Starting phenix.real_space_refine on Tue Apr 29 18:02:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dmb_7963/04_2025/6dmb_7963.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dmb_7963/04_2025/6dmb_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_7963/04_2025/6dmb_7963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dmb_7963/04_2025/6dmb_7963.map" model { file = "/net/cci-nas-00/data/ceres_data/6dmb_7963/04_2025/6dmb_7963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dmb_7963/04_2025/6dmb_7963.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG: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 dihedrals: 6 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.36, per 1000 atoms: 0.67 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: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.76 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: 2.49 Time building geometry restraints manager: 2.59 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: 4738 24.57 - 49.14: 227 49.14 - 73.71: 23 73.71 - 98.28: 6 98.28 - 122.85: 3 Dihedral angle restraints: 4997 sinusoidal: 2111 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 4994 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.760 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 : 13.898 122.852 3132 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.034 0.004 TRP A 337 HIS 0.011 0.002 HIS A 520 PHE 0.045 0.004 PHE A1015 TYR 0.032 0.003 TYR A 222 ARG 0.008 0.001 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.01317 ( 6) link_NAG-ASN : angle 6.67683 ( 18) link_BETA1-4 : bond 0.00204 ( 1) link_BETA1-4 : angle 1.04453 ( 3) hydrogen bonds : bond 0.15256 ( 389) hydrogen bonds : angle 6.79275 ( 1134) SS BOND : bond 0.00589 ( 3) SS BOND : angle 1.75782 ( 6) covalent geometry : bond 0.00887 ( 8142) covalent geometry : angle 1.36228 (11085) *********************** 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 : 0.847 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: 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: 0.7873 (mm-30) REVERT: A 416 THR cc_start: 0.8533 (p) cc_final: 0.8249 (t) REVERT: A 455 LEU cc_start: 0.8678 (mm) cc_final: 0.8429 (tt) REVERT: A 490 LEU cc_start: 0.8894 (mm) cc_final: 0.8401 (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: 0.8278 (m) REVERT: A 1029 LEU cc_start: 0.8798 (tt) cc_final: 0.8478 (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: 0.6996 (m-30) REVERT: A 1146 ASP cc_start: 0.7669 (t0) cc_final: 0.7237 (t0) REVERT: A 1165 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8641 (mt) outliers start: 16 outliers final: 4 residues processed: 226 average time/residue: 0.1895 time to fit residues: 58.5221 Evaluate side-chains 117 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 83 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 95 GLN A 178 HIS ** 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 853 GLN A 856 GLN A 929 ASN A1099 HIS A1112 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.109388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092675 restraints weight = 19562.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095095 restraints weight = 11349.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.096796 restraints weight = 7884.860| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8152 Z= 0.176 Angle : 0.881 11.366 11112 Z= 0.427 Chirality : 0.045 0.251 1289 Planarity : 0.006 0.071 1374 Dihedral : 9.173 59.089 1368 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.07 % Favored : 87.63 % Rotamer: Outliers : 6.07 % Allowed : 14.81 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.25), residues: 986 helix: -0.71 (0.21), residues: 567 sheet: -2.70 (0.70), residues: 46 loop : -3.75 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 236 HIS 0.005 0.001 HIS A 817 PHE 0.029 0.002 PHE A 800 TYR 0.021 0.002 TYR A 740 ARG 0.005 0.000 ARG A 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00864 ( 6) link_NAG-ASN : angle 4.92585 ( 18) link_BETA1-4 : bond 0.00123 ( 1) link_BETA1-4 : angle 0.64615 ( 3) hydrogen bonds : bond 0.05434 ( 389) hydrogen bonds : angle 5.02700 ( 1134) SS BOND : bond 0.00298 ( 3) SS BOND : angle 0.91960 ( 6) covalent geometry : bond 0.00389 ( 8142) covalent geometry : angle 0.85951 (11085) *********************** 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 183 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 432 LYS cc_start: 0.9031 (tmtt) cc_final: 0.8579 (tmtt) REVERT: A 455 LEU cc_start: 0.8311 (mm) cc_final: 0.8091 (tt) REVERT: A 456 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.7886 (t) REVERT: A 490 LEU cc_start: 0.8578 (mm) cc_final: 0.8143 (tt) REVERT: A 988 VAL cc_start: 0.9337 (t) cc_final: 0.8760 (m) outliers start: 50 outliers final: 22 residues processed: 169 average time/residue: 0.1641 time to fit residues: 40.4592 Evaluate side-chains 125 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 297 LEU Chi-restraints excluded: chain A residue 402 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 561 MET 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 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 1137 VAL 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 95 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 0.0670 chunk 78 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 289 HIS ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 GLN A 872 ASN A 889 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.107766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091366 restraints weight = 19913.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093733 restraints weight = 11581.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095454 restraints weight = 8004.853| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8152 Z= 0.185 Angle : 0.861 10.591 11112 Z= 0.414 Chirality : 0.045 0.295 1289 Planarity : 0.006 0.077 1374 Dihedral : 8.487 71.591 1364 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.27 % Favored : 87.42 % Rotamer: Outliers : 6.31 % Allowed : 17.23 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.27), residues: 986 helix: -0.04 (0.22), residues: 569 sheet: -2.09 (0.75), residues: 51 loop : -3.68 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 78 HIS 0.004 0.001 HIS A 520 PHE 0.023 0.002 PHE A1104 TYR 0.023 0.002 TYR A 740 ARG 0.005 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00790 ( 6) link_NAG-ASN : angle 4.55855 ( 18) link_BETA1-4 : bond 0.00069 ( 1) link_BETA1-4 : angle 0.65323 ( 3) hydrogen bonds : bond 0.05159 ( 389) hydrogen bonds : angle 4.77818 ( 1134) SS BOND : bond 0.00323 ( 3) SS BOND : angle 0.84860 ( 6) covalent geometry : bond 0.00408 ( 8142) covalent geometry : angle 0.84190 (11085) *********************** 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 161 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 109 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7025 (mtmp) REVERT: A 360 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8733 (pp) REVERT: A 374 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7755 (mm-30) REVERT: A 455 LEU cc_start: 0.8440 (mm) cc_final: 0.8195 (tt) REVERT: A 490 LEU cc_start: 0.8620 (mm) cc_final: 0.8170 (tt) REVERT: A 856 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7739 (tm-30) outliers start: 52 outliers final: 33 residues processed: 148 average time/residue: 0.1550 time to fit residues: 33.8163 Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 158 MET Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 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 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 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 815 ILE 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 950 HIS 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 1105 LEU Chi-restraints excluded: chain A residue 1134 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 66 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 41 optimal weight: 0.0970 chunk 72 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 856 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.109373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092927 restraints weight = 19593.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.095430 restraints weight = 11207.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.097186 restraints weight = 7669.484| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3777 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= 0.150 Angle : 0.829 10.769 11112 Z= 0.391 Chirality : 0.044 0.298 1289 Planarity : 0.006 0.076 1374 Dihedral : 7.998 59.008 1364 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 4.73 % Allowed : 20.75 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.27), residues: 986 helix: 0.23 (0.22), residues: 576 sheet: -1.96 (0.75), residues: 51 loop : -3.65 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 78 HIS 0.003 0.001 HIS A 520 PHE 0.020 0.002 PHE A 800 TYR 0.022 0.001 TYR A 740 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 6) link_NAG-ASN : angle 3.85614 ( 18) link_BETA1-4 : bond 0.00184 ( 1) link_BETA1-4 : angle 0.73310 ( 3) hydrogen bonds : bond 0.04663 ( 389) hydrogen bonds : angle 4.57205 ( 1134) SS BOND : bond 0.00175 ( 3) SS BOND : angle 0.66494 ( 6) covalent geometry : bond 0.00327 ( 8142) covalent geometry : angle 0.81522 (11085) *********************** 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 157 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8759 (pp) REVERT: A 455 LEU cc_start: 0.8385 (mm) cc_final: 0.8152 (tt) REVERT: A 490 LEU cc_start: 0.8568 (mm) cc_final: 0.8154 (tt) REVERT: A 493 ILE cc_start: 0.6441 (OUTLIER) cc_final: 0.6129 (mm) outliers start: 39 outliers final: 25 residues processed: 143 average time/residue: 0.1601 time to fit residues: 33.6547 Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 230 THR Chi-restraints excluded: chain A residue 254 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 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 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 950 HIS Chi-restraints excluded: chain A residue 992 GLU 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 1149 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.108716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.091955 restraints weight = 19680.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094441 restraints weight = 11487.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.096132 restraints weight = 7928.177| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8152 Z= 0.174 Angle : 0.885 20.323 11112 Z= 0.409 Chirality : 0.045 0.352 1289 Planarity : 0.006 0.075 1374 Dihedral : 8.186 59.304 1362 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 6.19 % Allowed : 20.02 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.28), residues: 986 helix: 0.46 (0.23), residues: 573 sheet: -1.95 (0.75), residues: 51 loop : -3.66 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 256 HIS 0.004 0.001 HIS A 520 PHE 0.021 0.002 PHE A 592 TYR 0.020 0.001 TYR A 740 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.01209 ( 6) link_NAG-ASN : angle 7.23499 ( 18) link_BETA1-4 : bond 0.00045 ( 1) link_BETA1-4 : angle 0.64028 ( 3) hydrogen bonds : bond 0.04788 ( 389) hydrogen bonds : angle 4.54785 ( 1134) SS BOND : bond 0.00265 ( 3) SS BOND : angle 0.77214 ( 6) covalent geometry : bond 0.00392 ( 8142) covalent geometry : angle 0.83694 (11085) *********************** 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 169 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 118 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8398 (m-40) cc_final: 0.6852 (p0) REVERT: A 156 GLN cc_start: 0.8583 (mp-120) cc_final: 0.8030 (mp-120) REVERT: A 198 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7016 (mtmp) REVERT: A 360 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8818 (pp) REVERT: A 374 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 455 LEU cc_start: 0.8292 (mm) cc_final: 0.8079 (tt) REVERT: A 490 LEU cc_start: 0.8553 (mm) cc_final: 0.8114 (tt) REVERT: A 493 ILE cc_start: 0.6559 (OUTLIER) cc_final: 0.6261 (mm) REVERT: A 905 GLN cc_start: 0.6847 (tp-100) cc_final: 0.6574 (tp40) REVERT: A 1048 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7401 (tt) REVERT: A 1076 ILE cc_start: 0.9118 (mm) cc_final: 0.8877 (mm) outliers start: 51 outliers final: 33 residues processed: 155 average time/residue: 0.1622 time to fit residues: 37.2836 Evaluate side-chains 136 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 158 MET 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 254 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 503 LEU Chi-restraints excluded: chain A residue 517 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 815 ILE Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1008 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 61 optimal weight: 0.1980 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 91 optimal weight: 0.0170 chunk 19 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN ** A 872 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 = 0.3732 r_free = 0.3732 target = 0.111812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095179 restraints weight = 19352.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097737 restraints weight = 11130.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.099506 restraints weight = 7631.568| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8152 Z= 0.134 Angle : 0.824 14.968 11112 Z= 0.383 Chirality : 0.045 0.496 1289 Planarity : 0.005 0.076 1374 Dihedral : 7.572 59.244 1362 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 4.61 % Allowed : 22.33 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.28), residues: 986 helix: 0.65 (0.23), residues: 571 sheet: -1.87 (0.76), residues: 51 loop : -3.52 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 256 HIS 0.002 0.000 HIS A 201 PHE 0.018 0.001 PHE A 800 TYR 0.024 0.001 TYR A 740 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 6) link_NAG-ASN : angle 5.09546 ( 18) link_BETA1-4 : bond 0.00131 ( 1) link_BETA1-4 : angle 0.69487 ( 3) hydrogen bonds : bond 0.04119 ( 389) hydrogen bonds : angle 4.33106 ( 1134) SS BOND : bond 0.00074 ( 3) SS BOND : angle 0.50517 ( 6) covalent geometry : bond 0.00294 ( 8142) covalent geometry : angle 0.79882 (11085) *********************** 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 164 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8367 (m110) cc_final: 0.7159 (p0) REVERT: A 198 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6916 (mtmp) REVERT: A 346 THR cc_start: 0.8043 (m) cc_final: 0.7803 (p) REVERT: A 360 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8694 (pp) REVERT: A 374 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 490 LEU cc_start: 0.8407 (mm) cc_final: 0.7890 (tt) REVERT: A 493 ILE cc_start: 0.6436 (OUTLIER) cc_final: 0.6020 (mm) REVERT: A 1076 ILE cc_start: 0.9140 (mm) cc_final: 0.8838 (mm) REVERT: A 1077 LYS cc_start: 0.7980 (mppt) cc_final: 0.7677 (mtmt) outliers start: 38 outliers final: 26 residues processed: 156 average time/residue: 0.1504 time to fit residues: 34.6247 Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 171 THR 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 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 803 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1024 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 9.9990 chunk 77 optimal weight: 0.0000 chunk 4 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 496 ASN ** A 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.111001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094202 restraints weight = 19666.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096782 restraints weight = 11374.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098530 restraints weight = 7798.818| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8152 Z= 0.141 Angle : 0.835 13.883 11112 Z= 0.383 Chirality : 0.043 0.232 1289 Planarity : 0.006 0.110 1374 Dihedral : 7.367 58.474 1362 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 4.49 % Allowed : 24.03 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.28), residues: 986 helix: 0.76 (0.23), residues: 573 sheet: -1.80 (0.76), residues: 51 loop : -3.45 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 256 HIS 0.002 0.001 HIS A 520 PHE 0.017 0.001 PHE A 592 TYR 0.024 0.001 TYR A 740 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 6) link_NAG-ASN : angle 3.82286 ( 18) link_BETA1-4 : bond 0.00129 ( 1) link_BETA1-4 : angle 0.76335 ( 3) hydrogen bonds : bond 0.04188 ( 389) hydrogen bonds : angle 4.29087 ( 1134) SS BOND : bond 0.00125 ( 3) SS BOND : angle 0.60742 ( 6) covalent geometry : bond 0.00311 ( 8142) covalent geometry : angle 0.82129 (11085) *********************** 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 141 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8220 (m110) cc_final: 0.7483 (p0) REVERT: A 198 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.7015 (mtmp) REVERT: A 360 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8757 (pp) REVERT: A 374 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7596 (mm-30) REVERT: A 490 LEU cc_start: 0.8305 (mm) cc_final: 0.7848 (tt) REVERT: A 493 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.6209 (mm) REVERT: A 1076 ILE cc_start: 0.9155 (mm) cc_final: 0.8831 (mm) REVERT: A 1077 LYS cc_start: 0.8006 (mppt) cc_final: 0.7683 (mtmm) outliers start: 37 outliers final: 28 residues processed: 133 average time/residue: 0.1662 time to fit residues: 32.1809 Evaluate side-chains 131 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 493 ILE 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 761 LEU Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1008 SER Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1057 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 61 optimal weight: 0.2980 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 0.0870 overall best weight: 2.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 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 = 0.3647 r_free = 0.3647 target = 0.106127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.089526 restraints weight = 19929.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.091897 restraints weight = 11745.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093564 restraints weight = 8190.973| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8152 Z= 0.206 Angle : 0.868 14.035 11112 Z= 0.413 Chirality : 0.045 0.221 1289 Planarity : 0.006 0.100 1374 Dihedral : 7.646 58.454 1362 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.18 % Favored : 86.82 % Rotamer: Outliers : 4.73 % Allowed : 23.91 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.28), residues: 986 helix: 0.74 (0.23), residues: 576 sheet: -1.88 (0.74), residues: 51 loop : -3.50 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 129 HIS 0.006 0.001 HIS A 520 PHE 0.023 0.002 PHE A 592 TYR 0.025 0.002 TYR A 740 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 6) link_NAG-ASN : angle 3.47231 ( 18) link_BETA1-4 : bond 0.00064 ( 1) link_BETA1-4 : angle 0.61039 ( 3) hydrogen bonds : bond 0.04980 ( 389) hydrogen bonds : angle 4.41710 ( 1134) SS BOND : bond 0.00361 ( 3) SS BOND : angle 0.86639 ( 6) covalent geometry : bond 0.00472 ( 8142) covalent geometry : angle 0.85754 (11085) *********************** 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 132 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.835 Fit side-chains REVERT: A 154 ASN cc_start: 0.8378 (m110) cc_final: 0.7639 (p0) REVERT: A 198 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7207 (mtmp) REVERT: A 360 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8792 (pp) REVERT: A 490 LEU cc_start: 0.8482 (mm) cc_final: 0.8000 (tt) REVERT: A 493 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6397 (mm) REVERT: A 845 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9005 (tm) outliers start: 39 outliers final: 30 residues processed: 125 average time/residue: 0.1564 time to fit residues: 29.6914 Evaluate side-chains 119 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 430 ILE 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 503 LEU Chi-restraints excluded: chain A residue 517 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 761 LEU Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1008 SER 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 1149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 21 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 70 optimal weight: 0.0670 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 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 = 0.3707 r_free = 0.3707 target = 0.110351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093678 restraints weight = 19933.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096249 restraints weight = 11407.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097896 restraints weight = 7794.003| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8152 Z= 0.141 Angle : 0.824 14.128 11112 Z= 0.386 Chirality : 0.043 0.225 1289 Planarity : 0.006 0.092 1374 Dihedral : 7.293 58.656 1362 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 3.64 % Allowed : 25.49 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.28), residues: 986 helix: 0.96 (0.23), residues: 565 sheet: -1.77 (0.75), residues: 51 loop : -3.39 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 78 HIS 0.005 0.001 HIS A 817 PHE 0.033 0.002 PHE A1104 TYR 0.023 0.001 TYR A 740 ARG 0.002 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 6) link_NAG-ASN : angle 3.15608 ( 18) link_BETA1-4 : bond 0.00155 ( 1) link_BETA1-4 : angle 0.65388 ( 3) hydrogen bonds : bond 0.04229 ( 389) hydrogen bonds : angle 4.28004 ( 1134) SS BOND : bond 0.00141 ( 3) SS BOND : angle 0.62577 ( 6) covalent geometry : bond 0.00310 ( 8142) covalent geometry : angle 0.81509 (11085) *********************** 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 123 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.821 Fit side-chains REVERT: A 154 ASN cc_start: 0.8392 (m110) cc_final: 0.7676 (p0) REVERT: A 198 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7211 (mtmp) REVERT: A 360 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8694 (pp) REVERT: A 490 LEU cc_start: 0.8392 (mm) cc_final: 0.7926 (tt) REVERT: A 493 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6209 (mm) REVERT: A 845 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8882 (tm) outliers start: 30 outliers final: 23 residues processed: 116 average time/residue: 0.1557 time to fit residues: 26.9914 Evaluate side-chains 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 140 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 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 761 LEU Chi-restraints excluded: chain A residue 843 MET 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 72 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 77 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 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 = 0.3760 r_free = 0.3760 target = 0.113942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.097459 restraints weight = 19399.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.100034 restraints weight = 11156.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.101839 restraints weight = 7660.011| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5138 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= 0.129 Angle : 0.821 13.689 11112 Z= 0.381 Chirality : 0.042 0.216 1289 Planarity : 0.006 0.088 1374 Dihedral : 6.982 59.949 1362 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 3.40 % Allowed : 25.36 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.28), residues: 986 helix: 1.02 (0.23), residues: 568 sheet: -1.73 (0.74), residues: 51 loop : -3.25 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 387 HIS 0.004 0.000 HIS A 817 PHE 0.031 0.002 PHE A1104 TYR 0.024 0.001 TYR A 740 ARG 0.002 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 6) link_NAG-ASN : angle 2.94532 ( 18) link_BETA1-4 : bond 0.00300 ( 1) link_BETA1-4 : angle 0.80458 ( 3) hydrogen bonds : bond 0.03715 ( 389) hydrogen bonds : angle 4.19529 ( 1134) SS BOND : bond 0.00066 ( 3) SS BOND : angle 0.53239 ( 6) covalent geometry : bond 0.00273 ( 8142) covalent geometry : angle 0.81332 (11085) ********************** 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 141 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8285 (m110) cc_final: 0.7542 (p0) REVERT: A 183 LEU cc_start: 0.8097 (tt) cc_final: 0.7803 (mt) REVERT: A 198 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7096 (mtmp) REVERT: A 360 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8631 (pp) REVERT: A 490 LEU cc_start: 0.8307 (mm) cc_final: 0.7845 (tt) REVERT: A 561 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7845 (mmp) REVERT: A 1076 ILE cc_start: 0.9213 (mm) cc_final: 0.8857 (mm) REVERT: A 1077 LYS cc_start: 0.8015 (mppt) cc_final: 0.7602 (mtmt) outliers start: 28 outliers final: 20 residues processed: 134 average time/residue: 0.1552 time to fit residues: 30.6085 Evaluate side-chains 120 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 126 GLU 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 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 843 MET Chi-restraints excluded: chain A residue 845 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 31 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 98 optimal weight: 0.0570 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 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 = 0.3749 r_free = 0.3749 target = 0.113236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.097005 restraints weight = 19669.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.099556 restraints weight = 11311.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101335 restraints weight = 7735.456| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8152 Z= 0.135 Angle : 0.831 13.796 11112 Z= 0.389 Chirality : 0.042 0.210 1289 Planarity : 0.006 0.129 1374 Dihedral : 6.780 59.747 1360 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 3.40 % Allowed : 25.24 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.28), residues: 986 helix: 1.09 (0.23), residues: 570 sheet: -1.78 (0.74), residues: 51 loop : -3.19 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 387 HIS 0.004 0.001 HIS A 817 PHE 0.032 0.002 PHE A1104 TYR 0.025 0.001 TYR A 740 ARG 0.003 0.000 ARG A 536 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 6) link_NAG-ASN : angle 2.90871 ( 18) link_BETA1-4 : bond 0.00187 ( 1) link_BETA1-4 : angle 0.79295 ( 3) hydrogen bonds : bond 0.03784 ( 389) hydrogen bonds : angle 4.16363 ( 1134) SS BOND : bond 0.00113 ( 3) SS BOND : angle 0.57971 ( 6) covalent geometry : bond 0.00297 ( 8142) covalent geometry : angle 0.82374 (11085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.85 seconds wall clock time: 45 minutes 25.93 seconds (2725.93 seconds total)