Starting phenix.real_space_refine on Wed Sep 17 04:48:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vib_43256/09_2025/8vib_43256.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vib_43256/09_2025/8vib_43256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vib_43256/09_2025/8vib_43256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vib_43256/09_2025/8vib_43256.map" model { file = "/net/cci-nas-00/data/ceres_data/8vib_43256/09_2025/8vib_43256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vib_43256/09_2025/8vib_43256.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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: 3 Type Number sf(0) Gaussians C 2630 2.51 5 N 895 2.21 5 O 896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4421 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 234 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 1, 'TRANS': 45} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 6, 'ARG:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "G" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1554 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PTRANS': 5, 'TRANS': 308} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 928 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 717 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'ASN:plan1': 13, 'ASP:plan': 20, 'GLU:plan': 33, 'ARG:plan': 24, 'PHE:plan': 10, 'HIS:plan': 4, 'GLN:plan1': 18, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 510 Chain: "M" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 1420 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 266} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 931 Unresolved non-hydrogen angles: 1206 Unresolved non-hydrogen dihedrals: 749 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'UNK:plan-1': 7, 'GLN:plan1': 11, 'GLU:plan': 21, 'ASN:plan1': 22, 'ARG:plan': 20, 'PHE:plan': 14, 'ASP:plan': 11, 'TYR:plan': 5, 'HIS:plan': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 511 Chain: "N" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 456 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 3, 'TRANS': 89} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "P" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 389 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 5, 'ARG:plan': 7, 'GLN:plan1': 2, 'ASN:plan1': 1, 'TYR:plan': 2, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 100 Chain: "Q" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 368 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 8, 'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 1.56, per 1000 atoms: 0.35 Number of scatterers: 4421 At special positions: 0 Unit cell: (100.205, 92.025, 169.735, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 896 8.00 N 895 7.00 C 2630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 274.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 7 sheets defined 54.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'F' and resid 514 through 543 removed outlier: 3.637A pdb=" N GLY F 528 " --> pdb=" O ASN F 524 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA F 529 " --> pdb=" O GLN F 525 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP F 541 " --> pdb=" O ARG F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 560 removed outlier: 3.504A pdb=" N ASN F 557 " --> pdb=" O GLN F 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 17 removed outlier: 3.596A pdb=" N ILE G 12 " --> pdb=" O ASP G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'G' and resid 48 through 66 Processing helix chain 'G' and resid 73 through 84 removed outlier: 3.622A pdb=" N ARG G 78 " --> pdb=" O ASN G 74 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU G 81 " --> pdb=" O LEU G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 88 Processing helix chain 'G' and resid 90 through 101 Processing helix chain 'G' and resid 102 through 113 Processing helix chain 'G' and resid 114 through 122 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 138 through 149 removed outlier: 3.532A pdb=" N LEU G 148 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 164 removed outlier: 4.010A pdb=" N ASP G 156 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA G 162 " --> pdb=" O MET G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 181 removed outlier: 3.513A pdb=" N GLY G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 206 Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'G' and resid 222 through 234 removed outlier: 3.508A pdb=" N ALA G 226 " --> pdb=" O ASP G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 250 removed outlier: 3.944A pdb=" N LEU G 250 " --> pdb=" O SER G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 253 No H-bonds generated for 'chain 'G' and resid 251 through 253' Processing helix chain 'G' and resid 255 through 264 removed outlier: 3.632A pdb=" N ILE G 261 " --> pdb=" O GLU G 257 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA G 262 " --> pdb=" O SER G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 275 Processing helix chain 'G' and resid 279 through 293 removed outlier: 3.509A pdb=" N ALA G 291 " --> pdb=" O ARG G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 319 removed outlier: 3.916A pdb=" N VAL G 301 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN G 303 " --> pdb=" O SER G 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 74 removed outlier: 4.602A pdb=" N GLU M 59 " --> pdb=" O GLU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 96 removed outlier: 3.744A pdb=" N ASN M 95 " --> pdb=" O GLU M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 131 Processing helix chain 'M' and resid 147 through 173 removed outlier: 3.836A pdb=" N LEU M 160 " --> pdb=" O ARG M 156 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA M 161 " --> pdb=" O MET M 157 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA M 171 " --> pdb=" O ASP M 167 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE M 172 " --> pdb=" O ALA M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 225 Processing helix chain 'M' and resid 226 through 228 No H-bonds generated for 'chain 'M' and resid 226 through 228' Processing helix chain 'M' and resid 246 through 256 Processing helix chain 'M' and resid 271 through 277 removed outlier: 3.544A pdb=" N ILE M 275 " --> pdb=" O ARG M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 322 through 330 Processing helix chain 'N' and resid 46 through 59 removed outlier: 4.326A pdb=" N ASP N 55 " --> pdb=" O MET N 51 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU N 56 " --> pdb=" O GLN N 52 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET N 58 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP N 59 " --> pdb=" O ASP N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 81 Processing helix chain 'N' and resid 127 through 137 removed outlier: 3.718A pdb=" N ARG N 133 " --> pdb=" O SER N 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 84 Processing helix chain 'P' and resid 127 through 137 removed outlier: 4.257A pdb=" N ARG P 137 " --> pdb=" O ARG P 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 74 Processing helix chain 'Q' and resid 127 through 137 Processing sheet with id=AA1, first strand: chain 'M' and resid 78 through 81 removed outlier: 3.510A pdb=" N VAL M 199 " --> pdb=" O GLN M 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 78 through 81 removed outlier: 3.634A pdb=" N GLY M 213 " --> pdb=" O VAL M 206 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG M 181 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N HIS M 106 " --> pdb=" O TYR M 179 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR M 179 " --> pdb=" O HIS M 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 283 through 285 removed outlier: 6.646A pdb=" N GLN N 108 " --> pdb=" O THR N 123 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE N 125 " --> pdb=" O ILE N 106 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ILE N 106 " --> pdb=" O ILE N 125 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE N 99 " --> pdb=" O ILE N 106 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN N 108 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU N 97 " --> pdb=" O GLN N 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP N 98 " --> pdb=" O GLU N 67 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU N 68 " --> pdb=" O ASN M 264 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASN M 264 " --> pdb=" O LEU N 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 283 through 285 removed outlier: 6.646A pdb=" N GLN N 108 " --> pdb=" O THR N 123 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE N 125 " --> pdb=" O ILE N 106 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ILE N 106 " --> pdb=" O ILE N 125 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE N 99 " --> pdb=" O ILE N 106 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN N 108 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU N 97 " --> pdb=" O GLN N 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP N 98 " --> pdb=" O GLU N 67 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU N 68 " --> pdb=" O ASN M 264 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASN M 264 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN M 264 " --> pdb=" O ILE M 293 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ILE M 293 " --> pdb=" O ASN M 264 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE M 292 " --> pdb=" O THR M 303 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR M 303 " --> pdb=" O ILE M 292 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA M 294 " --> pdb=" O VAL M 301 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN M 305 " --> pdb=" O VAL M 317 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL M 317 " --> pdb=" O GLN M 305 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY M 307 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU M 315 " --> pdb=" O GLY M 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 65 through 66 removed outlier: 6.485A pdb=" N THR P 65 " --> pdb=" O LEU Q 100 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU Q 97 " --> pdb=" O GLY Q 109 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA Q 107 " --> pdb=" O ILE Q 99 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE Q 106 " --> pdb=" O ILE Q 125 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE Q 125 " --> pdb=" O ILE Q 106 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN Q 108 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU Q 110 " --> pdb=" O ARG Q 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'P' and resid 107 through 111 removed outlier: 6.417A pdb=" N GLU P 110 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE P 122 " --> pdb=" O GLU P 110 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1098 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: 0.71 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.29: 896 1.29 - 1.36: 886 1.36 - 1.44: 5 1.44 - 1.51: 961 1.51 - 1.59: 1665 Bond restraints: 4413 Sorted by residual: bond pdb=" C PRO F 544 " pdb=" N ARG F 545 " ideal model delta sigma weight residual 1.331 1.586 -0.256 1.23e-02 6.61e+03 4.32e+02 bond pdb=" N VAL G 167 " pdb=" CA VAL G 167 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.25e-02 6.40e+03 1.51e+01 bond pdb=" N VAL G 196 " pdb=" CA VAL G 196 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" N ASP G 243 " pdb=" CA ASP G 243 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.23e-02 6.61e+03 8.27e+00 bond pdb=" N ILE G 161 " pdb=" CA ILE G 161 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.04e+00 ... (remaining 4408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 5930 2.74 - 5.47: 190 5.47 - 8.21: 6 8.21 - 10.94: 5 10.94 - 13.68: 2 Bond angle restraints: 6133 Sorted by residual: angle pdb=" O PRO F 544 " pdb=" C PRO F 544 " pdb=" N ARG F 545 " ideal model delta sigma weight residual 123.03 136.71 -13.68 1.21e+00 6.83e-01 1.28e+02 angle pdb=" CA PRO F 544 " pdb=" C PRO F 544 " pdb=" N ARG F 545 " ideal model delta sigma weight residual 115.56 102.24 13.32 1.27e+00 6.20e-01 1.10e+02 angle pdb=" N GLU G 177 " pdb=" CA GLU G 177 " pdb=" C GLU G 177 " ideal model delta sigma weight residual 111.28 100.39 10.89 1.09e+00 8.42e-01 9.98e+01 angle pdb=" N GLU M 242 " pdb=" CA GLU M 242 " pdb=" C GLU M 242 " ideal model delta sigma weight residual 110.91 103.46 7.45 1.17e+00 7.31e-01 4.06e+01 angle pdb=" N GLU G 174 " pdb=" CA GLU G 174 " pdb=" C GLU G 174 " ideal model delta sigma weight residual 111.74 103.37 8.37 1.35e+00 5.49e-01 3.85e+01 ... (remaining 6128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.84: 2305 4.84 - 9.69: 199 9.69 - 14.53: 51 14.53 - 19.37: 12 19.37 - 24.22: 1 Dihedral angle restraints: 2568 sinusoidal: 1 harmonic: 2567 Sorted by residual: dihedral pdb=" C ASN M 233 " pdb=" N ASN M 233 " pdb=" CA ASN M 233 " pdb=" CB ASN M 233 " ideal model delta harmonic sigma weight residual -122.60 -135.54 12.94 0 2.50e+00 1.60e-01 2.68e+01 dihedral pdb=" CA VAL M 186 " pdb=" C VAL M 186 " pdb=" N LYS M 187 " pdb=" CA LYS M 187 " ideal model delta harmonic sigma weight residual -180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA PHE M 131 " pdb=" C PHE M 131 " pdb=" N GLY M 132 " pdb=" CA GLY M 132 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 641 0.074 - 0.147: 158 0.147 - 0.220: 37 0.220 - 0.294: 3 0.294 - 0.367: 1 Chirality restraints: 840 Sorted by residual: chirality pdb=" CA ASN M 233 " pdb=" N ASN M 233 " pdb=" C ASN M 233 " pdb=" CB ASN M 233 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA GLU G 211 " pdb=" N GLU G 211 " pdb=" C GLU G 211 " pdb=" CB GLU G 211 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ARG G 219 " pdb=" N ARG G 219 " pdb=" C ARG G 219 " pdb=" CB ARG G 219 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 837 not shown) Planarity restraints: 888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN M 233 " -0.024 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C ASN M 233 " 0.085 2.00e-02 2.50e+03 pdb=" O ASN M 233 " -0.031 2.00e-02 2.50e+03 pdb=" N PRO M 234 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 6 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C GLY G 6 " -0.058 2.00e-02 2.50e+03 pdb=" O GLY G 6 " 0.022 2.00e-02 2.50e+03 pdb=" N THR G 7 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE M 131 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C PHE M 131 " 0.051 2.00e-02 2.50e+03 pdb=" O PHE M 131 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY M 132 " -0.017 2.00e-02 2.50e+03 ... (remaining 885 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 1536 2.82 - 3.34: 4365 3.34 - 3.86: 6481 3.86 - 4.38: 6058 4.38 - 4.90: 10159 Nonbonded interactions: 28599 Sorted by model distance: nonbonded pdb=" O ASN M 233 " pdb=" N PRO M 235 " model vdw 2.305 3.120 nonbonded pdb=" O ASP G 8 " pdb=" N VAL G 11 " model vdw 2.319 3.120 nonbonded pdb=" O GLN M 244 " pdb=" N TRP M 246 " model vdw 2.332 3.120 nonbonded pdb=" O ASP M 243 " pdb=" N ASN M 245 " model vdw 2.345 3.120 nonbonded pdb=" O ASP G 8 " pdb=" N SER G 10 " model vdw 2.350 3.120 ... (remaining 28594 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 'P' and (resid 63 through 137 and (name N or name CA or name C or name O \ or name CB ))) selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.030 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5466 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 : 0.009 0.256 4413 Z= 0.681 Angle : 1.125 13.680 6133 Z= 0.853 Chirality : 0.067 0.367 840 Planarity : 0.005 0.049 888 Dihedral : 5.118 24.217 888 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.92 % Allowed : 5.62 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.30), residues: 872 helix: 0.91 (0.26), residues: 424 sheet: -1.15 (0.54), residues: 96 loop : -1.42 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 76 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP F 554 Details of bonding type rmsd covalent geometry : bond 0.00872 ( 4413) covalent geometry : angle 1.12468 ( 6133) hydrogen bonds : bond 0.18632 ( 362) hydrogen bonds : angle 7.85719 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.208 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0231 time to fit residues: 1.2733 Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 40.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.067052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038926 restraints weight = 49576.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038926 restraints weight = 50104.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038926 restraints weight = 50104.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038926 restraints weight = 50104.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.038926 restraints weight = 50104.645| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.7634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4413 Z= 0.358 Angle : 0.778 7.994 6133 Z= 0.502 Chirality : 0.045 0.152 840 Planarity : 0.006 0.026 888 Dihedral : 6.942 32.167 888 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.22 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.27), residues: 872 helix: -0.04 (0.23), residues: 456 sheet: -1.86 (0.58), residues: 54 loop : -1.75 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 76 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP F 554 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 4413) covalent geometry : angle 0.77805 ( 6133) hydrogen bonds : bond 0.06944 ( 362) hydrogen bonds : angle 8.02918 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.176 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0204 time to fit residues: 1.1434 Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 32 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.053988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.040047 restraints weight = 100293.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.039924 restraints weight = 103692.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.039711 restraints weight = 116754.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.039673 restraints weight = 120047.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.039648 restraints weight = 120775.672| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3952 moved from start: 0.7561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 4413 Z= 0.111 Angle : 0.407 4.472 6133 Z= 0.257 Chirality : 0.042 0.140 840 Planarity : 0.002 0.013 888 Dihedral : 4.454 18.913 888 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.36 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.29), residues: 872 helix: 1.51 (0.24), residues: 468 sheet: -1.25 (0.62), residues: 57 loop : -1.61 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 76 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP F 554 Details of bonding type rmsd covalent geometry : bond 0.00147 ( 4413) covalent geometry : angle 0.40697 ( 6133) hydrogen bonds : bond 0.03174 ( 362) hydrogen bonds : angle 5.35945 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.173 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0210 time to fit residues: 1.1654 Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 7 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 28 optimal weight: 40.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.061822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.035945 restraints weight = 51217.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.035977 restraints weight = 49862.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.035976 restraints weight = 48858.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 13)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.035976 restraints weight = 48847.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.035976 restraints weight = 48847.287| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 1.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4413 Z= 0.267 Angle : 0.631 6.261 6133 Z= 0.406 Chirality : 0.043 0.165 840 Planarity : 0.004 0.021 888 Dihedral : 6.129 24.968 888 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.37 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.29), residues: 872 helix: 1.03 (0.23), residues: 469 sheet: -1.94 (0.64), residues: 56 loop : -1.77 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 76 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP F 554 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4413) covalent geometry : angle 0.63116 ( 6133) hydrogen bonds : bond 0.05815 ( 362) hydrogen bonds : angle 7.20005 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.156 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0201 time to fit residues: 1.1717 Evaluate side-chains 25 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 2 optimal weight: 40.0000 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 55 optimal weight: 0.0050 chunk 29 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.047727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.043941 restraints weight = 142968.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043975 restraints weight = 137256.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043975 restraints weight = 131785.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043975 restraints weight = 131774.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043975 restraints weight = 131774.932| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 1.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 4413 Z= 0.237 Angle : 0.551 4.257 6133 Z= 0.356 Chirality : 0.042 0.137 840 Planarity : 0.003 0.014 888 Dihedral : 5.861 19.866 888 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.83 % Favored : 90.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.28), residues: 872 helix: 1.10 (0.23), residues: 471 sheet: -1.37 (0.70), residues: 50 loop : -2.34 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 76 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP F 554 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4413) covalent geometry : angle 0.55135 ( 6133) hydrogen bonds : bond 0.04430 ( 362) hydrogen bonds : angle 6.69015 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.154 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0207 time to fit residues: 1.1130 Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.045892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030897 restraints weight = 81620.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030897 restraints weight = 91330.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030897 restraints weight = 91330.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030897 restraints weight = 91330.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.030897 restraints weight = 91330.595| |-----------------------------------------------------------------------------| r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 1.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4413 Z= 0.286 Angle : 0.595 4.983 6133 Z= 0.387 Chirality : 0.042 0.134 840 Planarity : 0.003 0.017 888 Dihedral : 6.134 22.257 888 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.35 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.29), residues: 872 helix: 1.02 (0.24), residues: 463 sheet: -1.29 (0.71), residues: 51 loop : -2.50 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 76 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP F 554 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4413) covalent geometry : angle 0.59504 ( 6133) hydrogen bonds : bond 0.05573 ( 362) hydrogen bonds : angle 7.24199 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.279 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0172 time to fit residues: 1.0935 Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 32 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.029805 restraints weight = 63888.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.029804 restraints weight = 64372.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.029804 restraints weight = 64380.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.029804 restraints weight = 64378.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.029804 restraints weight = 64378.289| |-----------------------------------------------------------------------------| r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 1.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 4413 Z= 0.198 Angle : 0.479 4.946 6133 Z= 0.310 Chirality : 0.042 0.135 840 Planarity : 0.003 0.015 888 Dihedral : 5.402 19.853 888 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.83 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.29), residues: 872 helix: 1.26 (0.24), residues: 466 sheet: -1.41 (0.64), residues: 62 loop : -2.38 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 76 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP F 554 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4413) covalent geometry : angle 0.47875 ( 6133) hydrogen bonds : bond 0.03967 ( 362) hydrogen bonds : angle 6.40500 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0192 time to fit residues: 1.0456 Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 20 optimal weight: 0.2980 chunk 2 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.044067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.030327 restraints weight = 66019.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.029713 restraints weight = 77379.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.029160 restraints weight = 118263.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.029052 restraints weight = 147622.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.029006 restraints weight = 146442.145| |-----------------------------------------------------------------------------| r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 1.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4413 Z= 0.309 Angle : 0.621 7.201 6133 Z= 0.401 Chirality : 0.043 0.158 840 Planarity : 0.004 0.023 888 Dihedral : 6.353 25.032 888 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.69 % Allowed : 12.61 % Favored : 86.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.28), residues: 872 helix: 0.67 (0.24), residues: 450 sheet: -1.66 (0.81), residues: 34 loop : -2.63 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 76 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP F 554 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 4413) covalent geometry : angle 0.62109 ( 6133) hydrogen bonds : bond 0.05948 ( 362) hydrogen bonds : angle 7.63099 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.164 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0202 time to fit residues: 1.1117 Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 40.0000 chunk 51 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.045675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.028647 restraints weight = 71978.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.028647 restraints weight = 69839.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.028647 restraints weight = 69839.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.028647 restraints weight = 69839.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.028647 restraints weight = 69839.905| |-----------------------------------------------------------------------------| r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 1.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4413 Z= 0.263 Angle : 0.551 7.237 6133 Z= 0.356 Chirality : 0.042 0.157 840 Planarity : 0.003 0.015 888 Dihedral : 5.958 24.057 888 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.55 % Favored : 88.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.29), residues: 872 helix: 0.62 (0.23), residues: 459 sheet: -1.74 (0.86), residues: 34 loop : -2.66 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 76 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP F 554 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4413) covalent geometry : angle 0.55111 ( 6133) hydrogen bonds : bond 0.04922 ( 362) hydrogen bonds : angle 7.13234 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.172 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0204 time to fit residues: 1.1441 Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 20.0000 chunk 55 optimal weight: 0.0470 chunk 51 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.043648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.031419 restraints weight = 85366.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.030659 restraints weight = 93288.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.030267 restraints weight = 125411.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.030128 restraints weight = 156264.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.030040 restraints weight = 156423.169| |-----------------------------------------------------------------------------| r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 1.8409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4413 Z= 0.296 Angle : 0.598 6.351 6133 Z= 0.389 Chirality : 0.043 0.175 840 Planarity : 0.004 0.025 888 Dihedral : 6.339 28.023 888 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.69 % Allowed : 13.42 % Favored : 85.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.29), residues: 872 helix: 0.55 (0.24), residues: 441 sheet: -1.75 (0.78), residues: 37 loop : -2.77 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 76 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP F 554 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 4413) covalent geometry : angle 0.59820 ( 6133) hydrogen bonds : bond 0.05724 ( 362) hydrogen bonds : angle 7.67243 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.169 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0204 time to fit residues: 1.1353 Evaluate side-chains 24 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 55 optimal weight: 0.0970 chunk 31 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 overall best weight: 4.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028114 restraints weight = 73721.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028114 restraints weight = 71294.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028114 restraints weight = 71294.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028114 restraints weight = 71294.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.028114 restraints weight = 71294.759| |-----------------------------------------------------------------------------| r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 1.8662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4413 Z= 0.264 Angle : 0.544 5.734 6133 Z= 0.355 Chirality : 0.042 0.161 840 Planarity : 0.003 0.020 888 Dihedral : 5.996 24.594 888 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.81 % Favored : 87.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.29), residues: 872 helix: 0.57 (0.23), residues: 454 sheet: -2.17 (0.86), residues: 34 loop : -2.82 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR G 76 PHE 0.000 0.000 PHE G 26 TRP 0.000 0.000 TRP F 554 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4413) covalent geometry : angle 0.54447 ( 6133) hydrogen bonds : bond 0.04999 ( 362) hydrogen bonds : angle 7.30691 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1148.22 seconds wall clock time: 20 minutes 19.49 seconds (1219.49 seconds total)