_final: 0.7702 (tpm170) REVERT: E 82 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8398 (ttp) REVERT: B 91 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.4816 (pmt170) REVERT: D 179 MET cc_start: 0.6516 (mmm) cc_final: 0.6149 (tpt) outliers start: 45 outliers final: 20 residues processed: 185 average time/residue: 1.3988 time to fit residues: 276.8267 Evaluate side-chains 167 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 A residue 321 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 82 MET 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 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: 2.9990 chunk 51 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 62 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.214476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168927 restraints weight = 13129.784| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.54 r_work: 0.3683 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11355 Z= 0.186 Angle : 0.619 8.759 15461 Z= 0.311 Chirality : 0.044 0.273 1774 Planarity : 0.005 0.050 1952 Dihedral : 4.809 50.681 1535 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.04 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: 1.16 (0.23), residues: 1410 helix: 1.73 (0.25), residues: 412 sheet: 0.98 (0.24), residues: 480 loop : -0.13 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 167 HIS 0.003 0.001 HIS A 356 PHE 0.020 0.002 PHE C 36 TYR 0.015 0.002 TYR E 150 ARG 0.007 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 607) hydrogen bonds : angle 4.48981 ( 1779) SS BOND : bond 0.00507 ( 8) SS BOND : angle 1.00611 ( 16) covalent geometry : bond 0.00425 (11347) covalent geometry : angle 0.61807 (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 193 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 1.147 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: 0.8169 (ttp-170) cc_final: 0.7715 (tpm170) REVERT: A 321 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8256 (mp) REVERT: A 366 GLN cc_start: 0.8200 (mt0) cc_final: 0.7954 (mt0) REVERT: B 91 ARG cc_start: 0.6014 (OUTLIER) cc_final: 0.4718 (pmt170) REVERT: F 57 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8540 (m) REVERT: D 179 MET cc_start: 0.6562 (mmm) cc_final: 0.6215 (tpt) outliers start: 42 outliers final: 16 residues processed: 181 average time/residue: 1.7597 time to fit residues: 340.5786 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 : 1.205 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 321 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 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** B 322 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.214693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.169199 restraints weight = 13201.038| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.56 r_work: 0.3679 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1449 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= 0.196 Angle : 0.632 12.202 15461 Z= 0.317 Chirality : 0.045 0.342 1774 Planarity : 0.005 0.060 1952 Dihedral : 4.906 54.027 1535 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.96 % Allowed : 24.33 % 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: 1.19 (0.23), residues: 1410 helix: 1.79 (0.26), residues: 412 sheet: 0.98 (0.24), residues: 480 loop : -0.14 (0.29), residues: 518 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 0.021 0.002 PHE C 36 TYR 0.017 0.002 TYR E 150 ARG 0.007 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 607) hydrogen bonds : angle 4.44963 ( 1779) SS BOND : bond 0.00510 ( 8) SS BOND : angle 1.08144 ( 16) covalent geometry : bond 0.00445 (11347) covalent geometry : angle 0.63120 (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 198 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8245 (ttp-170) cc_final: 0.7737 (tpm170) REVERT: A 366 GLN cc_start: 0.8232 (mt0) cc_final: 0.7966 (mt0) REVERT: B 91 ARG cc_start: 0.5990 (OUTLIER) cc_final: 0.4622 (pmt170) REVERT: F 57 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8553 (m) REVERT: D 179 MET cc_start: 0.6624 (mmm) cc_final: 0.6276 (tpt) outliers start: 49 outliers final: 20 residues processed: 187 average time/residue: 1.3883 time to fit residues: 279.3516 Evaluate side-chains 168 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 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 269 ILE Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain F residue 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: 5.9990 chunk 125 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 30 optimal weight: 0.0030 chunk 15 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- 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** D 142 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.214218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.169854 restraints weight = 13238.715| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.43 r_work: 0.3658 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11355 Z= 0.236 Angle : 0.656 10.459 15461 Z= 0.331 Chirality : 0.046 0.313 1774 Planarity : 0.005 0.057 1952 Dihedral : 5.064 56.591 1535 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.64 % Allowed : 24.90 % 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: 1.16 (0.23), residues: 1410 helix: 1.81 (0.26), residues: 411 sheet: 0.84 (0.24), residues: 484 loop : -0.06 (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 0.019 0.002 TYR E 150 ARG 0.007 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 607) hydrogen bonds : angle 4.49232 ( 1779) SS BOND : bond 0.00550 ( 8) SS BOND : angle 1.16495 ( 16) covalent geometry : bond 0.00538 (11347) covalent geometry : angle 0.65492 (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 194 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 1.303 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: 0.8295 (ttp-170) cc_final: 0.7765 (tpm170) REVERT: A 366 GLN cc_start: 0.8215 (mt0) cc_final: 0.7946 (mt0) REVERT: B 91 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.4647 (pmt170) REVERT: F 57 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8545 (m) REVERT: D 18 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7171 (ttm-80) outliers start: 45 outliers final: 25 residues processed: 179 average time/residue: 1.3529 time to fit residues: 260.8014 Evaluate side-chains 172 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 249 ILE 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 43 optimal weight: 40.0000 chunk 123 optimal weight: 0.9980 chunk 3 optimal weight: 50.0000 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 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 = 0.214993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.170693 restraints weight = 13365.290| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.45 r_work: 0.3640 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11355 Z= 0.183 Angle : 0.643 12.004 15461 Z= 0.322 Chirality : 0.044 0.281 1774 Planarity : 0.005 0.068 1952 Dihedral : 4.995 55.552 1535 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.96 % Allowed : 25.38 % 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: 1.21 (0.23), residues: 1410 helix: 1.88 (0.25), residues: 412 sheet: 0.86 (0.24), residues: 484 loop : -0.05 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 47 HIS 0.003 0.001 HIS B 325 PHE 0.020 0.002 PHE C 36 TYR 0.020 0.002 TYR E 150 ARG 0.008 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 607) hydrogen bonds : angle 4.44882 ( 1779) SS BOND : bond 0.00487 ( 8) SS BOND : angle 0.99245 ( 16) covalent geometry : bond 0.00415 (11347) covalent geometry : angle 0.64227 (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 197 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8333 (ttp-170) cc_final: 0.7765 (tpm170) REVERT: A 366 GLN cc_start: 0.8163 (mt0) cc_final: 0.7870 (mt0) REVERT: C 140 LEU cc_start: 0.7924 (mp) cc_final: 0.7687 (mt) REVERT: B 91 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.4649 (pmt170) REVERT: F 57 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8537 (m) REVERT: D 179 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6502 (tpp) outliers start: 49 outliers final: 27 residues processed: 182 average time/residue: 1.4287 time to fit residues: 282.2488 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 : 1.234 ------------------------------------------------------------------------------- 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 94 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 277 LEU 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 64 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain 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 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 76 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 46 optimal weight: 40.0000 chunk 18 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 129 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 overall best weight: 2.3662 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.215153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.169617 restraints weight = 13141.851| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.50 r_work: 0.3677 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11355 Z= 0.177 Angle : 0.664 12.698 15461 Z= 0.331 Chirality : 0.045 0.299 1774 Planarity : 0.005 0.050 1952 Dihedral : 4.968 54.520 1535 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.56 % Allowed : 25.95 % Favored : 70.49 % 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: 1.75 (0.25), residues: 412 sheet: 0.90 (0.24), residues: 480 loop : -0.10 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.003 0.001 HIS B 325 PHE 0.024 0.002 PHE B 48 TYR 0.020 0.002 TYR E 150 ARG 0.009 0.001 ARG C 72 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 607) hydrogen bonds : angle 4.50952 ( 1779) SS BOND : bond 0.00485 ( 8) SS BOND : angle 0.97513 ( 16) covalent geometry : bond 0.00403 (11347) covalent geometry : angle 0.66326 (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 189 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8287 (ttp-170) cc_final: 0.7746 (tpm170) REVERT: A 366 GLN cc_start: 0.8175 (mt0) cc_final: 0.7876 (mt0) REVERT: C 140 LEU cc_start: 0.7876 (mp) cc_final: 0.7633 (mt) REVERT: B 71 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.5272 (pmt) REVERT: B 91 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.4602 (pmt170) REVERT: F 57 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8546 (m) REVERT: D 179 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6318 (tpt) outliers start: 44 outliers final: 27 residues processed: 178 average time/residue: 1.4685 time to fit residues: 280.2464 Evaluate side-chains 178 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 94 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 277 LEU 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 141 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 185 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 57 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 133 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4406 r_free = 0.4406 target = 0.215440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.170136 restraints weight = 13291.480| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.52 r_work: 0.3689 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11355 Z= 0.168 Angle : 0.668 13.723 15461 Z= 0.331 Chirality : 0.045 0.405 1774 Planarity : 0.005 0.050 1952 Dihedral : 4.940 53.702 1535 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.15 % Allowed : 26.43 % Favored : 70.41 % 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: 1.20 (0.23), residues: 1410 helix: 1.84 (0.25), residues: 412 sheet: 0.91 (0.24), residues: 480 loop : -0.09 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.003 0.001 HIS B 325 PHE 0.023 0.002 PHE B 48 TYR 0.023 0.001 TYR E 150 ARG 0.006 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 607) hydrogen bonds : angle 4.47348 ( 1779) SS BOND : bond 0.00479 ( 8) SS BOND : angle 0.96450 ( 16) covalent geometry : bond 0.00386 (11347) covalent geometry : angle 0.66747 (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 188 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8281 (ttp-170) cc_final: 0.7737 (tpm170) REVERT: A 366 GLN cc_start: 0.8176 (mt0) cc_final: 0.7876 (mt0) REVERT: B 91 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.4609 (pmt170) REVERT: F 57 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8543 (m) REVERT: D 179 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6380 (tpt) outliers start: 39 outliers final: 25 residues processed: 178 average time/residue: 1.5925 time to fit residues: 304.8568 Evaluate side-chains 174 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 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 76 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 85 optimal weight: 30.0000 chunk 92 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.216207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.170418 restraints weight = 13180.212| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.45 r_work: 0.3703 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11355 Z= 0.147 Angle : 0.677 13.653 15461 Z= 0.334 Chirality : 0.045 0.396 1774 Planarity : 0.005 0.058 1952 Dihedral : 4.888 52.308 1535 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.43 % Allowed : 27.08 % Favored : 70.49 % 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: 1.25 (0.23), residues: 1410 helix: 1.87 (0.25), residues: 415 sheet: 0.95 (0.24), residues: 482 loop : -0.07 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.004 0.001 HIS D 193 PHE 0.030 0.002 PHE B 48 TYR 0.022 0.001 TYR E 150 ARG 0.011 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 607) hydrogen bonds : angle 4.44772 ( 1779) SS BOND : bond 0.00431 ( 8) SS BOND : angle 0.77781 ( 16) covalent geometry : bond 0.00334 (11347) covalent geometry : angle 0.67684 (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 180 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.8235 (ttp-170) cc_final: 0.7685 (tpm170) REVERT: A 366 GLN cc_start: 0.8154 (mt0) cc_final: 0.7866 (mt0) REVERT: B 91 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.4652 (pmt170) REVERT: F 57 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8527 (m) REVERT: D 179 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6329 (tpt) outliers start: 30 outliers final: 23 residues processed: 172 average time/residue: 1.8180 time to fit residues: 336.5939 Evaluate side-chains 172 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 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 141 VAL 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 76 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 75 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 87 optimal weight: 0.0170 chunk 88 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- 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 = 0.4406 r_free = 0.4406 target = 0.215344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.169363 restraints weight = 13113.226| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.48 r_work: 0.3683 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11355 Z= 0.194 Angle : 0.703 13.454 15461 Z= 0.348 Chirality : 0.046 0.393 1774 Planarity : 0.005 0.060 1952 Dihedral : 5.021 54.849 1535 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.83 % Allowed : 27.16 % 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: 1.22 (0.23), residues: 1410 helix: 1.86 (0.25), residues: 412 sheet: 0.87 (0.24), residues: 484 loop : -0.02 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.003 0.001 HIS B 325 PHE 0.021 0.002 PHE C 36 TYR 0.022 0.002 TYR E 150 ARG 0.012 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 607) hydrogen bonds : angle 4.48369 ( 1779) SS BOND : bond 0.00504 ( 8) SS BOND : angle 1.05925 ( 16) covalent geometry : bond 0.00445 (11347) covalent geometry : angle 0.70214 (15445) =============================================================================== Job complete usr+sys time: 9814.43 seconds wall clock time: 176 minutes 21.89 seconds (10581.89 seconds total)