Starting phenix.real_space_refine on Fri Sep 11 09:25:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dmb_7963/09_2026/6dmb_7963.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dmb_7963/09_2026/6dmb_7963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dmb_7963/09_2026/6dmb_7963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dmb_7963/09_2026/6dmb_7963.map" model { file = "/net/cci-nas-00/data/ceres_data/6dmb_7963/09_2026/6dmb_7963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dmb_7963/09_2026/6dmb_7963.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6dmb_7963/09_2026/6dmb_7963.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dmb_7963/09_2026/6dmb_7963.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 768 atoms to isotropic. 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 42 5.16 5 C 5189 2.51 5 N 1290 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7945 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7777 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 946} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" 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 chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Unusual residues: {'NAG': 5, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.68, per 1000 atoms: 0.21 Number of scatterers: 7945 At special positions: 0 Unit cell: (94.917, 77.461, 141.83, 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 42 16.00 O 1424 8.00 N 1290 7.00 C 5189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " 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 B 1 " - " NAG B 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG B 1 " - " ASN A1000 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 236.3 milliseconds 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 60.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 74 through 96 removed outlier: 4.175A pdb=" N TRP A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.807A pdb=" N PHE A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.649A pdb=" N TRP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.685A pdb=" N ASP A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 234' Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.534A pdb=" N ASN A 258 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 259 " --> pdb=" O TRP A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 260 through 271 removed outlier: 4.069A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 removed outlier: 3.751A pdb=" N ALA A 285 " --> pdb=" O MET A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.790A pdb=" N ILE A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 411 removed outlier: 3.657A pdb=" N GLU A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 439 through 457 removed outlier: 3.661A pdb=" N LEU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 491 removed outlier: 3.842A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 506 through 526 removed outlier: 3.688A pdb=" N VAL A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 564 removed outlier: 3.890A pdb=" N THR A 544 " --> pdb=" O CYS A 540 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N SER A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 605 removed outlier: 4.022A pdb=" N GLN A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 4.147A pdb=" N SER A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP A 605 " --> pdb=" O TYR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.713A pdb=" N LYS A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 745 removed outlier: 3.619A pdb=" N LEU A 745 " --> pdb=" O PRO A 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 745' Processing helix chain 'A' and resid 746 through 749 Processing helix chain 'A' and resid 750 through 770 removed outlier: 4.205A pdb=" N ILE A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 Processing helix chain 'A' and resid 815 through 828 removed outlier: 3.654A pdb=" N TYR A 820 " --> pdb=" O GLN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 863 removed outlier: 3.688A pdb=" N TYR A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 888 removed outlier: 3.707A pdb=" N VAL A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 882 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 883 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 888 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 903 Processing helix chain 'A' and resid 919 through 930 removed outlier: 3.565A pdb=" N LEU A 923 " --> pdb=" O PHE A 919 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 925 " --> pdb=" O ILE A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 937 removed outlier: 3.861A pdb=" N SER A 937 " --> pdb=" O ALA A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1004 removed outlier: 3.760A pdb=" N ILE A 997 " --> pdb=" O LYS A 993 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A1003 " --> pdb=" O SER A 999 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1018 Processing helix chain 'A' and resid 1019 through 1022 Processing helix chain 'A' and resid 1026 through 1046 removed outlier: 3.510A pdb=" N PHE A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1075 removed outlier: 3.796A pdb=" N GLY A1075 " --> pdb=" O MET A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1106 removed outlier: 3.556A pdb=" N VAL A1084 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1122 removed outlier: 3.525A pdb=" N ALA A1118 " --> pdb=" O ARG A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1138 Processing helix chain 'A' and resid 1146 through 1155 Processing helix chain 'A' and resid 1155 through 1178 Proline residue: A1172 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 363 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 331 removed outlier: 4.751A pdb=" N SER A 331 " --> pdb=" O MET A 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348 removed outlier: 7.242A pdb=" N VAL A 347 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 975 through 978 removed outlier: 3.738A pdb=" N TYR A 804 " --> pdb=" O ASN A1011 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 1.00 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: 2419 1.34 - 1.46: 1964 1.46 - 1.59: 3690 1.59 - 1.71: 0 1.71 - 1.83: 69 Bond restraints: 8142 Sorted by residual: bond pdb=" CAY Y01 A1809 " pdb=" OAW Y01 A1809 " ideal model delta sigma weight residual 1.332 1.462 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" CAY Y01 A1808 " pdb=" OAW Y01 A1808 " ideal model delta sigma weight residual 1.332 1.452 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C ASP A 293 " pdb=" N ARG A 294 " ideal model delta sigma weight residual 1.331 1.252 0.079 1.59e-02 3.96e+03 2.47e+01 bond pdb=" CAX Y01 A1808 " pdb=" OAH Y01 A1808 " ideal model delta sigma weight residual 1.248 1.328 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" CAX Y01 A1809 " pdb=" OAH Y01 A1809 " ideal model delta sigma weight residual 1.248 1.328 -0.080 2.00e-02 2.50e+03 1.60e+01 ... (remaining 8137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 10629 3.01 - 6.01: 359 6.01 - 9.02: 83 9.02 - 12.02: 10 12.02 - 15.03: 4 Bond angle restraints: 11085 Sorted by residual: angle pdb=" C LEU A 458 " pdb=" N ARG A 459 " pdb=" CA ARG A 459 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" N VAL A 908 " pdb=" CA VAL A 908 " pdb=" C VAL A 908 " ideal model delta sigma weight residual 113.53 108.53 5.00 9.80e-01 1.04e+00 2.60e+01 angle pdb=" C GLU A 836 " pdb=" N ASN A 837 " pdb=" CA ASN A 837 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C LEU A1048 " pdb=" N ASN A1049 " pdb=" CA ASN A1049 " ideal model delta sigma weight residual 121.80 133.18 -11.38 2.44e+00 1.68e-01 2.18e+01 angle pdb=" N GLU A 947 " pdb=" CA GLU A 947 " pdb=" C GLU A 947 " ideal model delta sigma weight residual 110.91 116.30 -5.39 1.17e+00 7.31e-01 2.12e+01 ... (remaining 11080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.57: 4507 24.57 - 49.14: 206 49.14 - 73.71: 17 73.71 - 98.28: 3 98.28 - 122.85: 1 Dihedral angle restraints: 4734 sinusoidal: 1848 harmonic: 2886 Sorted by residual: dihedral pdb=" CA ASN A1049 " pdb=" C ASN A1049 " pdb=" N PRO A1050 " pdb=" CA PRO A1050 " ideal model delta harmonic sigma weight residual 180.00 -120.68 -59.32 0 5.00e+00 4.00e-02 1.41e+02 dihedral pdb=" CA LYS A 867 " pdb=" C LYS A 867 " pdb=" N ILE A 868 " pdb=" CA ILE A 868 " ideal model delta harmonic sigma weight residual -180.00 -132.90 -47.10 0 5.00e+00 4.00e-02 8.87e+01 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 166.11 -73.11 1 1.00e+01 1.00e-02 6.81e+01 ... (remaining 4731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1079 0.091 - 0.182: 193 0.182 - 0.273: 14 0.273 - 0.363: 2 0.363 - 0.454: 1 Chirality restraints: 1289 Sorted by residual: chirality pdb=" C1 NAG A1804 " pdb=" ND2 ASN A 875 " pdb=" C2 NAG A1804 " pdb=" O5 NAG A1804 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CB ILE A 531 " pdb=" CA ILE A 531 " pdb=" CG1 ILE A 531 " pdb=" CG2 ILE A 531 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG A1801 " pdb=" ND2 ASN A 312 " pdb=" C2 NAG A1801 " pdb=" O5 NAG A1801 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1286 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 869 " -0.063 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO A 870 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 870 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 870 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 812 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 813 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 813 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 813 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1081 " 0.051 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO A1082 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A1082 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1082 " 0.043 5.00e-02 4.00e+02 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1940 2.79 - 3.32: 7486 3.32 - 3.85: 12883 3.85 - 4.37: 13993 4.37 - 4.90: 23612 Nonbonded interactions: 59914 Sorted by model distance: nonbonded pdb=" O MET A 956 " pdb=" OG1 THR A 959 " model vdw 2.266 3.040 nonbonded pdb=" O GLY A 774 " pdb=" OH TYR A1021 " model vdw 2.275 3.040 nonbonded pdb=" O CYS A 998 " pdb=" OG1 THR A1002 " model vdw 2.295 3.040 nonbonded pdb=" O TYR A 452 " pdb=" OG1 THR A 456 " model vdw 2.317 3.040 nonbonded pdb=" O ASN A 120 " pdb=" OG SER A 494 " model vdw 2.338 3.040 ... (remaining 59909 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.800 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.130 8152 Z= 0.398 Angle : 1.388 15.377 11112 Z= 0.695 Chirality : 0.068 0.454 1289 Planarity : 0.009 0.095 1374 Dihedral : 13.388 122.852 2869 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.18 % Favored : 86.21 % Rotamer: Outliers : 1.94 % Allowed : 8.74 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 4.65 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.21), residues: 986 helix: -2.31 (0.17), residues: 525 sheet: -3.36 (0.56), residues: 52 loop : -3.90 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 255 TYR 0.032 0.003 TYR A 222 PHE 0.045 0.004 PHE A1015 TRP 0.034 0.004 TRP A 337 HIS 0.011 0.002 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00887 / 0.40 ( 8142) covalent geometry : angle 1.36228 / 0.69 (11085) SS BOND : bond 0.00589 / 0.28 ( 3) SS BOND : angle 1.75782 / 1.01 ( 6) hydrogen bonds : bond 0.15256 / 9.84 ( 389) hydrogen bonds : angle 6.79275 / 4.44 ( 1134) link_BETA1-4 : bond 0.00204 / 0.11 ( 1) link_BETA1-4 : angle 1.04453 / 0.60 ( 3) link_NAG-ASN : bond 0.01317 / 0.87 ( 6) link_NAG-ASN : angle 6.67683 / 3.86 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TRP cc_start: 0.7803 (m100) cc_final: 0.7107 (m-10) REVERT: A 183 LEU cc_start: 0.9037 (tp) cc_final: 0.8744 (tt) REVERT: A 374 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 416 THR cc_start: 0.8533 (p) cc_final: 0.8251 (t) REVERT: A 455 LEU cc_start: 0.8678 (mm) cc_final: 0.8428 (tt) REVERT: A 490 LEU cc_start: 0.8894 (mm) cc_final: 0.8400 (tt) REVERT: A 550 LEU cc_start: 0.9214 (tp) cc_final: 0.8872 (tp) REVERT: A 598 MET cc_start: 0.8044 (mmm) cc_final: 0.7783 (tmm) REVERT: A 988 VAL cc_start: 0.9322 (t) cc_final: 0.8273 (m) REVERT: A 1029 LEU cc_start: 0.8798 (tt) cc_final: 0.8477 (mm) REVERT: A 1076 ILE cc_start: 0.9051 (mm) cc_final: 0.8837 (mm) REVERT: A 1128 ASP cc_start: 0.7284 (m-30) cc_final: 0.6992 (m-30) REVERT: A 1146 ASP cc_start: 0.7669 (t0) cc_final: 0.7248 (t0) REVERT: A 1165 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8648 (mt) outliers start: 16 outliers final: 4 residues processed: 226 average time/residue: 0.0778 time to fit residues: 24.4872 Evaluate side-chains 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1165 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 95 GLN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 375 HIS A 409 GLN A 496 ASN A 584 ASN A 802 ASN A 828 ASN A 846 HIS A 856 GLN A 872 ASN A 929 ASN A1099 HIS A1112 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.110315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.093704 restraints weight = 19610.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096191 restraints weight = 11353.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.097868 restraints weight = 7817.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.099042 restraints weight = 6055.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.099822 restraints weight = 5043.678| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8152 Z= 0.152 Angle : 0.870 11.324 11112 Z= 0.418 Chirality : 0.044 0.250 1289 Planarity : 0.006 0.071 1374 Dihedral : 9.404 112.579 1105 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.46 % Favored : 88.24 % Rotamer: Outliers : 5.34 % Allowed : 15.41 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.25), residues: 986 helix: -0.81 (0.20), residues: 569 sheet: -2.72 (0.68), residues: 46 loop : -3.74 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 962 TYR 0.022 0.001 TYR A 740 PHE 0.029 0.002 PHE A 800 TRP 0.016 0.002 TRP A 236 HIS 0.006 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8142) covalent geometry : angle 0.84778 / 0.41 (11085) SS BOND : bond 0.00263 / 0.13 ( 3) SS BOND : angle 0.81756 / 0.48 ( 6) hydrogen bonds : bond 0.05377 / 3.50 ( 389) hydrogen bonds : angle 5.06224 / 3.35 ( 1134) link_BETA1-4 : bond 0.00382 / 0.20 ( 1) link_BETA1-4 : angle 0.75446 / 0.39 ( 3) link_NAG-ASN : bond 0.00933 / 0.59 ( 6) link_NAG-ASN : angle 4.98010 / 2.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TRP cc_start: 0.7605 (m100) cc_final: 0.7047 (m-10) REVERT: A 183 LEU cc_start: 0.8924 (tp) cc_final: 0.8603 (tt) REVERT: A 416 THR cc_start: 0.8322 (p) cc_final: 0.8107 (t) REVERT: A 432 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8563 (tmtt) REVERT: A 455 LEU cc_start: 0.8217 (mm) cc_final: 0.8015 (tt) REVERT: A 456 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.7861 (t) REVERT: A 490 LEU cc_start: 0.8509 (mm) cc_final: 0.8095 (tt) outliers start: 44 outliers final: 17 residues processed: 170 average time/residue: 0.0752 time to fit residues: 18.5932 Evaluate side-chains 118 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 950 HIS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 0.0370 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS A 289 HIS A 576 GLN A 584 ASN A 853 GLN A 856 GLN A 889 GLN ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.110143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093457 restraints weight = 19635.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.095872 restraints weight = 11329.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.097582 restraints weight = 7828.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.098697 restraints weight = 6033.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.099554 restraints weight = 5071.329| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8152 Z= 0.150 Angle : 0.839 11.680 11112 Z= 0.399 Chirality : 0.044 0.293 1289 Planarity : 0.006 0.072 1374 Dihedral : 8.662 112.591 1101 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.66 % Favored : 88.13 % Rotamer: Outliers : 5.46 % Allowed : 17.48 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.26), residues: 986 helix: -0.14 (0.21), residues: 577 sheet: -2.08 (0.75), residues: 51 loop : -3.64 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 255 TYR 0.021 0.001 TYR A 740 PHE 0.025 0.002 PHE A1104 TRP 0.018 0.002 TRP A 78 HIS 0.008 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 8142) covalent geometry : angle 0.82083 / 0.39 (11085) SS BOND : bond 0.00197 / 0.10 ( 3) SS BOND : angle 0.71931 / 0.41 ( 6) hydrogen bonds : bond 0.04736 / 3.09 ( 389) hydrogen bonds : angle 4.69947 / 3.12 ( 1134) link_BETA1-4 : bond 0.00119 / 0.06 ( 1) link_BETA1-4 : angle 0.70236 / 0.37 ( 3) link_NAG-ASN : bond 0.00812 / 0.52 ( 6) link_NAG-ASN : angle 4.37118 / 2.48 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8824 (tp) cc_final: 0.8526 (tt) REVERT: A 192 MET cc_start: 0.4488 (pmm) cc_final: 0.3990 (pmm) REVERT: A 281 MET cc_start: 0.8658 (ttp) cc_final: 0.8364 (ptp) REVERT: A 360 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8719 (pp) REVERT: A 416 THR cc_start: 0.8386 (p) cc_final: 0.8107 (t) REVERT: A 455 LEU cc_start: 0.8342 (mm) cc_final: 0.8121 (tt) REVERT: A 490 LEU cc_start: 0.8574 (mm) cc_final: 0.8152 (tt) outliers start: 45 outliers final: 25 residues processed: 155 average time/residue: 0.0700 time to fit residues: 16.0502 Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 ASN ** 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 = 0.3661 r_free = 0.3661 target = 0.107482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090839 restraints weight = 20075.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093315 restraints weight = 11521.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094984 restraints weight = 7895.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.096145 restraints weight = 6090.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096748 restraints weight = 5056.956| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8152 Z= 0.185 Angle : 0.841 10.652 11112 Z= 0.400 Chirality : 0.045 0.269 1289 Planarity : 0.006 0.074 1374 Dihedral : 8.236 112.689 1101 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % Rotamer: Outliers : 5.34 % Allowed : 20.27 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.27), residues: 986 helix: 0.15 (0.22), residues: 578 sheet: -1.95 (0.76), residues: 51 loop : -3.60 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.021 0.002 TYR A 740 PHE 0.020 0.002 PHE A 592 TRP 0.015 0.002 TRP A 78 HIS 0.007 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 8142) covalent geometry : angle 0.82942 / 0.40 (11085) SS BOND : bond 0.00286 / 0.14 ( 3) SS BOND : angle 0.87189 / 0.49 ( 6) hydrogen bonds : bond 0.04873 / 3.16 ( 389) hydrogen bonds : angle 4.63298 / 3.08 ( 1134) link_BETA1-4 : bond 0.00180 / 0.09 ( 1) link_BETA1-4 : angle 0.54915 / 0.29 ( 3) link_NAG-ASN : bond 0.00488 / 0.25 ( 6) link_NAG-ASN : angle 3.55473 / 1.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.4250 (pmm) cc_final: 0.3660 (pmm) REVERT: A 198 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6963 (mtmp) REVERT: A 254 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7554 (tt) REVERT: A 281 MET cc_start: 0.8738 (ttp) cc_final: 0.8465 (ptp) REVERT: A 360 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8727 (pp) REVERT: A 416 THR cc_start: 0.8450 (p) cc_final: 0.8145 (t) REVERT: A 455 LEU cc_start: 0.8391 (mm) cc_final: 0.8145 (tt) REVERT: A 490 LEU cc_start: 0.8551 (mm) cc_final: 0.8120 (tt) outliers start: 44 outliers final: 30 residues processed: 139 average time/residue: 0.0661 time to fit residues: 14.0784 Evaluate side-chains 131 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1160 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 584 ASN ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.111788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.095036 restraints weight = 19667.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.097661 restraints weight = 11266.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.099422 restraints weight = 7690.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100646 restraints weight = 5892.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.101480 restraints weight = 4877.289| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8152 Z= 0.143 Angle : 0.862 19.248 11112 Z= 0.390 Chirality : 0.044 0.254 1289 Planarity : 0.005 0.076 1374 Dihedral : 7.827 113.137 1099 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 4.85 % Allowed : 21.24 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.28), residues: 986 helix: 0.46 (0.22), residues: 574 sheet: -1.77 (0.77), residues: 51 loop : -3.46 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.023 0.001 TYR A 740 PHE 0.021 0.001 PHE A1153 TRP 0.017 0.001 TRP A 256 HIS 0.005 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8142) covalent geometry : angle 0.81828 / 0.38 (11085) SS BOND : bond 0.00094 / 0.04 ( 3) SS BOND : angle 0.53064 / 0.30 ( 6) hydrogen bonds : bond 0.04167 / 2.73 ( 389) hydrogen bonds : angle 4.44989 / 2.98 ( 1134) link_BETA1-4 : bond 0.00114 / 0.06 ( 1) link_BETA1-4 : angle 0.54877 / 0.28 ( 3) link_NAG-ASN : bond 0.02215 / 1.12 ( 6) link_NAG-ASN : angle 6.76964 / 3.25 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8273 (m-40) cc_final: 0.7518 (p0) REVERT: A 183 LEU cc_start: 0.8817 (tp) cc_final: 0.8531 (tt) REVERT: A 192 MET cc_start: 0.4003 (pmm) cc_final: 0.3294 (pmm) REVERT: A 198 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7023 (mtmp) REVERT: A 281 MET cc_start: 0.8721 (ttp) cc_final: 0.8468 (ptp) REVERT: A 360 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8673 (pp) REVERT: A 416 THR cc_start: 0.8417 (p) cc_final: 0.8091 (t) REVERT: A 454 CYS cc_start: 0.7758 (t) cc_final: 0.6913 (p) REVERT: A 455 LEU cc_start: 0.8022 (mm) cc_final: 0.7785 (tt) REVERT: A 490 LEU cc_start: 0.8509 (mm) cc_final: 0.8032 (tt) REVERT: A 493 ILE cc_start: 0.6398 (OUTLIER) cc_final: 0.6124 (mm) REVERT: A 914 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8677 (pt) REVERT: A 986 ASP cc_start: 0.8200 (m-30) cc_final: 0.7959 (t0) REVERT: A 1022 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8912 (mt) REVERT: A 1048 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7327 (tt) REVERT: A 1076 ILE cc_start: 0.9111 (mm) cc_final: 0.8850 (mm) outliers start: 40 outliers final: 23 residues processed: 150 average time/residue: 0.0669 time to fit residues: 15.1542 Evaluate side-chains 143 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 80 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.112056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.095547 restraints weight = 19607.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.098148 restraints weight = 11315.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099958 restraints weight = 7708.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101142 restraints weight = 5883.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.102055 restraints weight = 4879.634| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8152 Z= 0.133 Angle : 0.813 11.865 11112 Z= 0.374 Chirality : 0.044 0.345 1289 Planarity : 0.005 0.078 1374 Dihedral : 7.683 113.502 1099 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 4.85 % Allowed : 22.21 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.28), residues: 986 helix: 0.66 (0.22), residues: 573 sheet: -1.65 (0.78), residues: 51 loop : -3.43 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.023 0.001 TYR A 740 PHE 0.017 0.001 PHE A1153 TRP 0.012 0.001 TRP A 78 HIS 0.005 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8142) covalent geometry : angle 0.79300 / 0.37 (11085) SS BOND : bond 0.00079 / 0.04 ( 3) SS BOND : angle 0.53265 / 0.30 ( 6) hydrogen bonds : bond 0.04011 / 2.63 ( 389) hydrogen bonds : angle 4.34615 / 2.90 ( 1134) link_BETA1-4 : bond 0.00346 / 0.18 ( 1) link_BETA1-4 : angle 0.69376 / 0.34 ( 3) link_NAG-ASN : bond 0.00592 / 0.32 ( 6) link_NAG-ASN : angle 4.48877 / 2.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8327 (m-40) cc_final: 0.7644 (p0) REVERT: A 192 MET cc_start: 0.3902 (pmm) cc_final: 0.3252 (pmm) REVERT: A 198 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6916 (mtmp) REVERT: A 281 MET cc_start: 0.8711 (ttp) cc_final: 0.8480 (ptp) REVERT: A 346 THR cc_start: 0.8077 (m) cc_final: 0.7819 (p) REVERT: A 360 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8728 (pp) REVERT: A 490 LEU cc_start: 0.8416 (mm) cc_final: 0.7942 (tt) REVERT: A 986 ASP cc_start: 0.8055 (m-30) cc_final: 0.7771 (t0) REVERT: A 1022 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8883 (mt) REVERT: A 1076 ILE cc_start: 0.9112 (mm) cc_final: 0.8813 (mm) outliers start: 40 outliers final: 29 residues processed: 145 average time/residue: 0.0644 time to fit residues: 14.0613 Evaluate side-chains 133 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.0070 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 496 ASN A 584 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.111981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095912 restraints weight = 19553.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.098415 restraints weight = 11442.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.100125 restraints weight = 7884.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.101299 restraints weight = 6067.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.101967 restraints weight = 5012.265| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8152 Z= 0.135 Angle : 0.813 13.318 11112 Z= 0.373 Chirality : 0.042 0.214 1289 Planarity : 0.006 0.110 1374 Dihedral : 7.513 113.738 1099 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 4.85 % Allowed : 22.57 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.28), residues: 986 helix: 0.83 (0.22), residues: 574 sheet: -1.69 (0.76), residues: 51 loop : -3.39 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.024 0.001 TYR A 740 PHE 0.022 0.001 PHE A1153 TRP 0.012 0.001 TRP A 78 HIS 0.004 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 8142) covalent geometry : angle 0.80205 / 0.37 (11085) SS BOND : bond 0.00122 / 0.06 ( 3) SS BOND : angle 0.57404 / 0.32 ( 6) hydrogen bonds : bond 0.03974 / 2.60 ( 389) hydrogen bonds : angle 4.28001 / 2.85 ( 1134) link_BETA1-4 : bond 0.00224 / 0.12 ( 1) link_BETA1-4 : angle 0.63890 / 0.31 ( 3) link_NAG-ASN : bond 0.00422 / 0.24 ( 6) link_NAG-ASN : angle 3.41517 / 1.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8294 (m110) cc_final: 0.7625 (p0) REVERT: A 183 LEU cc_start: 0.8282 (tt) cc_final: 0.7988 (mt) REVERT: A 192 MET cc_start: 0.3742 (pmm) cc_final: 0.3132 (pmm) REVERT: A 198 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6990 (mtmp) REVERT: A 360 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8771 (pp) REVERT: A 490 LEU cc_start: 0.8364 (mm) cc_final: 0.7898 (tt) REVERT: A 493 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.6153 (mm) REVERT: A 587 MET cc_start: 0.8702 (tmm) cc_final: 0.8460 (ppp) REVERT: A 1076 ILE cc_start: 0.9118 (mm) cc_final: 0.8869 (mm) outliers start: 40 outliers final: 28 residues processed: 138 average time/residue: 0.0627 time to fit residues: 13.0936 Evaluate side-chains 126 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.111054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094347 restraints weight = 19990.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096757 restraints weight = 11890.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098435 restraints weight = 8368.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099577 restraints weight = 6525.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100389 restraints weight = 5478.948| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8152 Z= 0.151 Angle : 0.810 13.834 11112 Z= 0.376 Chirality : 0.043 0.206 1289 Planarity : 0.006 0.099 1374 Dihedral : 7.510 113.669 1099 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 4.98 % Allowed : 22.82 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.28), residues: 986 helix: 0.96 (0.23), residues: 569 sheet: -1.71 (0.74), residues: 51 loop : -3.30 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.024 0.001 TYR A 740 PHE 0.023 0.002 PHE A1153 TRP 0.012 0.001 TRP A 78 HIS 0.004 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 8142) covalent geometry : angle 0.80247 / 0.37 (11085) SS BOND : bond 0.00198 / 0.09 ( 3) SS BOND : angle 0.69090 / 0.39 ( 6) hydrogen bonds : bond 0.04204 / 2.73 ( 389) hydrogen bonds : angle 4.28299 / 2.84 ( 1134) link_BETA1-4 : bond 0.00102 / 0.05 ( 1) link_BETA1-4 : angle 0.52462 / 0.26 ( 3) link_NAG-ASN : bond 0.00406 / 0.23 ( 6) link_NAG-ASN : angle 2.92599 / 1.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8281 (m110) cc_final: 0.7298 (p0) REVERT: A 156 GLN cc_start: 0.8490 (mp-120) cc_final: 0.7923 (mp-120) REVERT: A 183 LEU cc_start: 0.8286 (tt) cc_final: 0.7981 (mt) REVERT: A 192 MET cc_start: 0.4052 (pmm) cc_final: 0.3369 (pmm) REVERT: A 198 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7037 (mtmp) REVERT: A 360 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8801 (pp) REVERT: A 490 LEU cc_start: 0.8359 (mm) cc_final: 0.7907 (tt) REVERT: A 493 ILE cc_start: 0.6753 (OUTLIER) cc_final: 0.6397 (mm) REVERT: A 963 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8055 (mm) REVERT: A 1022 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8867 (mt) REVERT: A 1076 ILE cc_start: 0.9157 (mm) cc_final: 0.8900 (mm) outliers start: 41 outliers final: 29 residues processed: 132 average time/residue: 0.0635 time to fit residues: 12.8418 Evaluate side-chains 129 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 0.0020 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 0.0050 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 ASN A 872 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.113683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.097348 restraints weight = 19413.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099964 restraints weight = 11042.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.101769 restraints weight = 7482.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.102987 restraints weight = 5682.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.103484 restraints weight = 4679.452| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8152 Z= 0.128 Angle : 0.802 13.772 11112 Z= 0.367 Chirality : 0.042 0.203 1289 Planarity : 0.006 0.091 1374 Dihedral : 7.274 113.671 1099 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 3.76 % Allowed : 24.51 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.28), residues: 986 helix: 1.05 (0.23), residues: 562 sheet: -1.67 (0.75), residues: 51 loop : -3.17 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.025 0.001 TYR A 740 PHE 0.024 0.001 PHE A 800 TRP 0.013 0.001 TRP A 78 HIS 0.004 0.001 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 8142) covalent geometry : angle 0.79617 / 0.37 (11085) SS BOND : bond 0.00059 / 0.03 ( 3) SS BOND : angle 0.50776 / 0.28 ( 6) hydrogen bonds : bond 0.03684 / 2.41 ( 389) hydrogen bonds : angle 4.19998 / 2.79 ( 1134) link_BETA1-4 : bond 0.00258 / 0.14 ( 1) link_BETA1-4 : angle 0.67436 / 0.34 ( 3) link_NAG-ASN : bond 0.00424 / 0.24 ( 6) link_NAG-ASN : angle 2.61549 / 1.27 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8321 (m110) cc_final: 0.7628 (p0) REVERT: A 183 LEU cc_start: 0.8323 (tt) cc_final: 0.7973 (mt) REVERT: A 192 MET cc_start: 0.4086 (pmm) cc_final: 0.3482 (pmm) REVERT: A 198 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7052 (mtmp) REVERT: A 360 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8630 (pp) REVERT: A 432 LYS cc_start: 0.8948 (tmtt) cc_final: 0.8596 (tmtt) REVERT: A 490 LEU cc_start: 0.8277 (mm) cc_final: 0.7837 (tt) REVERT: A 561 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7774 (mmp) REVERT: A 919 PHE cc_start: 0.8058 (t80) cc_final: 0.7841 (t80) REVERT: A 1066 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6920 (mm-30) REVERT: A 1076 ILE cc_start: 0.9259 (mm) cc_final: 0.8990 (mm) outliers start: 31 outliers final: 25 residues processed: 142 average time/residue: 0.0684 time to fit residues: 14.6129 Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 18 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 ASN A 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.115098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098719 restraints weight = 19718.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101210 restraints weight = 11718.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102929 restraints weight = 8175.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.104116 restraints weight = 6356.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104790 restraints weight = 5303.467| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8152 Z= 0.132 Angle : 0.807 14.290 11112 Z= 0.371 Chirality : 0.042 0.203 1289 Planarity : 0.006 0.086 1374 Dihedral : 7.206 113.715 1099 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 3.64 % Allowed : 25.00 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.28), residues: 986 helix: 1.07 (0.23), residues: 564 sheet: -1.71 (0.73), residues: 51 loop : -3.12 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.024 0.001 TYR A 740 PHE 0.027 0.001 PHE A1153 TRP 0.012 0.001 TRP A 78 HIS 0.020 0.001 HIS A 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8142) covalent geometry : angle 0.80134 / 0.37 (11085) SS BOND : bond 0.00102 / 0.05 ( 3) SS BOND : angle 0.57568 / 0.33 ( 6) hydrogen bonds : bond 0.03735 / 2.44 ( 389) hydrogen bonds : angle 4.19873 / 2.79 ( 1134) link_BETA1-4 : bond 0.00135 / 0.07 ( 1) link_BETA1-4 : angle 0.69666 / 0.35 ( 3) link_NAG-ASN : bond 0.00413 / 0.24 ( 6) link_NAG-ASN : angle 2.56946 / 1.25 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8313 (m110) cc_final: 0.7720 (p0) REVERT: A 183 LEU cc_start: 0.8232 (tt) cc_final: 0.7904 (mt) REVERT: A 192 MET cc_start: 0.3769 (pmm) cc_final: 0.3238 (pmm) REVERT: A 198 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6984 (mtmp) REVERT: A 360 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8716 (pp) REVERT: A 367 MET cc_start: 0.6938 (pmm) cc_final: 0.6338 (ptp) REVERT: A 432 LYS cc_start: 0.8935 (tmtt) cc_final: 0.8509 (tmtt) REVERT: A 490 LEU cc_start: 0.8261 (mm) cc_final: 0.7899 (tt) REVERT: A 919 PHE cc_start: 0.7814 (t80) cc_final: 0.7577 (t80) REVERT: A 1076 ILE cc_start: 0.9218 (mm) cc_final: 0.8987 (mm) outliers start: 30 outliers final: 26 residues processed: 135 average time/residue: 0.0662 time to fit residues: 13.6222 Evaluate side-chains 131 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1073 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.0050 chunk 51 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 39 optimal weight: 0.0470 chunk 76 optimal weight: 6.9990 overall best weight: 0.7896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 ASN A 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.114993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098674 restraints weight = 19738.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.101090 restraints weight = 11762.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.102740 restraints weight = 8286.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.103897 restraints weight = 6501.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.104694 restraints weight = 5462.332| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8152 Z= 0.135 Angle : 0.802 14.192 11112 Z= 0.370 Chirality : 0.042 0.203 1289 Planarity : 0.006 0.128 1374 Dihedral : 7.192 113.930 1099 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 3.52 % Allowed : 24.76 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.28), residues: 986 helix: 1.12 (0.23), residues: 562 sheet: -1.71 (0.74), residues: 51 loop : -3.06 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.022 0.001 TYR A 740 PHE 0.026 0.001 PHE A1153 TRP 0.029 0.001 TRP A 278 HIS 0.013 0.001 HIS A 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8142) covalent geometry : angle 0.79658 / 0.37 (11085) SS BOND : bond 0.00112 / 0.05 ( 3) SS BOND : angle 0.58531 / 0.33 ( 6) hydrogen bonds : bond 0.03692 / 2.41 ( 389) hydrogen bonds : angle 4.17243 / 2.78 ( 1134) link_BETA1-4 : bond 0.00158 / 0.08 ( 1) link_BETA1-4 : angle 0.65610 / 0.33 ( 3) link_NAG-ASN : bond 0.00413 / 0.24 ( 6) link_NAG-ASN : angle 2.52774 / 1.23 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1315.46 seconds wall clock time: 23 minutes 28.98 seconds (1408.98 seconds total)