Starting phenix.real_space_refine on Sun Jul 27 02:23:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k65_22689/07_2025/7k65_22689.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k65_22689/07_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_22689/07_2025/7k65_22689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k65_22689/07_2025/7k65_22689.map" model { file = "/net/cci-nas-00/data/ceres_data/7k65_22689/07_2025/7k65_22689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k65_22689/07_2025/7k65_22689.cif" } resolution = 3.4 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= -0.021 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 10} 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: {'GLN:plan1': 1, 'GLU:plan': 3, '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: 5.48, per 1000 atoms: 0.62 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: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.02 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: 2.99 Time building geometry restraints manager: 2.88 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: 1.480 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.710 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- 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 : 8.32 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 (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: -1.91 (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 TRP 0.007 0.001 TRP A 830 HIS 0.003 0.001 HIS A 187 PHE 0.015 0.001 PHE A 743 TYR 0.010 0.001 TYR A 995 ARG 0.003 0.000 ARG B 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 6) link_NAG-ASN : angle 3.23557 ( 18) link_BETA1-4 : bond 0.06414 ( 1) link_BETA1-4 : angle 20.37126 ( 3) hydrogen bonds : bond 0.13876 ( 510) hydrogen bonds : angle 6.35262 ( 1443) SS BOND : bond 0.15336 ( 4) SS BOND : angle 4.61892 ( 8) covalent geometry : bond 0.00641 ( 9027) covalent geometry : angle 0.80251 (12368) *********************** 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 : 0.935 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: 0.2112 time to fit residues: 75.6930 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 : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 258 ASN A1085 HIS B 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110798 restraints weight = 15358.178| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.98 r_work: 0.3218 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1576 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= 0.127 Angle : 0.619 10.903 12397 Z= 0.300 Chirality : 0.042 0.269 1481 Planarity : 0.004 0.039 1521 Dihedral : 6.328 61.670 1814 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.65 % Allowed : 16.24 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1114 helix: 0.77 (0.21), residues: 569 sheet: -0.63 (0.54), residues: 94 loop : -1.19 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 264 HIS 0.008 0.001 HIS A 936 PHE 0.015 0.001 PHE A1032 TYR 0.013 0.001 TYR B 59 ARG 0.004 0.000 ARG A 931 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 6) link_NAG-ASN : angle 3.47305 ( 18) link_BETA1-4 : bond 0.00879 ( 1) link_BETA1-4 : angle 6.91100 ( 3) hydrogen bonds : bond 0.04007 ( 510) hydrogen bonds : angle 4.74556 ( 1443) SS BOND : bond 0.00659 ( 4) SS BOND : angle 1.24504 ( 8) covalent geometry : bond 0.00273 ( 9027) covalent geometry : angle 0.59502 (12368) *********************** 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 235 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8547 (mm110) REVERT: A 181 ARG cc_start: 0.8177 (mmt-90) cc_final: 0.7930 (mmm160) REVERT: A 284 ASN cc_start: 0.9025 (m110) cc_final: 0.8745 (m110) REVERT: A 301 LYS cc_start: 0.9297 (pttt) cc_final: 0.9024 (ptpp) REVERT: A 351 GLN cc_start: 0.8829 (mt0) cc_final: 0.8392 (mt0) REVERT: A 969 ASP cc_start: 0.7694 (t0) cc_final: 0.7126 (t0) REVERT: A 972 ASP cc_start: 0.8439 (m-30) cc_final: 0.8197 (m-30) REVERT: A 975 GLU cc_start: 0.8870 (tp30) cc_final: 0.8494 (tp30) REVERT: A 1035 ASN cc_start: 0.8204 (t0) cc_final: 0.7833 (t0) REVERT: A 1102 MET cc_start: 0.9130 (mtt) cc_final: 0.8747 (mtm) REVERT: A 1136 ARG cc_start: 0.8541 (mtp180) cc_final: 0.7468 (ttm110) REVERT: A 1154 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8033 (mp) REVERT: B 29 PHE cc_start: 0.8686 (t80) cc_final: 0.8467 (t80) REVERT: B 104 TYR cc_start: 0.9225 (p90) cc_final: 0.8338 (p90) REVERT: B 106 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8038 (ttm-80) outliers start: 23 outliers final: 16 residues processed: 223 average time/residue: 0.1991 time to fit residues: 62.3683 Evaluate side-chains 204 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 357 GLN 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 1070 VAL 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 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 61 optimal weight: 0.0070 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.139797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109898 restraints weight = 15556.230| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 4.01 r_work: 0.3199 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9038 Z= 0.137 Angle : 0.587 9.160 12397 Z= 0.289 Chirality : 0.041 0.241 1481 Planarity : 0.004 0.037 1521 Dihedral : 5.648 62.057 1814 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.46 % Allowed : 18.43 % 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 (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: 0.32 (0.26), residues: 1114 helix: 1.27 (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 TRP 0.011 0.001 TRP A1037 HIS 0.004 0.001 HIS A 187 PHE 0.021 0.001 PHE A1032 TYR 0.010 0.001 TYR A 179 ARG 0.004 0.000 ARG A 427 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 6) link_NAG-ASN : angle 3.03636 ( 18) link_BETA1-4 : bond 0.00908 ( 1) link_BETA1-4 : angle 5.78417 ( 3) hydrogen bonds : bond 0.03713 ( 510) hydrogen bonds : angle 4.53499 ( 1443) SS BOND : bond 0.00322 ( 4) SS BOND : angle 1.46912 ( 8) covalent geometry : bond 0.00306 ( 9027) covalent geometry : angle 0.56742 (12368) *********************** 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 231 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.976 Fit side-chains REVERT: A 92 LEU cc_start: 0.8376 (mp) cc_final: 0.8155 (mp) REVERT: A 131 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8468 (mm110) REVERT: A 181 ARG cc_start: 0.8221 (mmt-90) cc_final: 0.7954 (mmm160) REVERT: A 284 ASN cc_start: 0.9034 (m110) cc_final: 0.8754 (m110) REVERT: A 301 LYS cc_start: 0.9279 (pttt) cc_final: 0.9000 (ptpp) REVERT: A 351 GLN cc_start: 0.8873 (mt0) cc_final: 0.8448 (mt0) REVERT: A 569 PHE cc_start: 0.8581 (m-10) cc_final: 0.8333 (m-10) REVERT: A 573 MET cc_start: 0.8945 (tmm) cc_final: 0.8728 (ttp) REVERT: A 892 ARG cc_start: 0.8128 (mmm160) cc_final: 0.7755 (mmm-85) REVERT: A 969 ASP cc_start: 0.7704 (t0) cc_final: 0.7367 (t0) REVERT: A 975 GLU cc_start: 0.8840 (tp30) cc_final: 0.8500 (tp30) REVERT: A 1035 ASN cc_start: 0.8238 (t0) cc_final: 0.7851 (t0) REVERT: A 1102 MET cc_start: 0.9121 (mtt) cc_final: 0.8603 (mtm) REVERT: A 1136 ARG cc_start: 0.8502 (mtp180) cc_final: 0.7471 (ttm110) REVERT: B 80 LEU cc_start: 0.7154 (tt) cc_final: 0.6736 (tp) REVERT: B 104 TYR cc_start: 0.9254 (p90) cc_final: 0.8725 (p90) outliers start: 30 outliers final: 22 residues processed: 213 average time/residue: 0.1844 time to fit residues: 57.3639 Evaluate side-chains 217 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 340 LEU Chi-restraints excluded: chain A residue 375 GLU 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 789 MET 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 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 B residue 21 SER Chi-restraints excluded: chain B residue 34 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 403 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 = 0.3754 r_free = 0.3754 target = 0.138077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107995 restraints weight = 15571.408| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.99 r_work: 0.3176 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9038 Z= 0.180 Angle : 0.607 8.306 12397 Z= 0.300 Chirality : 0.042 0.226 1481 Planarity : 0.004 0.038 1521 Dihedral : 5.621 62.423 1814 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.84 % Allowed : 19.47 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.46 (0.26), residues: 1114 helix: 1.44 (0.22), residues: 571 sheet: -0.49 (0.55), residues: 92 loop : -0.97 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1037 HIS 0.005 0.001 HIS A 936 PHE 0.022 0.002 PHE A1032 TYR 0.009 0.001 TYR A 179 ARG 0.004 0.000 ARG A 427 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 6) link_NAG-ASN : angle 2.71882 ( 18) link_BETA1-4 : bond 0.00707 ( 1) link_BETA1-4 : angle 5.25954 ( 3) hydrogen bonds : bond 0.03727 ( 510) hydrogen bonds : angle 4.46055 ( 1443) SS BOND : bond 0.00352 ( 4) SS BOND : angle 1.87361 ( 8) covalent geometry : bond 0.00407 ( 9027) covalent geometry : angle 0.59085 (12368) *********************** 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 238 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8188 (mp) REVERT: A 131 GLN cc_start: 0.8835 (mm110) cc_final: 0.8600 (mm110) REVERT: A 181 ARG cc_start: 0.8233 (mmt-90) cc_final: 0.7970 (mmm160) REVERT: A 284 ASN cc_start: 0.9025 (m110) cc_final: 0.8729 (m110) REVERT: A 301 LYS cc_start: 0.9259 (pttt) cc_final: 0.8996 (ptpp) REVERT: A 351 GLN cc_start: 0.8900 (mt0) cc_final: 0.8486 (mt0) REVERT: A 569 PHE cc_start: 0.8548 (m-10) cc_final: 0.8316 (m-10) REVERT: A 795 LYS cc_start: 0.9147 (tttt) cc_final: 0.8727 (tptt) REVERT: A 892 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7799 (mmm-85) REVERT: A 969 ASP cc_start: 0.7875 (t0) cc_final: 0.7540 (t0) REVERT: A 975 GLU cc_start: 0.8865 (tp30) cc_final: 0.8511 (tp30) REVERT: A 987 TYR cc_start: 0.8174 (m-80) cc_final: 0.7783 (m-80) REVERT: A 1035 ASN cc_start: 0.8334 (t0) cc_final: 0.7935 (t0) REVERT: A 1102 MET cc_start: 0.9133 (mtt) cc_final: 0.8604 (mtm) REVERT: A 1136 ARG cc_start: 0.8484 (mtp180) cc_final: 0.7429 (ttm110) REVERT: A 1154 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7910 (mp) REVERT: B 29 PHE cc_start: 0.8844 (t80) cc_final: 0.8291 (t80) REVERT: B 104 TYR cc_start: 0.9275 (p90) cc_final: 0.8351 (p90) REVERT: B 106 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8034 (ttm-80) outliers start: 42 outliers final: 26 residues processed: 216 average time/residue: 0.1902 time to fit residues: 59.3602 Evaluate side-chains 221 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 300 THR 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 462 LEU Chi-restraints excluded: chain A residue 463 VAL 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 874 VAL 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 A residue 1125 MET Chi-restraints excluded: chain A residue 1154 LEU 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 17 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 65 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 15 optimal weight: 0.0000 chunk 54 optimal weight: 0.8980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 403 GLN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.113312 restraints weight = 15386.445| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.98 r_work: 0.3251 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9038 Z= 0.104 Angle : 0.579 10.426 12397 Z= 0.281 Chirality : 0.042 0.551 1481 Planarity : 0.004 0.037 1521 Dihedral : 5.565 62.641 1814 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.76 % Allowed : 21.89 % 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 (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: 0.69 (0.26), residues: 1114 helix: 1.58 (0.22), residues: 572 sheet: -0.14 (0.57), residues: 92 loop : -0.87 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.009 0.001 HIS A 936 PHE 0.025 0.001 PHE A1032 TYR 0.009 0.001 TYR A 179 ARG 0.004 0.000 ARG A 427 Details of bonding type rmsd link_NAG-ASN : bond 0.01252 ( 6) link_NAG-ASN : angle 3.52394 ( 18) link_BETA1-4 : bond 0.00692 ( 1) link_BETA1-4 : angle 4.78663 ( 3) hydrogen bonds : bond 0.03374 ( 510) hydrogen bonds : angle 4.29681 ( 1443) SS BOND : bond 0.00345 ( 4) SS BOND : angle 1.24371 ( 8) covalent geometry : bond 0.00216 ( 9027) covalent geometry : angle 0.55828 (12368) *********************** 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 238 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8162 (mp) REVERT: A 131 GLN cc_start: 0.8751 (mm110) cc_final: 0.8433 (mt0) REVERT: A 142 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8506 (mp10) REVERT: A 181 ARG cc_start: 0.8196 (mmt-90) cc_final: 0.7942 (mmm160) REVERT: A 246 ASP cc_start: 0.9055 (t0) cc_final: 0.8768 (t0) REVERT: A 284 ASN cc_start: 0.9008 (m110) cc_final: 0.8724 (m110) REVERT: A 301 LYS cc_start: 0.9269 (pttt) cc_final: 0.8988 (ptpp) REVERT: A 351 GLN cc_start: 0.8867 (mt0) cc_final: 0.8441 (mt0) REVERT: A 420 PHE cc_start: 0.8553 (t80) cc_final: 0.8344 (t80) REVERT: A 435 MET cc_start: 0.8186 (tpp) cc_final: 0.7708 (tpp) REVERT: A 795 LYS cc_start: 0.9075 (tttt) cc_final: 0.8625 (tptt) REVERT: A 892 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7616 (mmm-85) REVERT: A 975 GLU cc_start: 0.8728 (tp30) cc_final: 0.8361 (tp30) REVERT: A 1035 ASN cc_start: 0.8245 (t0) cc_final: 0.7837 (t0) REVERT: A 1102 MET cc_start: 0.9045 (mtt) cc_final: 0.8814 (mtp) REVERT: A 1136 ARG cc_start: 0.8446 (mtp180) cc_final: 0.7743 (ttm110) REVERT: A 1154 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7807 (mp) REVERT: B 104 TYR cc_start: 0.9210 (p90) cc_final: 0.8801 (p90) REVERT: B 106 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8006 (ttm-80) REVERT: B 108 TRP cc_start: 0.8450 (m100) cc_final: 0.8213 (m100) outliers start: 24 outliers final: 15 residues processed: 223 average time/residue: 0.1903 time to fit residues: 60.7512 Evaluate side-chains 215 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 142 GLN 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 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 936 HIS Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1160 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- 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** B 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.142367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112226 restraints weight = 15390.585| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 4.04 r_work: 0.3240 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2591 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= 0.116 Angle : 0.572 7.697 12397 Z= 0.282 Chirality : 0.041 0.336 1481 Planarity : 0.004 0.036 1521 Dihedral : 5.459 62.134 1814 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.57 % Allowed : 22.24 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.79 (0.26), residues: 1114 helix: 1.65 (0.22), residues: 573 sheet: -0.17 (0.57), residues: 92 loop : -0.79 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.009 0.001 HIS A 936 PHE 0.024 0.001 PHE A1032 TYR 0.017 0.001 TYR A 179 ARG 0.005 0.000 ARG A 427 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 6) link_NAG-ASN : angle 2.65387 ( 18) link_BETA1-4 : bond 0.00707 ( 1) link_BETA1-4 : angle 4.45319 ( 3) hydrogen bonds : bond 0.03383 ( 510) hydrogen bonds : angle 4.27209 ( 1443) SS BOND : bond 0.00290 ( 4) SS BOND : angle 1.21745 ( 8) covalent geometry : bond 0.00259 ( 9027) covalent geometry : angle 0.55870 (12368) *********************** 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 238 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8171 (mp) REVERT: A 181 ARG cc_start: 0.8079 (mmt-90) cc_final: 0.7835 (mmm160) REVERT: A 246 ASP cc_start: 0.8956 (t0) cc_final: 0.8695 (t0) REVERT: A 284 ASN cc_start: 0.9055 (m110) cc_final: 0.8777 (m110) REVERT: A 301 LYS cc_start: 0.9273 (pttt) cc_final: 0.8993 (ptpp) REVERT: A 351 GLN cc_start: 0.8841 (mt0) cc_final: 0.8426 (mt0) REVERT: A 769 ARG cc_start: 0.9018 (mtp180) cc_final: 0.8235 (mtt-85) REVERT: A 795 LYS cc_start: 0.9085 (tttt) cc_final: 0.8620 (tptt) REVERT: A 834 PHE cc_start: 0.9079 (t80) cc_final: 0.8778 (t80) REVERT: A 892 ARG cc_start: 0.7998 (mmm160) cc_final: 0.7628 (mmm-85) REVERT: A 969 ASP cc_start: 0.8050 (t0) cc_final: 0.7599 (t0) REVERT: A 975 GLU cc_start: 0.8732 (tp30) cc_final: 0.8349 (tp30) REVERT: A 1035 ASN cc_start: 0.8245 (t0) cc_final: 0.7830 (t0) REVERT: A 1102 MET cc_start: 0.9022 (mtt) cc_final: 0.8710 (mtm) REVERT: A 1136 ARG cc_start: 0.8458 (mtp180) cc_final: 0.7451 (ttm110) REVERT: A 1154 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7769 (mp) REVERT: B 104 TYR cc_start: 0.9196 (p90) cc_final: 0.8846 (p90) REVERT: B 105 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.8258 (mmt90) REVERT: B 106 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8069 (ttm-80) REVERT: B 108 TRP cc_start: 0.8467 (m100) cc_final: 0.8235 (m100) outliers start: 31 outliers final: 24 residues processed: 222 average time/residue: 0.2485 time to fit residues: 81.8351 Evaluate side-chains 220 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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 309 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 375 GLU 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 520 GLU 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 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 1154 LEU Chi-restraints excluded: chain A residue 1160 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.141798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111532 restraints weight = 15622.383| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 4.07 r_work: 0.3229 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9038 Z= 0.125 Angle : 0.572 7.388 12397 Z= 0.283 Chirality : 0.041 0.262 1481 Planarity : 0.004 0.036 1521 Dihedral : 5.402 61.906 1814 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.26 % Allowed : 21.66 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.88 (0.26), residues: 1114 helix: 1.68 (0.22), residues: 580 sheet: -0.17 (0.57), residues: 92 loop : -0.70 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.008 0.001 HIS A 936 PHE 0.026 0.001 PHE A1032 TYR 0.014 0.001 TYR A 179 ARG 0.005 0.000 ARG A 427 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 6) link_NAG-ASN : angle 2.36529 ( 18) link_BETA1-4 : bond 0.00584 ( 1) link_BETA1-4 : angle 4.23155 ( 3) hydrogen bonds : bond 0.03365 ( 510) hydrogen bonds : angle 4.24912 ( 1443) SS BOND : bond 0.00265 ( 4) SS BOND : angle 1.48729 ( 8) covalent geometry : bond 0.00283 ( 9027) covalent geometry : angle 0.56079 (12368) *********************** 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 233 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8139 (mmt-90) cc_final: 0.7894 (mmm160) REVERT: A 246 ASP cc_start: 0.8965 (t0) cc_final: 0.8698 (t0) REVERT: A 284 ASN cc_start: 0.9071 (m110) cc_final: 0.8802 (m110) REVERT: A 301 LYS cc_start: 0.9248 (pttt) cc_final: 0.8983 (ptpp) REVERT: A 351 GLN cc_start: 0.8785 (mt0) cc_final: 0.8381 (mt0) REVERT: A 520 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8094 (pm20) REVERT: A 573 MET cc_start: 0.8596 (ttp) cc_final: 0.8351 (tmm) REVERT: A 769 ARG cc_start: 0.9045 (mtp180) cc_final: 0.8267 (mtt-85) REVERT: A 795 LYS cc_start: 0.9093 (tttt) cc_final: 0.8623 (tptt) REVERT: A 969 ASP cc_start: 0.8086 (t0) cc_final: 0.7765 (t0) REVERT: A 975 GLU cc_start: 0.8760 (tp30) cc_final: 0.8395 (tp30) REVERT: A 1035 ASN cc_start: 0.8264 (t0) cc_final: 0.7862 (t0) REVERT: A 1136 ARG cc_start: 0.8461 (mtp180) cc_final: 0.7662 (ttm110) REVERT: A 1154 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7670 (mp) REVERT: B 104 TYR cc_start: 0.9221 (p90) cc_final: 0.8883 (p90) REVERT: B 106 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8104 (ttm-80) REVERT: B 108 TRP cc_start: 0.8466 (m100) cc_final: 0.8181 (m100) outliers start: 37 outliers final: 29 residues processed: 214 average time/residue: 0.2047 time to fit residues: 63.0186 Evaluate side-chains 221 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 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 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 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 936 HIS 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 1070 VAL Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1160 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 936 HIS ** 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 = 0.3806 r_free = 0.3806 target = 0.141907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112377 restraints weight = 15455.139| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.96 r_work: 0.3235 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2793 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= 0.125 Angle : 0.587 7.259 12397 Z= 0.289 Chirality : 0.041 0.236 1481 Planarity : 0.004 0.035 1521 Dihedral : 5.384 61.700 1814 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.92 % Allowed : 22.47 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.86 (0.26), residues: 1114 helix: 1.68 (0.22), residues: 580 sheet: -0.08 (0.58), residues: 91 loop : -0.75 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.011 0.001 HIS A 936 PHE 0.028 0.001 PHE A1032 TYR 0.011 0.001 TYR A 179 ARG 0.004 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 6) link_NAG-ASN : angle 2.25978 ( 18) link_BETA1-4 : bond 0.00655 ( 1) link_BETA1-4 : angle 4.06426 ( 3) hydrogen bonds : bond 0.03389 ( 510) hydrogen bonds : angle 4.28694 ( 1443) SS BOND : bond 0.00449 ( 4) SS BOND : angle 2.99327 ( 8) covalent geometry : bond 0.00285 ( 9027) covalent geometry : angle 0.57322 (12368) *********************** REFINEMENT MACRO_CYCLE 8 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: 34 poor density : 199 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8109 (mmt-90) cc_final: 0.7887 (mmm160) REVERT: A 246 ASP cc_start: 0.8966 (t0) cc_final: 0.8698 (t0) REVERT: A 284 ASN cc_start: 0.9072 (m110) cc_final: 0.8809 (m110) REVERT: A 301 LYS cc_start: 0.9248 (pttt) cc_final: 0.8973 (ptpp) REVERT: A 351 GLN cc_start: 0.8795 (mt0) cc_final: 0.8401 (mt0) REVERT: A 769 ARG cc_start: 0.9032 (mtp180) cc_final: 0.8268 (mtt-85) REVERT: A 795 LYS cc_start: 0.9098 (tttt) cc_final: 0.8610 (tptt) REVERT: A 969 ASP cc_start: 0.8044 (t0) cc_final: 0.7623 (t0) REVERT: A 975 GLU cc_start: 0.8765 (tp30) cc_final: 0.8379 (tp30) REVERT: A 1035 ASN cc_start: 0.8268 (t0) cc_final: 0.7861 (t0) REVERT: A 1102 MET cc_start: 0.8361 (mtp) cc_final: 0.8134 (ptp) REVERT: A 1136 ARG cc_start: 0.8463 (mtp180) cc_final: 0.7677 (ttm110) REVERT: A 1154 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7670 (mp) REVERT: B 104 TYR cc_start: 0.9236 (p90) cc_final: 0.8877 (p90) REVERT: B 105 ARG cc_start: 0.8652 (mmt90) cc_final: 0.8440 (mmt90) REVERT: B 106 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8088 (ttm-80) REVERT: B 108 TRP cc_start: 0.8489 (m100) cc_final: 0.8208 (m100) outliers start: 34 outliers final: 29 residues processed: 218 average time/residue: 0.1870 time to fit residues: 58.7739 Evaluate side-chains 224 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 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 1054 PHE Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1160 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 0.0030 chunk 47 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5972 ------------------------------------------------------------------------------- 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 936 HIS ** 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 = 0.3831 r_free = 0.3831 target = 0.143909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114400 restraints weight = 15370.442| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.00 r_work: 0.3261 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9038 Z= 0.109 Angle : 0.594 9.058 12397 Z= 0.291 Chirality : 0.040 0.216 1481 Planarity : 0.004 0.035 1521 Dihedral : 5.310 61.651 1814 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.23 % Allowed : 23.39 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.91 (0.26), residues: 1114 helix: 1.67 (0.22), residues: 581 sheet: 0.02 (0.57), residues: 94 loop : -0.70 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 264 HIS 0.018 0.001 HIS A 936 PHE 0.028 0.001 PHE A1032 TYR 0.011 0.001 TYR A 179 ARG 0.007 0.000 ARG A 427 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 6) link_NAG-ASN : angle 2.20460 ( 18) link_BETA1-4 : bond 0.00660 ( 1) link_BETA1-4 : angle 3.87680 ( 3) hydrogen bonds : bond 0.03324 ( 510) hydrogen bonds : angle 4.25272 ( 1443) SS BOND : bond 0.00436 ( 4) SS BOND : angle 2.39106 ( 8) covalent geometry : bond 0.00239 ( 9027) covalent geometry : angle 0.58289 (12368) *********************** REFINEMENT MACRO_CYCLE 9 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 227 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8102 (mmt-90) cc_final: 0.7895 (mmm160) REVERT: A 246 ASP cc_start: 0.8932 (t0) cc_final: 0.8680 (t0) REVERT: A 284 ASN cc_start: 0.9116 (m110) cc_final: 0.8873 (m110) REVERT: A 301 LYS cc_start: 0.9233 (pttt) cc_final: 0.8966 (ptpp) REVERT: A 351 GLN cc_start: 0.8837 (mt0) cc_final: 0.8438 (mt0) REVERT: A 359 TYR cc_start: 0.8887 (t80) cc_final: 0.8682 (t80) REVERT: A 420 PHE cc_start: 0.8540 (t80) cc_final: 0.8260 (t80) REVERT: A 520 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: A 769 ARG cc_start: 0.9003 (mtp180) cc_final: 0.8223 (mtt-85) REVERT: A 795 LYS cc_start: 0.9051 (tttt) cc_final: 0.8516 (tptp) REVERT: A 969 ASP cc_start: 0.8052 (t0) cc_final: 0.7656 (t0) REVERT: A 975 GLU cc_start: 0.8734 (tp30) cc_final: 0.8343 (tp30) REVERT: A 1035 ASN cc_start: 0.8227 (t0) cc_final: 0.7832 (t0) REVERT: A 1136 ARG cc_start: 0.8408 (mtp180) cc_final: 0.7630 (ttm110) REVERT: A 1154 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7692 (mp) REVERT: B 104 TYR cc_start: 0.9199 (p90) cc_final: 0.8814 (p90) REVERT: B 105 ARG cc_start: 0.8646 (mmt90) cc_final: 0.8421 (mmt90) REVERT: B 106 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.7827 (ttm-80) REVERT: B 108 TRP cc_start: 0.8461 (m100) cc_final: 0.7833 (m100) outliers start: 28 outliers final: 24 residues processed: 215 average time/residue: 0.1848 time to fit residues: 57.2646 Evaluate side-chains 220 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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 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 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 888 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 108 optimal weight: 30.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 936 HIS ** 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 = 0.3798 r_free = 0.3798 target = 0.141301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111479 restraints weight = 15412.281| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.98 r_work: 0.3222 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9038 Z= 0.152 Angle : 0.633 9.138 12397 Z= 0.310 Chirality : 0.042 0.213 1481 Planarity : 0.004 0.035 1521 Dihedral : 5.330 61.181 1814 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.00 % Allowed : 24.19 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.88 (0.26), residues: 1114 helix: 1.64 (0.22), residues: 581 sheet: -0.08 (0.58), residues: 91 loop : -0.67 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1037 HIS 0.019 0.002 HIS A 936 PHE 0.027 0.002 PHE A1032 TYR 0.021 0.001 TYR B 37 ARG 0.004 0.000 ARG B 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 6) link_NAG-ASN : angle 2.16802 ( 18) link_BETA1-4 : bond 0.00628 ( 1) link_BETA1-4 : angle 3.79102 ( 3) hydrogen bonds : bond 0.03483 ( 510) hydrogen bonds : angle 4.33220 ( 1443) SS BOND : bond 0.00386 ( 4) SS BOND : angle 2.30054 ( 8) covalent geometry : bond 0.00350 ( 9027) covalent geometry : angle 0.62256 (12368) ********************** REFINEMENT MACRO_CYCLE 10 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 221 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7904 (mmm160) REVERT: A 246 ASP cc_start: 0.8959 (t0) cc_final: 0.8680 (t0) REVERT: A 284 ASN cc_start: 0.9079 (m110) cc_final: 0.8823 (m110) REVERT: A 301 LYS cc_start: 0.9238 (pttt) cc_final: 0.8964 (ptpp) REVERT: A 351 GLN cc_start: 0.8817 (mt0) cc_final: 0.8414 (mt0) REVERT: A 420 PHE cc_start: 0.8531 (t80) cc_final: 0.8230 (t80) REVERT: A 769 ARG cc_start: 0.9043 (mtp180) cc_final: 0.8265 (mtt-85) REVERT: A 795 LYS cc_start: 0.9115 (tttt) cc_final: 0.8574 (tptp) REVERT: A 969 ASP cc_start: 0.7970 (t0) cc_final: 0.7632 (t0) REVERT: A 975 GLU cc_start: 0.8733 (tp30) cc_final: 0.8380 (tp30) REVERT: A 1035 ASN cc_start: 0.8327 (t0) cc_final: 0.7908 (t0) REVERT: A 1102 MET cc_start: 0.8590 (ptp) cc_final: 0.8375 (ptm) REVERT: A 1136 ARG cc_start: 0.8453 (mtp180) cc_final: 0.7687 (ttm110) REVERT: B 104 TYR cc_start: 0.9234 (p90) cc_final: 0.8872 (p90) REVERT: B 105 ARG cc_start: 0.8645 (mmt90) cc_final: 0.8408 (mmt90) REVERT: B 106 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.7951 (ttm-80) REVERT: B 108 TRP cc_start: 0.8452 (m100) cc_final: 0.7847 (m100) outliers start: 26 outliers final: 26 residues processed: 208 average time/residue: 0.1860 time to fit residues: 55.4177 Evaluate side-chains 215 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 267 MET 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 888 LEU Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 1008 ILE 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 1160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 35 optimal weight: 0.0060 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 0.0020 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 overall best weight: 0.7606 ------------------------------------------------------------------------------- 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 936 HIS ** 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 = 0.3827 r_free = 0.3827 target = 0.143779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113542 restraints weight = 15415.072| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.08 r_work: 0.3257 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9038 Z= 0.114 Angle : 0.601 8.343 12397 Z= 0.295 Chirality : 0.041 0.199 1481 Planarity : 0.004 0.035 1521 Dihedral : 5.269 61.750 1814 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.00 % Allowed : 24.65 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.26), residues: 1114 helix: 1.67 (0.22), residues: 580 sheet: -0.02 (0.58), residues: 91 loop : -0.67 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 264 HIS 0.015 0.001 HIS A 936 PHE 0.027 0.001 PHE A1032 TYR 0.018 0.001 TYR A 908 ARG 0.007 0.000 ARG A 427 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 6) link_NAG-ASN : angle 2.13190 ( 18) link_BETA1-4 : bond 0.00695 ( 1) link_BETA1-4 : angle 3.68005 ( 3) hydrogen bonds : bond 0.03352 ( 510) hydrogen bonds : angle 4.26859 ( 1443) SS BOND : bond 0.00390 ( 4) SS BOND : angle 1.98649 ( 8) covalent geometry : bond 0.00256 ( 9027) covalent geometry : angle 0.59138 (12368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4527.75 seconds wall clock time: 81 minutes 24.47 seconds (4884.47 seconds total)