Starting phenix.real_space_refine on Sat Aug 23 01:40:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k65_22689/08_2025/7k65_22689.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k65_22689/08_2025/7k65_22689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k65_22689/08_2025/7k65_22689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k65_22689/08_2025/7k65_22689.map" model { file = "/net/cci-nas-00/data/ceres_data/7k65_22689/08_2025/7k65_22689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k65_22689/08_2025/7k65_22689.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.021 sd= 0.878 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5734 2.51 5 N 1415 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8796 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7666 Classifications: {'peptide': 1005} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 959} Chain breaks: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 3, 'ASN:plan1': 3, 'GLU:plan': 10, 'ASP:plan': 7, 'ARG:plan': 10, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 166 Chain: "B" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 858 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 244 Unusual residues: {'NAG': 5, 'Q7G': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 65 Time building chain proxies: 2.04, per 1000 atoms: 0.23 Number of scatterers: 8796 At special positions: 0 Unit cell: (122.844, 121.785, 95.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1600 8.00 N 1415 7.00 C 5734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 313 " distance=2.34 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 290 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1401 " - " ASN A 400 " " NAG A1402 " - " ASN A 127 " " NAG A1403 " - " ASN A 298 " " NAG A1404 " - " ASN A 861 " " NAG A1405 " - " ASN A 335 " " NAG C 1 " - " ASN A 986 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 229.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 60.7% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 60 through 83 Processing helix chain 'A' and resid 85 through 100 removed outlier: 3.785A pdb=" N VAL A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 110 through 115 removed outlier: 4.125A pdb=" N TRP A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 removed outlier: 4.018A pdb=" N ARG A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 173 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 201 through 210 removed outlier: 3.618A pdb=" N ILE A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 228 removed outlier: 4.823A pdb=" N TRP A 222 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU A 223 " --> pdb=" O CYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.690A pdb=" N PHE A 245 " --> pdb=" O TRP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.722A pdb=" N ILE A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.830A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 374 through 396 removed outlier: 3.543A pdb=" N ALA A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 421 Processing helix chain 'A' and resid 424 through 444 Processing helix chain 'A' and resid 452 through 478 removed outlier: 4.273A pdb=" N ALA A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 488 through 513 removed outlier: 3.966A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 520 No H-bonds generated for 'chain 'A' and resid 518 through 520' Processing helix chain 'A' and resid 521 through 549 removed outlier: 5.240A pdb=" N ALA A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N SER A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 577 Processing helix chain 'A' and resid 577 through 588 removed outlier: 3.666A pdb=" N ILE A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 726 Processing helix chain 'A' and resid 727 through 732 removed outlier: 3.957A pdb=" N LYS A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 754 Processing helix chain 'A' and resid 762 through 766 Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 797 through 800 Processing helix chain 'A' and resid 801 through 812 removed outlier: 3.836A pdb=" N PHE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 829 through 851 Processing helix chain 'A' and resid 863 through 874 Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 916 through 924 Processing helix chain 'A' and resid 942 through 947 removed outlier: 3.648A pdb=" N LEU A 947 " --> pdb=" O PRO A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 989 Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1005 through 1008 Processing helix chain 'A' and resid 1009 through 1034 Processing helix chain 'A' and resid 1035 through 1061 removed outlier: 3.594A pdb=" N ALA A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1079 Processing helix chain 'A' and resid 1080 through 1082 No H-bonds generated for 'chain 'A' and resid 1080 through 1082' Processing helix chain 'A' and resid 1083 through 1092 Processing helix chain 'A' and resid 1096 through 1125 removed outlier: 5.435A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) Proline residue: A1111 - end of helix removed outlier: 4.253A pdb=" N MET A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1129 Processing helix chain 'A' and resid 1131 through 1138 removed outlier: 3.515A pdb=" N VAL A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1154 Processing helix chain 'A' and resid 1155 through 1164 removed outlier: 3.767A pdb=" N VAL A1159 " --> pdb=" O VAL A1155 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.657A pdb=" N LYS B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.719A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 178 Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 334 Processing sheet with id=AA4, first strand: chain 'A' and resid 958 through 964 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 59 removed outlier: 6.578A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 97 " --> pdb=" O TYR B 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 59 removed outlier: 6.578A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1443 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: 1.13 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2716 1.34 - 1.46: 2196 1.46 - 1.58: 4039 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9027 Sorted by residual: bond pdb=" C11 Q7G A1406 " pdb=" C13 Q7G A1406 " ideal model delta sigma weight residual 1.527 1.392 0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C11 Q7G A1408 " pdb=" C13 Q7G A1408 " ideal model delta sigma weight residual 1.527 1.403 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C11 Q7G A1407 " pdb=" C13 Q7G A1407 " ideal model delta sigma weight residual 1.527 1.403 0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C11 Q7G A1409 " pdb=" C13 Q7G A1409 " ideal model delta sigma weight residual 1.527 1.405 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C13 Q7G A1406 " pdb=" C16 Q7G A1406 " ideal model delta sigma weight residual 1.509 1.396 0.113 2.00e-02 2.50e+03 3.19e+01 ... (remaining 9022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 12051 2.23 - 4.47: 250 4.47 - 6.70: 54 6.70 - 8.93: 9 8.93 - 11.16: 4 Bond angle restraints: 12368 Sorted by residual: angle pdb=" C02 Q7G A1408 " pdb=" C03 Q7G A1408 " pdb=" C74 Q7G A1408 " ideal model delta sigma weight residual 120.31 109.15 11.16 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C LYS A 334 " pdb=" N ASN A 335 " pdb=" CA ASN A 335 " ideal model delta sigma weight residual 122.40 127.45 -5.05 1.45e+00 4.76e-01 1.22e+01 angle pdb=" C ILE A 949 " pdb=" CA ILE A 949 " pdb=" CB ILE A 949 " ideal model delta sigma weight residual 111.00 114.37 -3.37 9.80e-01 1.04e+00 1.18e+01 angle pdb=" C02 Q7G A1407 " pdb=" C03 Q7G A1407 " pdb=" C74 Q7G A1407 " ideal model delta sigma weight residual 120.31 110.01 10.30 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C02 Q7G A1409 " pdb=" C03 Q7G A1409 " pdb=" C74 Q7G A1409 " ideal model delta sigma weight residual 120.31 110.07 10.24 3.00e+00 1.11e-01 1.17e+01 ... (remaining 12363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.27: 5264 18.27 - 36.54: 380 36.54 - 54.80: 54 54.80 - 73.07: 8 73.07 - 91.34: 19 Dihedral angle restraints: 5725 sinusoidal: 2470 harmonic: 3255 Sorted by residual: dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 313 " pdb=" CB CYS A 313 " ideal model delta sinusoidal sigma weight residual -86.00 0.84 -86.84 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CA ASN A 335 " pdb=" C ASN A 335 " pdb=" N ALA A 336 " pdb=" CA ALA A 336 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA CYS A 220 " pdb=" C CYS A 220 " pdb=" N PHE A 221 " pdb=" CA PHE A 221 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1423 0.109 - 0.218: 34 0.218 - 0.327: 14 0.327 - 0.435: 2 0.435 - 0.544: 8 Chirality restraints: 1481 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-02 2.50e+03 5.81e+02 chirality pdb=" C11 Q7G A1406 " pdb=" C08 Q7G A1406 " pdb=" C13 Q7G A1406 " pdb=" C19 Q7G A1406 " both_signs ideal model delta sigma weight residual False 2.88 2.33 0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" C11 Q7G A1408 " pdb=" C08 Q7G A1408 " pdb=" C13 Q7G A1408 " pdb=" C19 Q7G A1408 " both_signs ideal model delta sigma weight residual False 2.88 2.36 0.51 2.00e-01 2.50e+01 6.58e+00 ... (remaining 1478 not shown) Planarity restraints: 1527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G A1406 " -0.013 2.00e-02 2.50e+03 1.88e-02 4.41e+00 pdb=" C13 Q7G A1406 " 0.030 2.00e-02 2.50e+03 pdb=" C14 Q7G A1406 " -0.025 2.00e-02 2.50e+03 pdb=" C15 Q7G A1406 " 0.011 2.00e-02 2.50e+03 pdb=" C16 Q7G A1406 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 Q7G A1409 " 0.012 2.00e-02 2.50e+03 1.80e-02 4.04e+00 pdb=" C13 Q7G A1409 " -0.029 2.00e-02 2.50e+03 pdb=" C14 Q7G A1409 " 0.023 2.00e-02 2.50e+03 pdb=" C15 Q7G A1409 " -0.009 2.00e-02 2.50e+03 pdb=" C16 Q7G A1409 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 Q7G A1407 " 0.012 2.00e-02 2.50e+03 1.79e-02 4.00e+00 pdb=" C13 Q7G A1407 " -0.029 2.00e-02 2.50e+03 pdb=" C14 Q7G A1407 " 0.023 2.00e-02 2.50e+03 pdb=" C15 Q7G A1407 " -0.010 2.00e-02 2.50e+03 pdb=" C16 Q7G A1407 " 0.003 2.00e-02 2.50e+03 ... (remaining 1524 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1161 2.75 - 3.29: 9055 3.29 - 3.83: 14956 3.83 - 4.36: 16599 4.36 - 4.90: 28651 Nonbonded interactions: 70422 Sorted by model distance: nonbonded pdb=" O PRO A 929 " pdb=" NH1 ARG A 931 " model vdw 2.213 3.120 nonbonded pdb=" NE2 GLN A 875 " pdb=" O LEU A 947 " model vdw 2.225 3.120 nonbonded pdb=" O MET A 278 " pdb=" OG1 THR A 293 " model vdw 2.226 3.040 nonbonded pdb=" O LYS A 810 " pdb=" OG SER A 813 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR A 876 " pdb=" O LYS A 881 " model vdw 2.261 3.040 ... (remaining 70417 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.060 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.007 0.307 9038 Z= 0.374 Angle : 0.879 34.717 12397 Z= 0.419 Chirality : 0.064 0.544 1481 Planarity : 0.004 0.037 1521 Dihedral : 13.575 91.340 3625 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.24), residues: 1114 helix: -0.78 (0.19), residues: 566 sheet: -1.34 (0.51), residues: 99 loop : -1.75 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.010 0.001 TYR A 995 PHE 0.015 0.001 PHE A 743 TRP 0.007 0.001 TRP A 830 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00641 ( 9027) covalent geometry : angle 0.80251 (12368) SS BOND : bond 0.15336 ( 4) SS BOND : angle 4.61892 ( 8) hydrogen bonds : bond 0.13876 ( 510) hydrogen bonds : angle 6.35262 ( 1443) link_BETA1-4 : bond 0.06414 ( 1) link_BETA1-4 : angle 20.37126 ( 3) link_NAG-ASN : bond 0.00657 ( 6) link_NAG-ASN : angle 3.23557 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 131 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8450 (mt0) REVERT: A 181 ARG cc_start: 0.8106 (mmt-90) cc_final: 0.7903 (mmm160) REVERT: A 220 CYS cc_start: 0.6628 (p) cc_final: 0.6154 (p) REVERT: A 278 MET cc_start: 0.9002 (mmp) cc_final: 0.8718 (mmm) REVERT: A 284 ASN cc_start: 0.8992 (m110) cc_final: 0.8727 (m110) REVERT: A 301 LYS cc_start: 0.9270 (pttt) cc_final: 0.9032 (ptpp) REVERT: A 325 GLU cc_start: 0.8323 (pm20) cc_final: 0.8115 (pm20) REVERT: A 351 GLN cc_start: 0.8188 (mt0) cc_final: 0.7857 (mt0) REVERT: A 443 MET cc_start: 0.7941 (mmp) cc_final: 0.7425 (mmm) REVERT: A 892 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7979 (mmm160) REVERT: A 949 ILE cc_start: 0.8757 (tt) cc_final: 0.8183 (tt) REVERT: A 969 ASP cc_start: 0.7753 (t0) cc_final: 0.7299 (t0) REVERT: A 972 ASP cc_start: 0.8255 (m-30) cc_final: 0.8046 (m-30) REVERT: A 975 GLU cc_start: 0.8419 (tp30) cc_final: 0.8105 (tp30) REVERT: A 1035 ASN cc_start: 0.8100 (t0) cc_final: 0.7780 (t0) REVERT: A 1102 MET cc_start: 0.9049 (mtt) cc_final: 0.8600 (mtm) REVERT: A 1136 ARG cc_start: 0.8615 (mtp180) cc_final: 0.8012 (ttm-80) REVERT: A 1163 PHE cc_start: 0.7534 (m-80) cc_final: 0.7328 (m-10) REVERT: A 1164 PHE cc_start: 0.6847 (t80) cc_final: 0.6063 (t80) REVERT: B 29 PHE cc_start: 0.8601 (t80) cc_final: 0.8391 (t80) REVERT: B 82 MET cc_start: 0.7056 (mtt) cc_final: 0.6735 (tmm) REVERT: B 104 TYR cc_start: 0.9045 (p90) cc_final: 0.8319 (p90) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.0834 time to fit residues: 30.2037 Evaluate side-chains 194 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 0.4980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1085 HIS A1152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.109127 restraints weight = 15489.377| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.99 r_work: 0.3195 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9038 Z= 0.150 Angle : 0.631 10.790 12397 Z= 0.307 Chirality : 0.043 0.269 1481 Planarity : 0.004 0.039 1521 Dihedral : 6.340 61.975 1814 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.88 % Allowed : 16.36 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.26), residues: 1114 helix: 0.77 (0.21), residues: 569 sheet: -0.70 (0.53), residues: 94 loop : -1.18 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 931 TYR 0.014 0.001 TYR B 59 PHE 0.015 0.002 PHE A1164 TRP 0.009 0.001 TRP A 264 HIS 0.009 0.001 HIS A 936 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9027) covalent geometry : angle 0.60746 (12368) SS BOND : bond 0.00536 ( 4) SS BOND : angle 1.38579 ( 8) hydrogen bonds : bond 0.04014 ( 510) hydrogen bonds : angle 4.76006 ( 1443) link_BETA1-4 : bond 0.00806 ( 1) link_BETA1-4 : angle 6.81450 ( 3) link_NAG-ASN : bond 0.00627 ( 6) link_NAG-ASN : angle 3.42740 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8547 (mm110) REVERT: A 181 ARG cc_start: 0.8196 (mmt-90) cc_final: 0.7948 (mmm160) REVERT: A 284 ASN cc_start: 0.9031 (m110) cc_final: 0.8742 (m110) REVERT: A 301 LYS cc_start: 0.9300 (pttt) cc_final: 0.9029 (ptpp) REVERT: A 351 GLN cc_start: 0.8846 (mt0) cc_final: 0.8409 (mt0) REVERT: A 573 MET cc_start: 0.8940 (tmm) cc_final: 0.8730 (ttp) REVERT: A 969 ASP cc_start: 0.7678 (t0) cc_final: 0.7108 (t0) REVERT: A 972 ASP cc_start: 0.8479 (m-30) cc_final: 0.8222 (m-30) REVERT: A 975 GLU cc_start: 0.8888 (tp30) cc_final: 0.8514 (tp30) REVERT: A 1035 ASN cc_start: 0.8255 (t0) cc_final: 0.7862 (t0) REVERT: A 1102 MET cc_start: 0.9061 (mtt) cc_final: 0.8742 (mtm) REVERT: A 1136 ARG cc_start: 0.8522 (mtp180) cc_final: 0.7461 (ttm110) REVERT: A 1154 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8045 (mp) REVERT: B 29 PHE cc_start: 0.8735 (t80) cc_final: 0.8506 (t80) REVERT: B 104 TYR cc_start: 0.9245 (p90) cc_final: 0.8418 (p90) REVERT: B 106 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8080 (ttm-80) outliers start: 25 outliers final: 17 residues processed: 220 average time/residue: 0.0724 time to fit residues: 22.5676 Evaluate side-chains 203 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1154 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111186 restraints weight = 15249.783| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.97 r_work: 0.3219 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9038 Z= 0.120 Angle : 0.575 9.050 12397 Z= 0.283 Chirality : 0.041 0.239 1481 Planarity : 0.004 0.037 1521 Dihedral : 5.593 62.279 1814 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.00 % Allowed : 18.89 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.26), residues: 1114 helix: 1.31 (0.22), residues: 571 sheet: -0.51 (0.54), residues: 95 loop : -0.98 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 931 TYR 0.009 0.001 TYR A 179 PHE 0.020 0.001 PHE A1032 TRP 0.010 0.001 TRP A 264 HIS 0.006 0.001 HIS A 936 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9027) covalent geometry : angle 0.55567 (12368) SS BOND : bond 0.00418 ( 4) SS BOND : angle 1.38998 ( 8) hydrogen bonds : bond 0.03650 ( 510) hydrogen bonds : angle 4.51328 ( 1443) link_BETA1-4 : bond 0.00864 ( 1) link_BETA1-4 : angle 5.68538 ( 3) link_NAG-ASN : bond 0.00473 ( 6) link_NAG-ASN : angle 3.01282 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.322 Fit side-chains REVERT: A 92 LEU cc_start: 0.8302 (mp) cc_final: 0.8085 (mp) REVERT: A 131 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8361 (mt0) REVERT: A 181 ARG cc_start: 0.8207 (mmt-90) cc_final: 0.7949 (mmm160) REVERT: A 284 ASN cc_start: 0.9016 (m110) cc_final: 0.8731 (m110) REVERT: A 301 LYS cc_start: 0.9264 (pttt) cc_final: 0.8985 (ptpp) REVERT: A 351 GLN cc_start: 0.8863 (mt0) cc_final: 0.8431 (mt0) REVERT: A 427 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8391 (mtp85) REVERT: A 769 ARG cc_start: 0.9055 (mtp180) cc_final: 0.8215 (mtt-85) REVERT: A 892 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7719 (mmm-85) REVERT: A 969 ASP cc_start: 0.7646 (t0) cc_final: 0.7311 (t0) REVERT: A 975 GLU cc_start: 0.8848 (tp30) cc_final: 0.8483 (tp30) REVERT: A 1035 ASN cc_start: 0.8239 (t0) cc_final: 0.7852 (t0) REVERT: A 1102 MET cc_start: 0.9104 (mtt) cc_final: 0.8778 (mtp) REVERT: A 1136 ARG cc_start: 0.8469 (mtp180) cc_final: 0.7453 (ttm110) REVERT: A 1154 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7919 (mp) REVERT: B 80 LEU cc_start: 0.7170 (tt) cc_final: 0.6764 (tp) REVERT: B 104 TYR cc_start: 0.9228 (p90) cc_final: 0.8706 (p90) outliers start: 26 outliers final: 13 residues processed: 215 average time/residue: 0.0694 time to fit residues: 21.7800 Evaluate side-chains 206 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 GLN A1006 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.138413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.108403 restraints weight = 15681.350| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.99 r_work: 0.3184 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9038 Z= 0.171 Angle : 0.621 8.468 12397 Z= 0.303 Chirality : 0.042 0.219 1481 Planarity : 0.004 0.037 1521 Dihedral : 5.714 62.194 1814 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.26 % Allowed : 19.47 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.26), residues: 1114 helix: 1.45 (0.22), residues: 571 sheet: -0.48 (0.55), residues: 92 loop : -0.95 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 105 TYR 0.009 0.001 TYR A 179 PHE 0.024 0.001 PHE A1032 TRP 0.011 0.001 TRP A1037 HIS 0.007 0.001 HIS A 936 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9027) covalent geometry : angle 0.60543 (12368) SS BOND : bond 0.00331 ( 4) SS BOND : angle 1.95686 ( 8) hydrogen bonds : bond 0.03677 ( 510) hydrogen bonds : angle 4.43223 ( 1443) link_BETA1-4 : bond 0.00709 ( 1) link_BETA1-4 : angle 5.18378 ( 3) link_NAG-ASN : bond 0.00440 ( 6) link_NAG-ASN : angle 2.81268 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 131 GLN cc_start: 0.8835 (mm110) cc_final: 0.8598 (mm110) REVERT: A 181 ARG cc_start: 0.8227 (mmt-90) cc_final: 0.7957 (mmm160) REVERT: A 284 ASN cc_start: 0.9066 (m110) cc_final: 0.8733 (m110) REVERT: A 301 LYS cc_start: 0.9277 (pttt) cc_final: 0.9004 (ptpp) REVERT: A 351 GLN cc_start: 0.8892 (mt0) cc_final: 0.8482 (mt0) REVERT: A 569 PHE cc_start: 0.8556 (m-10) cc_final: 0.8353 (m-10) REVERT: A 769 ARG cc_start: 0.9059 (mtp180) cc_final: 0.8269 (mtt-85) REVERT: A 795 LYS cc_start: 0.9145 (tttt) cc_final: 0.8732 (tptt) REVERT: A 975 GLU cc_start: 0.8861 (tp30) cc_final: 0.8518 (tp30) REVERT: A 1035 ASN cc_start: 0.8331 (t0) cc_final: 0.7883 (t0) REVERT: A 1102 MET cc_start: 0.9131 (mtt) cc_final: 0.8807 (mtp) REVERT: A 1136 ARG cc_start: 0.8489 (mtp180) cc_final: 0.7445 (ttm110) REVERT: B 29 PHE cc_start: 0.8822 (t80) cc_final: 0.8350 (t80) REVERT: B 104 TYR cc_start: 0.9268 (p90) cc_final: 0.8746 (p90) REVERT: B 105 ARG cc_start: 0.8736 (mmm-85) cc_final: 0.8486 (mmt90) REVERT: B 106 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8140 (ttm-80) outliers start: 37 outliers final: 25 residues processed: 216 average time/residue: 0.0763 time to fit residues: 23.6339 Evaluate side-chains 216 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1037 TRP Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110636 restraints weight = 15443.041| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.99 r_work: 0.3215 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9038 Z= 0.124 Angle : 0.569 7.629 12397 Z= 0.280 Chirality : 0.040 0.200 1481 Planarity : 0.004 0.036 1521 Dihedral : 5.561 62.563 1814 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.03 % Allowed : 20.39 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.26), residues: 1114 helix: 1.58 (0.22), residues: 571 sheet: -0.31 (0.56), residues: 92 loop : -0.91 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.008 0.001 TYR A 179 PHE 0.023 0.001 PHE A1032 TRP 0.011 0.001 TRP A 264 HIS 0.005 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9027) covalent geometry : angle 0.55558 (12368) SS BOND : bond 0.00344 ( 4) SS BOND : angle 1.41203 ( 8) hydrogen bonds : bond 0.03448 ( 510) hydrogen bonds : angle 4.33515 ( 1443) link_BETA1-4 : bond 0.00645 ( 1) link_BETA1-4 : angle 4.76402 ( 3) link_NAG-ASN : bond 0.00762 ( 6) link_NAG-ASN : angle 2.52075 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 131 GLN cc_start: 0.8763 (mm110) cc_final: 0.8511 (mm110) REVERT: A 179 TYR cc_start: 0.8704 (m-80) cc_final: 0.8434 (m-10) REVERT: A 181 ARG cc_start: 0.8224 (mmt-90) cc_final: 0.7975 (mmm160) REVERT: A 246 ASP cc_start: 0.9001 (t0) cc_final: 0.8740 (t0) REVERT: A 284 ASN cc_start: 0.9032 (m110) cc_final: 0.8699 (m110) REVERT: A 301 LYS cc_start: 0.9250 (pttt) cc_final: 0.8988 (ptpp) REVERT: A 351 GLN cc_start: 0.8869 (mt0) cc_final: 0.8463 (mt0) REVERT: A 795 LYS cc_start: 0.9123 (tttt) cc_final: 0.8659 (tptt) REVERT: A 892 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7739 (mmm160) REVERT: A 969 ASP cc_start: 0.8015 (t0) cc_final: 0.7691 (t0) REVERT: A 975 GLU cc_start: 0.8789 (tp30) cc_final: 0.8406 (tp30) REVERT: A 1035 ASN cc_start: 0.8304 (t0) cc_final: 0.7885 (t0) REVERT: A 1102 MET cc_start: 0.9080 (mtt) cc_final: 0.8814 (mtp) REVERT: A 1136 ARG cc_start: 0.8465 (mtp180) cc_final: 0.7435 (ttm110) REVERT: A 1154 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7874 (mp) REVERT: B 104 TYR cc_start: 0.9234 (p90) cc_final: 0.8784 (p90) REVERT: B 106 ARG cc_start: 0.8486 (ttm-80) cc_final: 0.8176 (ttm-80) outliers start: 35 outliers final: 25 residues processed: 217 average time/residue: 0.0717 time to fit residues: 22.5866 Evaluate side-chains 215 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 34 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112466 restraints weight = 15493.282| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.97 r_work: 0.3237 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9038 Z= 0.114 Angle : 0.572 7.215 12397 Z= 0.279 Chirality : 0.040 0.188 1481 Planarity : 0.004 0.036 1521 Dihedral : 5.453 62.105 1814 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.49 % Allowed : 20.16 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.26), residues: 1114 helix: 1.66 (0.22), residues: 572 sheet: -0.31 (0.56), residues: 92 loop : -0.83 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 529 TYR 0.008 0.001 TYR A 987 PHE 0.025 0.001 PHE A1032 TRP 0.011 0.001 TRP A 264 HIS 0.006 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9027) covalent geometry : angle 0.56040 (12368) SS BOND : bond 0.00307 ( 4) SS BOND : angle 1.29813 ( 8) hydrogen bonds : bond 0.03364 ( 510) hydrogen bonds : angle 4.25938 ( 1443) link_BETA1-4 : bond 0.00733 ( 1) link_BETA1-4 : angle 4.33981 ( 3) link_NAG-ASN : bond 0.00580 ( 6) link_NAG-ASN : angle 2.39835 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8633 (m-80) cc_final: 0.8265 (m-10) REVERT: A 181 ARG cc_start: 0.8189 (mmt-90) cc_final: 0.7981 (mmm160) REVERT: A 246 ASP cc_start: 0.8956 (t0) cc_final: 0.8705 (t0) REVERT: A 284 ASN cc_start: 0.9024 (m110) cc_final: 0.8703 (m110) REVERT: A 301 LYS cc_start: 0.9258 (pttt) cc_final: 0.8997 (ptpp) REVERT: A 351 GLN cc_start: 0.8858 (mt0) cc_final: 0.8425 (mt0) REVERT: A 427 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8486 (mtp85) REVERT: A 435 MET cc_start: 0.8203 (tpp) cc_final: 0.7781 (tpp) REVERT: A 573 MET cc_start: 0.8618 (ttp) cc_final: 0.8415 (tmm) REVERT: A 769 ARG cc_start: 0.9030 (mtp180) cc_final: 0.8266 (mtt-85) REVERT: A 795 LYS cc_start: 0.9090 (tttt) cc_final: 0.8624 (tptt) REVERT: A 892 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7667 (mmm160) REVERT: A 969 ASP cc_start: 0.8006 (t0) cc_final: 0.7541 (t0) REVERT: A 975 GLU cc_start: 0.8730 (tp30) cc_final: 0.8350 (tp30) REVERT: A 1035 ASN cc_start: 0.8260 (t0) cc_final: 0.7850 (t0) REVERT: A 1102 MET cc_start: 0.9032 (mtt) cc_final: 0.8827 (mtp) REVERT: A 1136 ARG cc_start: 0.8461 (mtp180) cc_final: 0.7671 (ttm110) REVERT: B 104 TYR cc_start: 0.9214 (p90) cc_final: 0.8830 (p90) REVERT: B 105 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8287 (mmt90) REVERT: B 106 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8062 (ttm-80) REVERT: B 108 TRP cc_start: 0.8472 (m100) cc_final: 0.8214 (m100) outliers start: 39 outliers final: 30 residues processed: 217 average time/residue: 0.0706 time to fit residues: 22.2656 Evaluate side-chains 223 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 936 HIS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 34 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.142276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.112850 restraints weight = 15392.651| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.96 r_work: 0.3234 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9038 Z= 0.117 Angle : 0.570 7.202 12397 Z= 0.280 Chirality : 0.040 0.171 1481 Planarity : 0.004 0.036 1521 Dihedral : 5.382 61.718 1814 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.15 % Allowed : 21.31 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.26), residues: 1114 helix: 1.70 (0.22), residues: 573 sheet: -0.18 (0.57), residues: 92 loop : -0.77 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 529 TYR 0.008 0.001 TYR A 987 PHE 0.026 0.001 PHE A1032 TRP 0.012 0.001 TRP A 264 HIS 0.006 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9027) covalent geometry : angle 0.55999 (12368) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.29379 ( 8) hydrogen bonds : bond 0.03348 ( 510) hydrogen bonds : angle 4.26455 ( 1443) link_BETA1-4 : bond 0.00721 ( 1) link_BETA1-4 : angle 4.08943 ( 3) link_NAG-ASN : bond 0.00503 ( 6) link_NAG-ASN : angle 2.25979 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ASP cc_start: 0.8996 (t0) cc_final: 0.8746 (t0) REVERT: A 284 ASN cc_start: 0.9059 (m110) cc_final: 0.8782 (m110) REVERT: A 301 LYS cc_start: 0.9250 (pttt) cc_final: 0.8982 (ptpp) REVERT: A 351 GLN cc_start: 0.8859 (mt0) cc_final: 0.8429 (mt0) REVERT: A 520 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: A 769 ARG cc_start: 0.9047 (mtp180) cc_final: 0.8275 (mtt-85) REVERT: A 795 LYS cc_start: 0.9116 (tttt) cc_final: 0.8601 (tptp) REVERT: A 892 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7726 (mmm160) REVERT: A 969 ASP cc_start: 0.8131 (t0) cc_final: 0.7716 (t0) REVERT: A 975 GLU cc_start: 0.8747 (tp30) cc_final: 0.8367 (tp30) REVERT: A 1035 ASN cc_start: 0.8233 (t0) cc_final: 0.7823 (t0) REVERT: A 1136 ARG cc_start: 0.8471 (mtp180) cc_final: 0.7707 (ttm110) REVERT: A 1154 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7721 (mp) REVERT: B 34 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7908 (ptp) REVERT: B 104 TYR cc_start: 0.9225 (p90) cc_final: 0.8892 (p90) REVERT: B 105 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8420 (mmm-85) REVERT: B 106 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8227 (ttm-80) outliers start: 36 outliers final: 29 residues processed: 217 average time/residue: 0.0870 time to fit residues: 27.0758 Evaluate side-chains 220 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1160 LEU Chi-restraints excluded: chain B residue 34 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2229 > 50: distance: 75 - 96: 25.760 distance: 79 - 82: 4.857 distance: 80 - 105: 7.212 distance: 82 - 83: 14.194 distance: 83 - 84: 11.756 distance: 83 - 86: 5.241 distance: 84 - 85: 22.101 distance: 84 - 89: 41.956 distance: 86 - 87: 9.226 distance: 86 - 88: 13.646 distance: 89 - 90: 24.944 distance: 90 - 91: 13.309 distance: 90 - 93: 16.115 distance: 91 - 92: 19.376 distance: 91 - 96: 11.662 distance: 93 - 94: 11.040 distance: 93 - 95: 18.751 distance: 96 - 97: 8.333 distance: 97 - 98: 10.239 distance: 97 - 100: 6.728 distance: 98 - 99: 6.582 distance: 98 - 105: 17.296 distance: 100 - 101: 7.692 distance: 101 - 102: 15.707 distance: 102 - 103: 9.138 distance: 102 - 104: 7.494 distance: 105 - 106: 4.846 distance: 106 - 107: 9.646 distance: 106 - 109: 16.576 distance: 107 - 108: 8.120 distance: 107 - 112: 3.247 distance: 108 - 138: 8.028 distance: 109 - 110: 23.334 distance: 109 - 111: 9.378 distance: 112 - 113: 9.048 distance: 113 - 114: 17.932 distance: 113 - 116: 6.600 distance: 114 - 115: 16.996 distance: 114 - 120: 18.866 distance: 115 - 146: 7.939 distance: 116 - 117: 8.441 distance: 117 - 118: 29.026 distance: 117 - 119: 3.979 distance: 120 - 121: 14.399 distance: 120 - 126: 10.795 distance: 121 - 122: 4.621 distance: 121 - 124: 10.877 distance: 122 - 123: 13.908 distance: 124 - 125: 6.458 distance: 125 - 126: 20.780 distance: 127 - 128: 12.237 distance: 128 - 129: 5.618 distance: 128 - 131: 14.437 distance: 129 - 130: 9.862 distance: 130 - 159: 15.254 distance: 131 - 132: 4.986 distance: 132 - 133: 12.765 distance: 132 - 134: 10.402 distance: 133 - 135: 4.800 distance: 134 - 136: 5.223 distance: 135 - 137: 10.843 distance: 136 - 137: 12.396 distance: 138 - 139: 6.991 distance: 139 - 140: 4.980 distance: 139 - 142: 21.805 distance: 140 - 141: 7.436 distance: 140 - 146: 6.536 distance: 141 - 163: 11.636 distance: 142 - 143: 7.610 distance: 143 - 144: 23.809 distance: 143 - 145: 12.658 distance: 146 - 147: 5.766 distance: 147 - 148: 7.732 distance: 147 - 150: 12.637 distance: 148 - 149: 13.259 distance: 148 - 151: 8.352 distance: 149 - 170: 10.516 distance: 151 - 152: 3.148 distance: 152 - 153: 7.997 distance: 152 - 155: 4.373 distance: 153 - 154: 3.029 distance: 153 - 159: 4.582 distance: 154 - 173: 9.855 distance: 155 - 156: 7.023 distance: 156 - 157: 21.458 distance: 156 - 158: 8.609