Starting phenix.real_space_refine on Thu Mar 6 02:10:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vib_43256/03_2025/8vib_43256.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vib_43256/03_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_43256/03_2025/8vib_43256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vib_43256/03_2025/8vib_43256.map" model { file = "/net/cci-nas-00/data/ceres_data/8vib_43256/03_2025/8vib_43256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vib_43256/03_2025/8vib_43256.cif" } resolution = 4.6 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 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} 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: {'GLN:plan1': 18, 'ASP:plan': 20, 'TYR:plan': 1, 'ASN:plan1': 13, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 33, 'ARG:plan': 24} 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: {'GLN:plan1': 11, 'HIS:plan': 8, 'ASN:plan1': 22, 'TYR:plan': 5, 'UNK:plan-1': 7, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 14, 'GLU:plan': 21, 'ARG:plan': 20} 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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 8} 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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5, 'ARG%COO:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} 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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 5.93, per 1000 atoms: 1.34 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: 1.28 Conformation dependent library (CDL) restraints added in 862.1 milliseconds 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: 0.67 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: 1.50 Time building geometry restraints manager: 1.51 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: 86.820 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.870 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.980 ------------------------------------------------------------------------------- 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= 0.648 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 (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 (0.30), 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 TRP 0.000 0.000 TRP F 554 PHE 0.000 0.000 PHE G 26 TYR 0.000 0.000 TYR G 76 *********************** 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 : 0.516 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0401 time to fit residues: 2.4900 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 : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 2.7184 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.057229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.047110 restraints weight = 114298.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046119 restraints weight = 116718.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.045869 restraints weight = 199449.821| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4022 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4413 Z= 0.242 Angle : 0.632 6.485 6133 Z= 0.403 Chirality : 0.043 0.163 840 Planarity : 0.004 0.025 888 Dihedral : 5.533 30.396 888 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.28 % Favored : 94.38 % 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 : 2.94 % 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: -0.43 (0.28), residues: 872 helix: 0.74 (0.23), residues: 462 sheet: -2.26 (0.55), residues: 63 loop : -1.25 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 554 PHE 0.000 0.000 PHE G 26 TYR 0.000 0.000 TYR G 76 *********************** 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 : 0.470 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0409 time to fit residues: 2.5072 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 : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 29 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.058586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.037819 restraints weight = 57272.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.037264 restraints weight = 53331.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.036977 restraints weight = 58864.781| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 1.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4413 Z= 0.304 Angle : 0.694 8.303 6133 Z= 0.443 Chirality : 0.044 0.177 840 Planarity : 0.004 0.018 888 Dihedral : 6.351 28.610 888 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.80 % Favored : 91.74 % 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 (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: -0.67 (0.29), residues: 872 helix: 0.71 (0.23), residues: 469 sheet: -2.09 (0.59), residues: 59 loop : -1.76 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 554 PHE 0.000 0.000 PHE G 26 TYR 0.000 0.000 TYR G 76 *********************** 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 25 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.530 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0487 time to fit residues: 2.9301 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 : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 54 optimal weight: 0.2980 chunk 53 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 chunk 80 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.053341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.038109 restraints weight = 61523.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.037298 restraints weight = 74037.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037271 restraints weight = 77715.379| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 1.1553 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= 0.193 Angle : 0.487 5.128 6133 Z= 0.313 Chirality : 0.042 0.129 840 Planarity : 0.003 0.015 888 Dihedral : 5.106 21.233 888 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.19 % Favored : 93.58 % 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 (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: 0.23 (0.29), residues: 872 helix: 1.62 (0.24), residues: 471 sheet: -1.23 (0.71), residues: 52 loop : -1.77 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 554 PHE 0.000 0.000 PHE G 26 TYR 0.000 0.000 TYR G 76 *********************** 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 : 0.505 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0459 time to fit residues: 2.8471 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 : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 chunk 30 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.092300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.081660 restraints weight = 99036.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080619 restraints weight = 117475.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080579 restraints weight = 135861.006| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 1.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4413 Z= 0.246 Angle : 0.556 4.980 6133 Z= 0.357 Chirality : 0.042 0.129 840 Planarity : 0.003 0.016 888 Dihedral : 5.622 23.787 888 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.94 % 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 (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: -0.06 (0.29), residues: 872 helix: 1.57 (0.23), residues: 466 sheet: -1.27 (0.70), residues: 53 loop : -2.16 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 554 PHE 0.000 0.000 PHE G 26 TYR 0.000 0.000 TYR G 76 *********************** 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 : 0.624 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0483 time to fit residues: 3.2101 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 : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.2956 r_free = 0.2956 target = 0.046110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.030877 restraints weight = 78572.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.030877 restraints weight = 88208.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.030877 restraints weight = 88208.645| |-----------------------------------------------------------------------------| r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 1.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4413 Z= 0.352 Angle : 0.661 5.218 6133 Z= 0.431 Chirality : 0.042 0.140 840 Planarity : 0.004 0.019 888 Dihedral : 6.477 24.305 888 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.21 % Favored : 89.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.28), residues: 872 helix: 0.62 (0.23), residues: 458 sheet: -1.75 (0.68), residues: 52 loop : -2.72 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 554 PHE 0.000 0.000 PHE G 26 TYR 0.000 0.000 TYR G 76 *********************** 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 : 0.947 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0990 time to fit residues: 6.0596 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 : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 40.0000 chunk 75 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.2949 r_free = 0.2949 target = 0.046210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.037490 restraints weight = 110185.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.037490 restraints weight = 125022.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.037490 restraints weight = 125023.163| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 1.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4413 Z= 0.211 Angle : 0.490 5.401 6133 Z= 0.318 Chirality : 0.041 0.131 840 Planarity : 0.003 0.019 888 Dihedral : 5.430 25.516 888 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.60 % Favored : 90.94 % 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 (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: -0.66 (0.29), residues: 872 helix: 1.13 (0.24), residues: 466 sheet: -1.83 (0.74), residues: 40 loop : -2.47 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 554 PHE 0.000 0.000 PHE G 26 TYR 0.000 0.000 TYR G 76 *********************** 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 : 0.588 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0512 time to fit residues: 3.3460 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 : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 21 optimal weight: 0.0570 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 30.0000 overall best weight: 5.3904 ------------------------------------------------------------------------------- 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 = 0.2930 r_free = 0.2930 target = 0.044717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.031361 restraints weight = 75991.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.030385 restraints weight = 94839.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.029933 restraints weight = 144601.208| |-----------------------------------------------------------------------------| r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 1.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4413 Z= 0.325 Angle : 0.633 7.679 6133 Z= 0.411 Chirality : 0.042 0.161 840 Planarity : 0.004 0.022 888 Dihedral : 6.309 24.953 888 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.57 % Allowed : 11.81 % Favored : 87.61 % 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 (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: -1.44 (0.28), residues: 872 helix: 0.56 (0.24), residues: 450 sheet: -2.27 (0.75), residues: 40 loop : -2.78 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 554 PHE 0.000 0.000 PHE G 26 TYR 0.000 0.000 TYR G 76 *********************** 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 : 0.511 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0432 time to fit residues: 2.6631 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 : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 0.0670 chunk 31 optimal weight: 40.0000 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 27 optimal weight: 50.0000 overall best weight: 4.8126 ------------------------------------------------------------------------------- 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 = 0.2971 r_free = 0.2971 target = 0.045555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.028715 restraints weight = 72291.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.028715 restraints weight = 71105.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.028715 restraints weight = 71105.253| |-----------------------------------------------------------------------------| r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 1.7580 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= 0.260 Angle : 0.546 6.241 6133 Z= 0.356 Chirality : 0.042 0.168 840 Planarity : 0.003 0.019 888 Dihedral : 5.867 29.805 888 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.78 % Favored : 88.76 % 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 (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: -1.34 (0.28), residues: 872 helix: 0.61 (0.23), residues: 460 sheet: -2.59 (0.75), residues: 41 loop : -2.73 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 554 PHE 0.000 0.000 PHE G 26 TYR 0.000 0.000 TYR G 76 *********************** 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 : 0.491 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0434 time to fit residues: 2.6844 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 : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 37 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.2902 r_free = 0.2902 target = 0.043270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.028729 restraints weight = 72425.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.028728 restraints weight = 81657.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.028728 restraints weight = 81690.915| |-----------------------------------------------------------------------------| r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 1.8641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4413 Z= 0.389 Angle : 0.700 7.296 6133 Z= 0.459 Chirality : 0.043 0.183 840 Planarity : 0.004 0.027 888 Dihedral : 6.866 29.720 888 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.57 % Allowed : 14.56 % Favored : 84.86 % 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 (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: -2.17 (0.27), residues: 872 helix: -0.04 (0.23), residues: 435 sheet: -2.92 (0.68), residues: 47 loop : -2.95 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 554 PHE 0.000 0.000 PHE G 26 TYR 0.000 0.000 TYR G 76 ********************** 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 : 0.517 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0427 time to fit residues: 2.5959 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 : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 17 optimal weight: 30.0000 chunk 23 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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 = 0.2952 r_free = 0.2952 target = 0.044503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.028203 restraints weight = 73583.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.028264 restraints weight = 71665.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.028300 restraints weight = 69072.188| |-----------------------------------------------------------------------------| r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 1.8694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4413 Z= 0.259 Angle : 0.559 6.163 6133 Z= 0.363 Chirality : 0.042 0.173 840 Planarity : 0.003 0.023 888 Dihedral : 6.246 29.634 888 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.57 % Allowed : 12.27 % Favored : 87.16 % 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 (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: -1.92 (0.28), residues: 872 helix: 0.24 (0.23), residues: 457 sheet: -2.34 (0.85), residues: 34 loop : -3.20 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP F 554 PHE 0.000 0.000 PHE G 26 TYR 0.000 0.000 TYR G 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2287.50 seconds wall clock time: 41 minutes 59.83 seconds (2519.83 seconds total)