Starting phenix.real_space_refine on Mon Jan 13 23:20:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vib_43256/01_2025/8vib_43256.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vib_43256/01_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_43256/01_2025/8vib_43256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vib_43256/01_2025/8vib_43256.map" model { file = "/net/cci-nas-00/data/ceres_data/8vib_43256/01_2025/8vib_43256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vib_43256/01_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-5571/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: 5.64, per 1000 atoms: 1.28 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: 1.21 Conformation dependent library (CDL) restraints added in 801.0 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: 0.64 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: 1.30 Time building geometry restraints manager: 1.37 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: 7.960 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: 17.500 Find NCS groups from input model: 0.090 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- 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 : 0.467 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0412 time to fit residues: 2.3946 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 : 0.455 ------------------------------------------------------------------------------- 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 = 0.057230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.047081 restraints weight = 114298.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046295 restraints weight = 120488.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.046122 restraints weight = 168042.882| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4080 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 : 0.462 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0406 time to fit residues: 2.4820 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 : 0.462 ------------------------------------------------------------------------------- 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: 1.9990 chunk 8 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 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 = 0.3308 r_free = 0.3308 target = 0.053850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039163 restraints weight = 62087.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.038349 restraints weight = 73310.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.038185 restraints weight = 82693.468| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 1.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4413 Z= 0.328 Angle : 0.726 6.870 6133 Z= 0.468 Chirality : 0.044 0.162 840 Planarity : 0.005 0.024 888 Dihedral : 6.467 28.909 888 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.91 % 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: -0.80 (0.28), residues: 872 helix: 0.61 (0.23), residues: 469 sheet: -2.10 (0.60), residues: 59 loop : -1.83 (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 : 0.438 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0456 time to fit residues: 2.6950 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 : 0.529 ------------------------------------------------------------------------------- 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: 9.9990 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- 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 = 0.3014 r_free = 0.3014 target = 0.048321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.031268 restraints weight = 62158.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.031082 restraints weight = 72827.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.031082 restraints weight = 81662.820| |-----------------------------------------------------------------------------| r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 1.2202 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= 0.250 Angle : 0.557 5.613 6133 Z= 0.364 Chirality : 0.042 0.147 840 Planarity : 0.003 0.018 888 Dihedral : 5.577 21.693 888 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.57 % Favored : 92.09 % 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: -0.27 (0.29), residues: 872 helix: 1.29 (0.23), residues: 466 sheet: -1.23 (0.71), residues: 50 loop : -2.09 (0.33), residues: 356 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 : 0.507 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0466 time to fit residues: 2.9349 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 : 0.510 ------------------------------------------------------------------------------- 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: 10.0000 chunk 14 optimal weight: 30.0000 chunk 30 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 overall best weight: 8.7994 ------------------------------------------------------------------------------- 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 = 0.2913 r_free = 0.2913 target = 0.044412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.029207 restraints weight = 64427.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.029207 restraints weight = 77076.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.029207 restraints weight = 77076.634| |-----------------------------------------------------------------------------| r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 1.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 4413 Z= 0.488 Angle : 0.897 7.048 6133 Z= 0.579 Chirality : 0.045 0.148 840 Planarity : 0.006 0.027 888 Dihedral : 8.353 39.552 888 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.92 % Allowed : 12.61 % Favored : 86.47 % 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 (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: -2.69 (0.26), residues: 872 helix: -0.79 (0.23), residues: 429 sheet: -1.90 (0.65), residues: 58 loop : -2.96 (0.30), residues: 385 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 : 0.467 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0411 time to fit residues: 2.5179 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 : 0.469 ------------------------------------------------------------------------------- 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: 9.9990 chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 50 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3030 r_free = 0.3030 target = 0.047225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.029126 restraints weight = 57253.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.029126 restraints weight = 57255.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.029126 restraints weight = 57255.555| |-----------------------------------------------------------------------------| r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 1.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4413 Z= 0.319 Angle : 0.642 6.647 6133 Z= 0.419 Chirality : 0.042 0.164 840 Planarity : 0.004 0.026 888 Dihedral : 6.871 26.191 888 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.10 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 (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: -2.33 (0.27), residues: 872 helix: -0.42 (0.23), residues: 454 sheet: -2.36 (0.68), residues: 45 loop : -2.91 (0.31), residues: 373 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 : 0.521 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0411 time to fit residues: 2.5204 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 : 0.468 ------------------------------------------------------------------------------- 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: 9.9990 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 30 optimal weight: 30.0000 chunk 75 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.2911 r_free = 0.2911 target = 0.043674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.029026 restraints weight = 71719.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.028822 restraints weight = 81869.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.028822 restraints weight = 92450.632| |-----------------------------------------------------------------------------| r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 1.7615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4413 Z= 0.399 Angle : 0.731 8.892 6133 Z= 0.477 Chirality : 0.043 0.175 840 Planarity : 0.005 0.032 888 Dihedral : 7.495 35.759 888 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.69 % Allowed : 14.56 % Favored : 84.75 % 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 (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: -2.61 (0.27), residues: 872 helix: -0.55 (0.23), residues: 432 sheet: -2.10 (0.81), residues: 38 loop : -3.12 (0.30), residues: 402 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 : 0.502 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0543 time to fit residues: 3.1626 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 : 0.500 ------------------------------------------------------------------------------- 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: 20.0000 chunk 70 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 20.0000 overall best weight: 7.3388 ------------------------------------------------------------------------------- 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 = 0.2913 r_free = 0.2913 target = 0.043442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.027909 restraints weight = 72041.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.027176 restraints weight = 70756.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.027188 restraints weight = 70332.033| |-----------------------------------------------------------------------------| r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 1.8954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4413 Z= 0.383 Angle : 0.733 7.985 6133 Z= 0.476 Chirality : 0.043 0.188 840 Planarity : 0.005 0.029 888 Dihedral : 7.470 30.109 888 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.57 % Allowed : 13.99 % Favored : 85.44 % 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 (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: -3.13 (0.27), residues: 872 helix: -0.96 (0.22), residues: 435 sheet: -2.57 (0.82), residues: 38 loop : -3.39 (0.30), residues: 399 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 : 0.463 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0417 time to fit residues: 2.4921 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 : 0.462 ------------------------------------------------------------------------------- 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: 20.0000 chunk 28 optimal weight: 0.0170 chunk 54 optimal weight: 20.0000 chunk 31 optimal weight: 40.0000 chunk 18 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 72 optimal weight: 0.0870 chunk 14 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 50.0000 overall best weight: 7.0204 ------------------------------------------------------------------------------- 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 = 0.2868 r_free = 0.2868 target = 0.042412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.029490 restraints weight = 78963.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.028748 restraints weight = 94613.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.028458 restraints weight = 130391.300| |-----------------------------------------------------------------------------| r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 1.9584 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= 0.386 Angle : 0.725 9.332 6133 Z= 0.469 Chirality : 0.044 0.200 840 Planarity : 0.005 0.029 888 Dihedral : 7.497 36.099 888 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.69 % Allowed : 16.28 % Favored : 83.03 % 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 : 0.35 % 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: -3.20 (0.27), residues: 872 helix: -1.00 (0.23), residues: 420 sheet: -3.09 (0.73), residues: 45 loop : -3.31 (0.30), residues: 407 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 : 0.459 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0421 time to fit residues: 2.5626 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 : 0.468 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 75 optimal weight: 0.0670 chunk 16 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 overall best weight: 6.0126 ------------------------------------------------------------------------------- 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 = 0.2863 r_free = 0.2863 target = 0.042464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.030121 restraints weight = 88725.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.029884 restraints weight = 97399.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 12)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.029884 restraints weight = 104176.354| |-----------------------------------------------------------------------------| r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 1.9939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4413 Z= 0.329 Angle : 0.665 8.445 6133 Z= 0.427 Chirality : 0.043 0.204 840 Planarity : 0.004 0.025 888 Dihedral : 7.079 31.345 888 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.46 % Allowed : 15.37 % Favored : 84.17 % 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 (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: -3.13 (0.27), residues: 872 helix: -0.88 (0.23), residues: 434 sheet: -2.37 (0.81), residues: 40 loop : -3.52 (0.30), residues: 398 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 : 0.513 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0407 time to fit residues: 2.4861 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 : 0.466 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.2945 r_free = 0.2945 target = 0.044400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.035945 restraints weight = 97311.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.036107 restraints weight = 84407.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.036231 restraints weight = 73120.249| |-----------------------------------------------------------------------------| r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 1.9662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 4413 Z= 0.148 Angle : 0.468 5.995 6133 Z= 0.298 Chirality : 0.042 0.144 840 Planarity : 0.003 0.019 888 Dihedral : 5.697 26.642 888 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.55 % Favored : 88.99 % 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: -1.94 (0.28), residues: 872 helix: 0.23 (0.23), residues: 458 sheet: -1.92 (0.83), residues: 40 loop : -3.29 (0.31), residues: 374 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: 1863.76 seconds wall clock time: 35 minutes 1.98 seconds (2101.98 seconds total)