Starting phenix.real_space_refine on Fri Aug 2 18:59:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vib_43256/08_2024/8vib_43256.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vib_43256/08_2024/8vib_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vib_43256/08_2024/8vib_43256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vib_43256/08_2024/8vib_43256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vib_43256/08_2024/8vib_43256.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vib_43256/08_2024/8vib_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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 6.24, per 1000 atoms: 1.41 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 - 3.50 Amino acid : False - 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: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.68 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: 1.43 Time building geometry restraints manager: 2.05 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: 97.67 - 105.47: 41 105.47 - 113.28: 2462 113.28 - 121.09: 2211 121.09 - 128.90: 1417 128.90 - 136.71: 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: 7.930 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 20.950 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.050 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.485 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0442 time to fit residues: 2.6232 Evaluate side-chains 24 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 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 fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.414 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0365 time to fit residues: 2.2514 Evaluate side-chains 24 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 40.0000 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 40.0000 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 1.0538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4413 Z= 0.339 Angle : 0.734 7.794 6133 Z= 0.474 Chirality : 0.044 0.147 840 Planarity : 0.005 0.023 888 Dihedral : 6.637 30.592 888 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.82 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 : 0.12 % 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: -0.88 (0.28), residues: 872 helix: 0.56 (0.23), residues: 466 sheet: -2.11 (0.59), residues: 57 loop : -1.89 (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 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.519 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0439 time to fit residues: 2.8104 Evaluate side-chains 25 residues out of total 776 non-(ALA, GLY, PRO) need fitting. 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 77 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 22 optimal weight: 30.0000 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 1.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 4413 Z= 0.176 Angle : 0.460 4.580 6133 Z= 0.298 Chirality : 0.041 0.130 840 Planarity : 0.003 0.014 888 Dihedral : 5.032 22.990 888 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.08 % Favored : 93.69 % 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: 0.26 (0.29), residues: 872 helix: 1.66 (0.24), residues: 469 sheet: -1.33 (0.69), residues: 52 loop : -1.73 (0.34), residues: 351 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.461 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0371 time to fit residues: 2.3416 Evaluate side-chains 25 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 50.0000 chunk 61 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 20 optimal weight: 0.0020 overall best weight: 5.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 1.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4413 Z= 0.320 Angle : 0.670 5.076 6133 Z= 0.433 Chirality : 0.043 0.137 840 Planarity : 0.004 0.018 888 Dihedral : 6.811 29.945 888 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.21 % Favored : 89.45 % 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: -1.00 (0.28), residues: 872 helix: 0.73 (0.23), residues: 466 sheet: -1.93 (0.63), residues: 55 loop : -2.44 (0.32), residues: 351 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 fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.525 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0439 time to fit residues: 2.6886 Evaluate side-chains 24 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.0060 chunk 74 optimal weight: 0.0370 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 0.0980 chunk 83 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 1.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 4413 Z= 0.087 Angle : 0.406 5.166 6133 Z= 0.255 Chirality : 0.041 0.130 840 Planarity : 0.002 0.014 888 Dihedral : 4.704 18.997 888 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.73 % Favored : 94.04 % 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: 0.54 (0.30), residues: 872 helix: 2.02 (0.24), residues: 470 sheet: -1.44 (0.65), residues: 57 loop : -1.78 (0.35), residues: 345 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 25 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.496 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0419 time to fit residues: 2.6436 Evaluate side-chains 25 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.0980 overall best weight: 6.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 1.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4413 Z= 0.352 Angle : 0.639 5.031 6133 Z= 0.422 Chirality : 0.042 0.136 840 Planarity : 0.004 0.018 888 Dihedral : 6.048 26.343 888 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.21 % Favored : 89.45 % 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: -0.72 (0.29), residues: 872 helix: 1.03 (0.24), residues: 452 sheet: -2.22 (0.64), residues: 51 loop : -2.22 (0.33), residues: 369 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 fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.506 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0416 time to fit residues: 2.5854 Evaluate side-chains 24 residues out of total 776 non-(ALA, GLY, PRO) need fitting. 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 24 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 77 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 1.5021 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= 0.158 Angle : 0.440 4.586 6133 Z= 0.284 Chirality : 0.042 0.129 840 Planarity : 0.002 0.015 888 Dihedral : 5.039 17.688 888 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.45 % Favored : 92.20 % 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: -0.13 (0.29), residues: 872 helix: 1.50 (0.24), residues: 468 sheet: -1.30 (0.72), residues: 50 loop : -2.19 (0.33), residues: 354 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 fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.507 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0419 time to fit residues: 2.5897 Evaluate side-chains 24 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 1.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4413 Z= 0.214 Angle : 0.505 5.568 6133 Z= 0.326 Chirality : 0.042 0.134 840 Planarity : 0.003 0.014 888 Dihedral : 5.389 26.068 888 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.86 % Favored : 89.79 % 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: -0.34 (0.29), residues: 872 helix: 1.46 (0.24), residues: 463 sheet: -1.97 (0.71), residues: 40 loop : -2.35 (0.32), residues: 369 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 fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.507 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0418 time to fit residues: 2.5782 Evaluate side-chains 24 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 1.7610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4413 Z= 0.336 Angle : 0.670 7.962 6133 Z= 0.432 Chirality : 0.043 0.170 840 Planarity : 0.004 0.021 888 Dihedral : 6.709 25.814 888 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.42 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: -1.85 (0.27), residues: 872 helix: 0.16 (0.23), residues: 447 sheet: -2.72 (0.75), residues: 40 loop : -2.82 (0.31), 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 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 fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.533 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0452 time to fit residues: 2.7457 Evaluate side-chains 24 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 10.0000 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 chunk 70 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 overall best weight: 4.6390 ------------------------------------------------------------------------------- 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 = 0.2914 r_free = 0.2914 target = 0.044260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.030062 restraints weight = 82171.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.029915 restraints weight = 90558.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.029915 restraints weight = 98952.088| |-----------------------------------------------------------------------------| r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 1.7941 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= 0.253 Angle : 0.541 6.780 6133 Z= 0.351 Chirality : 0.042 0.161 840 Planarity : 0.003 0.024 888 Dihedral : 5.906 30.953 888 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.47 % Favored : 88.07 % 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: -1.43 (0.28), residues: 872 helix: 0.55 (0.23), residues: 461 sheet: -2.58 (0.75), residues: 40 loop : -2.80 (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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1198.79 seconds wall clock time: 21 minutes 44.37 seconds (1304.37 seconds total)