Starting phenix.real_space_refine on Sat Sep 12 12:00:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w5s_21546/09_2026/6w5s_21546.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5s_21546/09_2026/6w5s_21546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w5s_21546/09_2026/6w5s_21546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5s_21546/09_2026/6w5s_21546.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5s_21546/09_2026/6w5s_21546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5s_21546/09_2026/6w5s_21546.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6w5s_21546/09_2026/6w5s_21546.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w5s_21546/09_2026/6w5s_21546.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 6691 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 75 5.16 5 C 6276 2.51 5 N 1534 2.21 5 O 1814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9700 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9360 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1194, 9338 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 1194, 9338 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 9558 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 206 Unusual residues: {'CLR': 1, 'NAG': 9, 'POV': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 579 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 579 " occ=0.50 residue: pdb=" N AARG A1032 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1032 " occ=0.50 Time building chain proxies: 3.54, per 1000 atoms: 0.36 Number of scatterers: 9700 At special positions: 0 Unit cell: (101.374, 88.006, 157.074, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 1 15.00 O 1814 8.00 N 1534 7.00 C 6276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.02 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.02 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " 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 ALPHA1-3 " NAG C 2 " - " MAN C 3 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1401 " - " ASN A 452 " " NAG A1402 " - " ASN A 459 " " NAG A1405 " - " ASN A 524 " " NAG A1409 " - " ASN A 598 " " NAG A1410 " - " ASN A 916 " " NAG A1414 " - " ASN A 961 " " NAG A1415 " - " ASN A 968 " " NAG A1416 " - " ASN A1064 " " NAG A1419 " - " ASN A 158 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " " NAG D 1 " - " ASN A 931 " " NAG E 1 " - " ASN A 222 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 818.5 milliseconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 7 sheets defined 58.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.693A pdb=" N CYS A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.900A pdb=" N THR A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.897A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 149 through 161 removed outlier: 3.675A pdb=" N ALA A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 185 through 195 removed outlier: 3.735A pdb=" N TRP A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 268 through 291 removed outlier: 3.539A pdb=" N TRP A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 349 removed outlier: 3.785A pdb=" N CYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 436 through 453 removed outlier: 3.711A pdb=" N ILE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.574A pdb=" N TYR A 487 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.661A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.615A pdb=" N VAL A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 542 through 546' Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 574 through 593 removed outlier: 3.671A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.694A pdb=" N ASP A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 639 removed outlier: 3.642A pdb=" N ILE A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 679 Processing helix chain 'A' and resid 685 through 711 Proline residue: A 691 - end of helix Processing helix chain 'A' and resid 719 through 750 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 754 through 792 removed outlier: 3.636A pdb=" N THR A 759 " --> pdb=" O PRO A 755 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 780 " --> pdb=" O ILE A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 removed outlier: 3.525A pdb=" N ASN A 823 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 830 removed outlier: 3.895A pdb=" N LEU A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 852 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 870 through 883 removed outlier: 4.213A pdb=" N ASP A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 918 through 930 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 983 through 988 removed outlier: 4.302A pdb=" N GLN A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 removed outlier: 4.318A pdb=" N MET A 996 " --> pdb=" O GLY A 992 " (cutoff:3.500A) Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1028 through 1031 Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.698A pdb=" N GLY A1070 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1093 through 1117 Processing helix chain 'A' and resid 1120 through 1146 Processing helix chain 'A' and resid 1152 through 1177 removed outlier: 4.147A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A1163 " --> pdb=" O MET A1159 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1202 removed outlier: 4.018A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1214 Processing helix chain 'A' and resid 1218 through 1225 Processing helix chain 'A' and resid 1225 through 1252 Proline residue: A1245 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.524A pdb=" N CYS A 42 " --> pdb=" O TYR A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 125 removed outlier: 6.247A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 144 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR A 146 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA6, first strand: chain 'A' and resid 1023 through 1025 removed outlier: 5.889A pdb=" N ASN A1024 " --> pdb=" O GLY A1034 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 959 483 hydrogen bonds defined for protein. 1387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3004 1.34 - 1.46: 2507 1.46 - 1.59: 4330 1.59 - 1.71: 2 1.71 - 1.84: 105 Bond restraints: 9948 Sorted by residual: bond pdb=" C31 POV A1421 " pdb=" O31 POV A1421 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C21 POV A1421 " pdb=" O21 POV A1421 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C1 NAG A1410 " pdb=" O5 NAG A1410 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.70e+00 bond pdb=" O12 POV A1421 " pdb=" P POV A1421 " ideal model delta sigma weight residual 1.657 1.608 0.049 2.00e-02 2.50e+03 6.03e+00 ... (remaining 9943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 13508 4.95 - 9.90: 34 9.90 - 14.84: 0 14.84 - 19.79: 0 19.79 - 24.74: 1 Bond angle restraints: 13543 Sorted by residual: angle pdb=" N ASN A 70 " pdb=" CA ASN A 70 " pdb=" C ASN A 70 " ideal model delta sigma weight residual 110.80 86.06 24.74 2.13e+00 2.20e-01 1.35e+02 angle pdb=" N LYS A 142 " pdb=" CA LYS A 142 " pdb=" C LYS A 142 " ideal model delta sigma weight residual 111.14 118.85 -7.71 1.08e+00 8.57e-01 5.10e+01 angle pdb=" N LYS A 822 " pdb=" CA LYS A 822 " pdb=" C LYS A 822 " ideal model delta sigma weight residual 111.36 118.57 -7.21 1.09e+00 8.42e-01 4.38e+01 angle pdb=" C ASN A 70 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta sigma weight residual 120.56 113.02 7.54 1.26e+00 6.30e-01 3.58e+01 angle pdb=" N SER A 863 " pdb=" CA SER A 863 " pdb=" C SER A 863 " ideal model delta sigma weight residual 113.97 107.18 6.79 1.28e+00 6.10e-01 2.81e+01 ... (remaining 13538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 5598 35.93 - 71.86: 129 71.86 - 107.80: 6 107.80 - 143.73: 2 143.73 - 179.66: 2 Dihedral angle restraints: 5737 sinusoidal: 2249 harmonic: 3488 Sorted by residual: dihedral pdb=" CD BARG A 579 " pdb=" NE BARG A 579 " pdb=" CZ BARG A 579 " pdb=" NH1BARG A 579 " ideal model delta sinusoidal sigma weight residual 0.00 -179.66 179.66 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CB CYS A 240 " pdb=" SG CYS A 240 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual -86.00 1.75 -87.75 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 914 " pdb=" CB CYS A 914 " ideal model delta sinusoidal sigma weight residual -86.00 -14.78 -71.22 1 1.00e+01 1.00e-02 6.51e+01 ... (remaining 5734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.939: 1575 0.939 - 1.877: 0 1.877 - 2.816: 0 2.816 - 3.755: 0 3.755 - 4.694: 1 Chirality restraints: 1576 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 2.29 -4.69 2.00e-02 2.50e+03 5.51e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.10e+02 chirality pdb=" C1 MAN C 3 " pdb=" O3 NAG C 2 " pdb=" C2 MAN C 3 " pdb=" O5 MAN C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-02 2.50e+03 1.22e+02 ... (remaining 1573 not shown) Planarity restraints: 1711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG E 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.084 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.339 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG D 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.044 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.511 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.264 2.00e-02 2.50e+03 2.19e-01 6.01e+02 pdb=" C7 NAG B 2 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.365 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.008 2.00e-02 2.50e+03 ... (remaining 1708 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 74 2.54 - 3.13: 8226 3.13 - 3.72: 14433 3.72 - 4.31: 21333 4.31 - 4.90: 35516 Nonbonded interactions: 79582 Sorted by model distance: nonbonded pdb=" OE2 GLU A 164 " pdb=" NE2 GLN A 241 " model vdw 1.946 3.120 nonbonded pdb=" O PHE A 821 " pdb=" OG SER A 826 " model vdw 2.026 3.040 nonbonded pdb=" O GLN A 119 " pdb=" SD MET A 217 " model vdw 2.032 3.400 nonbonded pdb=" NH2 ARG A 78 " pdb=" OE1 GLN A 81 " model vdw 2.055 3.120 nonbonded pdb=" O CYS A 909 " pdb=" OG SER A 918 " model vdw 2.066 3.040 ... (remaining 79577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.850 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 : 0.005 0.223 9982 Z= 0.280 Angle : 0.918 31.637 13630 Z= 0.488 Chirality : 0.129 4.694 1576 Planarity : 0.013 0.303 1698 Dihedral : 14.820 179.661 3450 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 31.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.58 % Favored : 92.00 % Rotamer: Outliers : 2.70 % Allowed : 3.67 % Favored : 93.63 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.22), residues: 1194 helix: -1.31 (0.19), residues: 626 sheet: -1.98 (0.56), residues: 88 loop : -3.30 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 372 TYR 0.013 0.001 TYR A 570 PHE 0.012 0.001 PHE A1079 TRP 0.018 0.002 TRP A 949 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.26 ( 9948) covalent geometry : angle 0.82899 / 0.47 (13543) SS BOND : bond 0.00364 / 0.22 ( 15) SS BOND : angle 2.88284 / 2.11 ( 30) hydrogen bonds : bond 0.16287 / 10.19 ( 483) hydrogen bonds : angle 6.75309 / 4.64 ( 1387) link_ALPHA1-3 : bond 0.00402 / 0.21 ( 1) link_ALPHA1-3 : angle 2.48497 / 1.30 ( 3) link_ALPHA1-4 : bond 0.00030 / 0.02 ( 1) link_ALPHA1-4 : angle 1.35425 / 0.71 ( 3) link_BETA1-4 : bond 0.00662 / 0.35 ( 4) link_BETA1-4 : angle 4.05345 / 2.44 ( 12) link_NAG-ASN : bond 0.06199 / 2.95 ( 13) link_NAG-ASN : angle 6.59698 / 5.81 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.272 Fit side-chains REVERT: A 156 MET cc_start: 0.8738 (ttt) cc_final: 0.8538 (ttm) REVERT: A 233 GLU cc_start: 0.7428 (mp0) cc_final: 0.6874 (pm20) REVERT: A 260 TRP cc_start: 0.6129 (m-10) cc_final: 0.5482 (m-90) REVERT: A 586 GLU cc_start: 0.6921 (tp30) cc_final: 0.6641 (tp30) REVERT: A 822 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8388 (tttp) REVERT: A 1158 VAL cc_start: 0.9175 (t) cc_final: 0.8971 (t) outliers start: 27 outliers final: 10 residues processed: 173 average time/residue: 0.5251 time to fit residues: 97.7080 Evaluate side-chains 118 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 822 LYS Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1161 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.0970 chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN A 92 GLN A 103 ASN A 122 ASN A 136 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN A 553 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN A 884 HIS A 906 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 HIS A1046 GLN A1137 ASN A1193 HIS A1239 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123724 restraints weight = 27019.916| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 5.78 r_work: 0.2878 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9982 Z= 0.151 Angle : 0.820 12.406 13630 Z= 0.383 Chirality : 0.048 0.311 1576 Planarity : 0.005 0.042 1698 Dihedral : 11.719 177.892 1364 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 2.51 % Allowed : 11.39 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.23), residues: 1194 helix: -0.07 (0.20), residues: 638 sheet: -1.61 (0.54), residues: 88 loop : -2.50 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 989 TYR 0.023 0.002 TYR A 570 PHE 0.012 0.001 PHE A1038 TRP 0.022 0.002 TRP A 273 HIS 0.009 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 9948) covalent geometry : angle 0.79764 / 0.38 (13543) SS BOND : bond 0.00330 / 0.20 ( 15) SS BOND : angle 2.05795 / 1.33 ( 30) hydrogen bonds : bond 0.05112 / 3.28 ( 483) hydrogen bonds : angle 5.16112 / 3.59 ( 1387) link_ALPHA1-3 : bond 0.01476 / 0.78 ( 1) link_ALPHA1-3 : angle 1.44774 / 0.80 ( 3) link_ALPHA1-4 : bond 0.01643 / 0.86 ( 1) link_ALPHA1-4 : angle 4.66369 / 2.53 ( 3) link_BETA1-4 : bond 0.00940 / 0.48 ( 4) link_BETA1-4 : angle 3.13696 / 1.80 ( 12) link_NAG-ASN : bond 0.00637 / 0.34 ( 13) link_NAG-ASN : angle 2.45319 / 2.13 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8374 (ttt) cc_final: 0.8137 (ttm) REVERT: A 192 TYR cc_start: 0.7367 (t80) cc_final: 0.6919 (t80) REVERT: A 260 TRP cc_start: 0.6143 (m-10) cc_final: 0.5196 (m-90) REVERT: A 265 LEU cc_start: 0.7415 (mp) cc_final: 0.7189 (mm) REVERT: A 288 PHE cc_start: 0.7154 (m-10) cc_final: 0.5732 (OUTLIER) REVERT: A 466 ASP cc_start: 0.8446 (t0) cc_final: 0.7872 (m-30) REVERT: A 498 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8427 (ptmt) REVERT: A 586 GLU cc_start: 0.7993 (tp30) cc_final: 0.7318 (tp30) REVERT: A 862 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7791 (pt0) outliers start: 25 outliers final: 11 residues processed: 127 average time/residue: 0.4355 time to fit residues: 59.9567 Evaluate side-chains 105 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1114 MET Chi-restraints excluded: chain A residue 1161 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.0020 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 117 GLN A 145 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.160939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120618 restraints weight = 25956.257| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 5.87 r_work: 0.2834 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9982 Z= 0.155 Angle : 0.774 14.186 13630 Z= 0.362 Chirality : 0.048 0.314 1576 Planarity : 0.005 0.046 1698 Dihedral : 10.590 176.649 1346 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer: Outliers : 2.80 % Allowed : 13.22 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.24), residues: 1194 helix: 0.49 (0.20), residues: 638 sheet: -1.24 (0.56), residues: 88 loop : -2.10 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.017 0.002 TYR A 570 PHE 0.016 0.001 PHE A 345 TRP 0.017 0.002 TRP A 273 HIS 0.007 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9948) covalent geometry : angle 0.75171 / 0.36 (13543) SS BOND : bond 0.00290 / 0.18 ( 15) SS BOND : angle 1.88681 / 1.09 ( 30) hydrogen bonds : bond 0.05103 / 3.23 ( 483) hydrogen bonds : angle 4.98505 / 3.46 ( 1387) link_ALPHA1-3 : bond 0.01496 / 0.79 ( 1) link_ALPHA1-3 : angle 1.83880 / 1.00 ( 3) link_ALPHA1-4 : bond 0.00884 / 0.47 ( 1) link_ALPHA1-4 : angle 5.18389 / 2.82 ( 3) link_BETA1-4 : bond 0.01041 / 0.52 ( 4) link_BETA1-4 : angle 3.16315 / 1.81 ( 12) link_NAG-ASN : bond 0.00457 / 0.21 ( 13) link_NAG-ASN : angle 2.23115 / 1.90 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 92 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: A 192 TYR cc_start: 0.7369 (t80) cc_final: 0.6967 (t80) REVERT: A 241 GLN cc_start: 0.7494 (tm-30) cc_final: 0.6980 (tm-30) REVERT: A 260 TRP cc_start: 0.6168 (m-10) cc_final: 0.5209 (m-90) REVERT: A 466 ASP cc_start: 0.8349 (t0) cc_final: 0.7743 (m-30) REVERT: A 586 GLU cc_start: 0.8055 (tp30) cc_final: 0.7363 (tp30) REVERT: A 666 SER cc_start: 0.8986 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 1111 LEU cc_start: 0.8603 (tm) cc_final: 0.7933 (mt) REVERT: A 1158 VAL cc_start: 0.9020 (t) cc_final: 0.8754 (m) REVERT: A 1166 GLU cc_start: 0.7921 (tp30) cc_final: 0.7455 (tm-30) REVERT: A 1179 MET cc_start: 0.7983 (mmm) cc_final: 0.7595 (mpp) outliers start: 28 outliers final: 10 residues processed: 124 average time/residue: 0.4716 time to fit residues: 63.2693 Evaluate side-chains 105 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1043 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.160629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118600 restraints weight = 22762.267| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 5.37 r_work: 0.2847 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9982 Z= 0.194 Angle : 0.793 13.539 13630 Z= 0.373 Chirality : 0.049 0.328 1576 Planarity : 0.005 0.048 1698 Dihedral : 10.199 175.534 1342 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.23 % Favored : 93.52 % Rotamer: Outliers : 2.80 % Allowed : 14.96 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.24), residues: 1194 helix: 0.64 (0.20), residues: 638 sheet: -0.58 (0.61), residues: 78 loop : -1.94 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.019 0.002 TYR A1037 PHE 0.015 0.002 PHE A1224 TRP 0.017 0.002 TRP A 949 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 ( 9948) covalent geometry : angle 0.76567 / 0.37 (13543) SS BOND : bond 0.00292 / 0.18 ( 15) SS BOND : angle 2.10003 / 1.40 ( 30) hydrogen bonds : bond 0.05468 / 3.43 ( 483) hydrogen bonds : angle 5.01298 / 3.47 ( 1387) link_ALPHA1-3 : bond 0.01112 / 0.59 ( 1) link_ALPHA1-3 : angle 1.79599 / 0.98 ( 3) link_ALPHA1-4 : bond 0.00786 / 0.41 ( 1) link_ALPHA1-4 : angle 5.09108 / 2.77 ( 3) link_BETA1-4 : bond 0.01051 / 0.53 ( 4) link_BETA1-4 : angle 3.06429 / 1.71 ( 12) link_NAG-ASN : bond 0.00532 / 0.24 ( 13) link_NAG-ASN : angle 2.74784 / 2.12 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7413 (t80) cc_final: 0.7013 (t80) REVERT: A 241 GLN cc_start: 0.6877 (tm-30) cc_final: 0.6349 (tm-30) REVERT: A 260 TRP cc_start: 0.6078 (m-10) cc_final: 0.5163 (m-90) REVERT: A 466 ASP cc_start: 0.8315 (t0) cc_final: 0.7717 (m-30) REVERT: A 586 GLU cc_start: 0.7963 (tp30) cc_final: 0.7280 (tp30) REVERT: A 666 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8753 (p) REVERT: A 1179 MET cc_start: 0.7875 (mmm) cc_final: 0.7526 (mpp) outliers start: 28 outliers final: 13 residues processed: 110 average time/residue: 0.4912 time to fit residues: 58.2651 Evaluate side-chains 105 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1043 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 0.0870 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN A 92 GLN A 145 GLN A 200 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122607 restraints weight = 30856.951| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 6.35 r_work: 0.2850 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9982 Z= 0.135 Angle : 0.737 11.673 13630 Z= 0.344 Chirality : 0.047 0.312 1576 Planarity : 0.004 0.048 1698 Dihedral : 9.931 177.169 1342 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 2.51 % Allowed : 15.54 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1194 helix: 0.91 (0.21), residues: 639 sheet: -0.34 (0.61), residues: 78 loop : -1.69 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.017 0.001 TYR A 571 PHE 0.011 0.001 PHE A1167 TRP 0.014 0.001 TRP A 949 HIS 0.007 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9948) covalent geometry : angle 0.71286 / 0.34 (13543) SS BOND : bond 0.00285 / 0.16 ( 15) SS BOND : angle 1.76171 / 1.05 ( 30) hydrogen bonds : bond 0.04797 / 3.03 ( 483) hydrogen bonds : angle 4.87879 / 3.37 ( 1387) link_ALPHA1-3 : bond 0.01114 / 0.59 ( 1) link_ALPHA1-3 : angle 1.65628 / 0.90 ( 3) link_ALPHA1-4 : bond 0.00754 / 0.40 ( 1) link_ALPHA1-4 : angle 4.99179 / 2.72 ( 3) link_BETA1-4 : bond 0.01121 / 0.57 ( 4) link_BETA1-4 : angle 2.94107 / 1.62 ( 12) link_NAG-ASN : bond 0.00522 / 0.25 ( 13) link_NAG-ASN : angle 2.46804 / 1.88 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7435 (t80) cc_final: 0.6987 (t80) REVERT: A 241 GLN cc_start: 0.6860 (tm-30) cc_final: 0.6302 (tm-30) REVERT: A 260 TRP cc_start: 0.6001 (m-10) cc_final: 0.5096 (m-90) REVERT: A 466 ASP cc_start: 0.8308 (t0) cc_final: 0.7634 (m-30) REVERT: A 506 TYR cc_start: 0.7999 (m-80) cc_final: 0.7721 (m-80) REVERT: A 578 GLN cc_start: 0.8435 (mm110) cc_final: 0.8077 (mt0) REVERT: A 586 GLU cc_start: 0.8080 (tp30) cc_final: 0.7396 (tp30) REVERT: A 666 SER cc_start: 0.9133 (OUTLIER) cc_final: 0.8784 (p) REVERT: A 869 ASP cc_start: 0.6460 (p0) cc_final: 0.6197 (t0) REVERT: A 1158 VAL cc_start: 0.9033 (t) cc_final: 0.8796 (m) REVERT: A 1179 MET cc_start: 0.7876 (mmm) cc_final: 0.7473 (mpp) outliers start: 25 outliers final: 14 residues processed: 113 average time/residue: 0.4760 time to fit residues: 58.1891 Evaluate side-chains 110 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122183 restraints weight = 28275.931| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 6.03 r_work: 0.2813 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9982 Z= 0.146 Angle : 0.733 10.611 13630 Z= 0.344 Chirality : 0.047 0.321 1576 Planarity : 0.004 0.048 1698 Dihedral : 9.678 176.425 1339 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.48 % Favored : 93.27 % Rotamer: Outliers : 2.41 % Allowed : 16.22 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1194 helix: 1.04 (0.21), residues: 637 sheet: -0.27 (0.62), residues: 78 loop : -1.54 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.017 0.001 TYR A 571 PHE 0.024 0.001 PHE A 345 TRP 0.015 0.001 TRP A 949 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9948) covalent geometry : angle 0.70948 / 0.34 (13543) SS BOND : bond 0.00478 / 0.25 ( 15) SS BOND : angle 1.79582 / 1.10 ( 30) hydrogen bonds : bond 0.04876 / 3.07 ( 483) hydrogen bonds : angle 4.86732 / 3.36 ( 1387) link_ALPHA1-3 : bond 0.01055 / 0.56 ( 1) link_ALPHA1-3 : angle 1.61353 / 0.88 ( 3) link_ALPHA1-4 : bond 0.00788 / 0.41 ( 1) link_ALPHA1-4 : angle 4.88176 / 2.66 ( 3) link_BETA1-4 : bond 0.00996 / 0.50 ( 4) link_BETA1-4 : angle 2.96060 / 1.61 ( 12) link_NAG-ASN : bond 0.00485 / 0.22 ( 13) link_NAG-ASN : angle 2.38489 / 1.84 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7388 (t80) cc_final: 0.6902 (t80) REVERT: A 241 GLN cc_start: 0.6850 (tm-30) cc_final: 0.6366 (tm-30) REVERT: A 260 TRP cc_start: 0.5981 (m-10) cc_final: 0.5088 (m-90) REVERT: A 466 ASP cc_start: 0.8314 (t0) cc_final: 0.7616 (m-30) REVERT: A 506 TYR cc_start: 0.8055 (m-80) cc_final: 0.7724 (m-80) REVERT: A 578 GLN cc_start: 0.8436 (mm110) cc_final: 0.8077 (mt0) REVERT: A 586 GLU cc_start: 0.8070 (tp30) cc_final: 0.7379 (tp30) REVERT: A 666 SER cc_start: 0.9142 (OUTLIER) cc_final: 0.8785 (p) REVERT: A 748 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8057 (mt) REVERT: A 869 ASP cc_start: 0.6484 (p0) cc_final: 0.6219 (t0) REVERT: A 987 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8327 (mptt) REVERT: A 1179 MET cc_start: 0.7873 (mmm) cc_final: 0.7474 (mpp) REVERT: A 1234 LEU cc_start: 0.8219 (tt) cc_final: 0.7945 (tp) outliers start: 24 outliers final: 16 residues processed: 112 average time/residue: 0.4716 time to fit residues: 57.1152 Evaluate side-chains 112 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 6 optimal weight: 0.0770 chunk 80 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN A 530 HIS ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.166316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125770 restraints weight = 27255.310| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 5.77 r_work: 0.2920 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9982 Z= 0.121 Angle : 0.690 9.596 13630 Z= 0.324 Chirality : 0.045 0.306 1576 Planarity : 0.004 0.048 1698 Dihedral : 9.377 177.530 1339 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.02 % Rotamer: Outliers : 2.03 % Allowed : 16.60 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.25), residues: 1194 helix: 1.32 (0.21), residues: 633 sheet: -0.09 (0.62), residues: 78 loop : -1.47 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 161 TYR 0.016 0.001 TYR A 571 PHE 0.025 0.001 PHE A 345 TRP 0.013 0.001 TRP A 949 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9948) covalent geometry : angle 0.67089 / 0.32 (13543) SS BOND : bond 0.00205 / 0.11 ( 15) SS BOND : angle 1.50909 / 0.90 ( 30) hydrogen bonds : bond 0.04280 / 2.72 ( 483) hydrogen bonds : angle 4.73670 / 3.28 ( 1387) link_ALPHA1-3 : bond 0.00668 / 0.35 ( 1) link_ALPHA1-3 : angle 1.43071 / 0.78 ( 3) link_ALPHA1-4 : bond 0.00951 / 0.50 ( 1) link_ALPHA1-4 : angle 4.54580 / 2.48 ( 3) link_BETA1-4 : bond 0.00908 / 0.46 ( 4) link_BETA1-4 : angle 2.85185 / 1.53 ( 12) link_NAG-ASN : bond 0.00459 / 0.23 ( 13) link_NAG-ASN : angle 2.02853 / 1.56 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7427 (t80) cc_final: 0.6982 (t80) REVERT: A 241 GLN cc_start: 0.6943 (tm-30) cc_final: 0.6370 (tm-30) REVERT: A 466 ASP cc_start: 0.8205 (t0) cc_final: 0.7589 (m-30) REVERT: A 506 TYR cc_start: 0.8069 (m-80) cc_final: 0.7708 (m-80) REVERT: A 578 GLN cc_start: 0.8381 (mm110) cc_final: 0.8079 (mt0) REVERT: A 586 GLU cc_start: 0.8053 (tp30) cc_final: 0.7408 (tp30) REVERT: A 666 SER cc_start: 0.9107 (OUTLIER) cc_final: 0.8791 (p) REVERT: A 748 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8072 (mt) REVERT: A 869 ASP cc_start: 0.6449 (p0) cc_final: 0.6183 (t0) REVERT: A 1158 VAL cc_start: 0.8962 (t) cc_final: 0.8696 (m) REVERT: A 1179 MET cc_start: 0.7898 (mmm) cc_final: 0.7494 (mpp) REVERT: A 1234 LEU cc_start: 0.8181 (tt) cc_final: 0.7966 (tp) outliers start: 20 outliers final: 11 residues processed: 121 average time/residue: 0.4640 time to fit residues: 60.9124 Evaluate side-chains 111 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120922 restraints weight = 26013.973| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 5.86 r_work: 0.2832 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9982 Z= 0.172 Angle : 0.738 9.605 13630 Z= 0.350 Chirality : 0.048 0.320 1576 Planarity : 0.005 0.049 1698 Dihedral : 9.383 175.701 1339 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.48 % Favored : 93.27 % Rotamer: Outliers : 2.12 % Allowed : 17.18 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1194 helix: 1.25 (0.21), residues: 638 sheet: -0.02 (0.63), residues: 78 loop : -1.43 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.019 0.001 TYR A1037 PHE 0.015 0.001 PHE A1167 TRP 0.015 0.001 TRP A 949 HIS 0.005 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 9948) covalent geometry : angle 0.71403 / 0.34 (13543) SS BOND : bond 0.00515 / 0.37 ( 15) SS BOND : angle 2.26555 / 1.33 ( 30) hydrogen bonds : bond 0.04997 / 3.14 ( 483) hydrogen bonds : angle 4.84172 / 3.35 ( 1387) link_ALPHA1-3 : bond 0.00695 / 0.37 ( 1) link_ALPHA1-3 : angle 1.61701 / 0.89 ( 3) link_ALPHA1-4 : bond 0.00950 / 0.50 ( 1) link_ALPHA1-4 : angle 4.26175 / 2.33 ( 3) link_BETA1-4 : bond 0.00853 / 0.42 ( 4) link_BETA1-4 : angle 2.66183 / 1.44 ( 12) link_NAG-ASN : bond 0.00432 / 0.19 ( 13) link_NAG-ASN : angle 2.35885 / 1.99 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 92 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6854 (tp40) REVERT: A 192 TYR cc_start: 0.7444 (t80) cc_final: 0.7010 (t80) REVERT: A 241 GLN cc_start: 0.7013 (tm-30) cc_final: 0.6536 (tm-30) REVERT: A 260 TRP cc_start: 0.5722 (m-10) cc_final: 0.4847 (m-90) REVERT: A 466 ASP cc_start: 0.8402 (t0) cc_final: 0.7798 (m-30) REVERT: A 506 TYR cc_start: 0.8034 (m-80) cc_final: 0.7730 (m-80) REVERT: A 586 GLU cc_start: 0.8087 (tp30) cc_final: 0.7403 (tp30) REVERT: A 666 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8815 (p) REVERT: A 748 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8141 (mt) REVERT: A 857 ASP cc_start: 0.8290 (m-30) cc_final: 0.7957 (t70) REVERT: A 869 ASP cc_start: 0.6529 (p0) cc_final: 0.6248 (t0) REVERT: A 987 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8379 (mptt) REVERT: A 1179 MET cc_start: 0.7933 (mmm) cc_final: 0.7526 (mpp) REVERT: A 1234 LEU cc_start: 0.8252 (tt) cc_final: 0.8014 (tp) outliers start: 21 outliers final: 13 residues processed: 115 average time/residue: 0.4617 time to fit residues: 57.5757 Evaluate side-chains 110 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 106 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN A 823 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119228 restraints weight = 25379.602| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 5.68 r_work: 0.2860 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9982 Z= 0.131 Angle : 0.701 9.576 13630 Z= 0.332 Chirality : 0.046 0.324 1576 Planarity : 0.004 0.052 1698 Dihedral : 9.323 177.059 1339 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.02 % Rotamer: Outliers : 1.83 % Allowed : 17.66 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1194 helix: 1.41 (0.21), residues: 637 sheet: -0.08 (0.57), residues: 90 loop : -1.46 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.017 0.001 TYR A 571 PHE 0.021 0.001 PHE A 93 TRP 0.014 0.001 TRP A 949 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9948) covalent geometry : angle 0.68047 / 0.33 (13543) SS BOND : bond 0.00256 / 0.17 ( 15) SS BOND : angle 1.94040 / 1.13 ( 30) hydrogen bonds : bond 0.04608 / 2.91 ( 483) hydrogen bonds : angle 4.79161 / 3.32 ( 1387) link_ALPHA1-3 : bond 0.00678 / 0.36 ( 1) link_ALPHA1-3 : angle 1.53694 / 0.85 ( 3) link_ALPHA1-4 : bond 0.00997 / 0.52 ( 1) link_ALPHA1-4 : angle 3.97171 / 2.17 ( 3) link_BETA1-4 : bond 0.00853 / 0.43 ( 4) link_BETA1-4 : angle 2.54109 / 1.36 ( 12) link_NAG-ASN : bond 0.00455 / 0.21 ( 13) link_NAG-ASN : angle 2.17321 / 1.82 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 92 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6914 (tp40) REVERT: A 192 TYR cc_start: 0.7432 (t80) cc_final: 0.7011 (t80) REVERT: A 241 GLN cc_start: 0.6962 (tm-30) cc_final: 0.6351 (tm-30) REVERT: A 466 ASP cc_start: 0.8377 (t0) cc_final: 0.7749 (m-30) REVERT: A 506 TYR cc_start: 0.7954 (m-80) cc_final: 0.7704 (m-80) REVERT: A 586 GLU cc_start: 0.8073 (tp30) cc_final: 0.7413 (tp30) REVERT: A 666 SER cc_start: 0.9142 (OUTLIER) cc_final: 0.8801 (p) REVERT: A 748 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8140 (mt) REVERT: A 869 ASP cc_start: 0.6422 (p0) cc_final: 0.6161 (t0) REVERT: A 987 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8343 (mptt) REVERT: A 1158 VAL cc_start: 0.8968 (t) cc_final: 0.8700 (m) REVERT: A 1179 MET cc_start: 0.7901 (mmm) cc_final: 0.7475 (mpp) REVERT: A 1234 LEU cc_start: 0.8168 (tt) cc_final: 0.7952 (tp) outliers start: 18 outliers final: 13 residues processed: 106 average time/residue: 0.4870 time to fit residues: 55.8382 Evaluate side-chains 111 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 13 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.160433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119227 restraints weight = 27094.951| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 5.84 r_work: 0.2830 rms_B_bonded: 5.26 restraints_weight: 2.0000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9982 Z= 0.136 Angle : 0.702 9.574 13630 Z= 0.332 Chirality : 0.046 0.324 1576 Planarity : 0.004 0.052 1698 Dihedral : 9.265 176.670 1339 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer: Outliers : 1.83 % Allowed : 17.66 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.25), residues: 1194 helix: 1.46 (0.21), residues: 637 sheet: -0.14 (0.57), residues: 92 loop : -1.45 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.016 0.001 TYR A 571 PHE 0.015 0.001 PHE A 93 TRP 0.014 0.001 TRP A 949 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9948) covalent geometry : angle 0.68231 / 0.33 (13543) SS BOND : bond 0.00240 / 0.16 ( 15) SS BOND : angle 1.93803 / 1.13 ( 30) hydrogen bonds : bond 0.04638 / 2.92 ( 483) hydrogen bonds : angle 4.78715 / 3.32 ( 1387) link_ALPHA1-3 : bond 0.00645 / 0.34 ( 1) link_ALPHA1-3 : angle 1.54155 / 0.85 ( 3) link_ALPHA1-4 : bond 0.01002 / 0.53 ( 1) link_ALPHA1-4 : angle 3.69235 / 2.03 ( 3) link_BETA1-4 : bond 0.00851 / 0.42 ( 4) link_BETA1-4 : angle 2.44822 / 1.31 ( 12) link_NAG-ASN : bond 0.00452 / 0.20 ( 13) link_NAG-ASN : angle 2.14288 / 1.80 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 92 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7060 (tp40) REVERT: A 192 TYR cc_start: 0.7436 (t80) cc_final: 0.7014 (t80) REVERT: A 241 GLN cc_start: 0.6989 (tm-30) cc_final: 0.6473 (tm-30) REVERT: A 466 ASP cc_start: 0.8417 (t0) cc_final: 0.7771 (m-30) REVERT: A 506 TYR cc_start: 0.7975 (m-80) cc_final: 0.7718 (m-80) REVERT: A 586 GLU cc_start: 0.8134 (tp30) cc_final: 0.7458 (tp30) REVERT: A 666 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8808 (p) REVERT: A 748 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8142 (mt) REVERT: A 857 ASP cc_start: 0.8290 (m-30) cc_final: 0.7961 (t70) REVERT: A 869 ASP cc_start: 0.6519 (p0) cc_final: 0.6220 (t0) REVERT: A 987 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8351 (mptt) REVERT: A 1179 MET cc_start: 0.7935 (mmm) cc_final: 0.7495 (mpp) REVERT: A 1234 LEU cc_start: 0.8190 (tt) cc_final: 0.7983 (tp) outliers start: 18 outliers final: 14 residues processed: 106 average time/residue: 0.4536 time to fit residues: 52.2926 Evaluate side-chains 111 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1069 MET Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1142 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 0.0000 chunk 23 optimal weight: 0.0370 chunk 15 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.161516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120769 restraints weight = 26325.949| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 5.67 r_work: 0.2850 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9982 Z= 0.125 Angle : 0.687 9.561 13630 Z= 0.326 Chirality : 0.046 0.321 1576 Planarity : 0.004 0.052 1698 Dihedral : 9.190 177.208 1339 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.98 % Favored : 93.77 % Rotamer: Outliers : 1.74 % Allowed : 18.15 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1194 helix: 1.53 (0.21), residues: 637 sheet: -0.09 (0.57), residues: 92 loop : -1.41 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.016 0.001 TYR A 571 PHE 0.018 0.001 PHE A 93 TRP 0.014 0.001 TRP A 949 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9948) covalent geometry : angle 0.66864 / 0.32 (13543) SS BOND : bond 0.00229 / 0.14 ( 15) SS BOND : angle 1.83483 / 1.07 ( 30) hydrogen bonds : bond 0.04445 / 2.81 ( 483) hydrogen bonds : angle 4.75430 / 3.30 ( 1387) link_ALPHA1-3 : bond 0.00562 / 0.30 ( 1) link_ALPHA1-3 : angle 1.49303 / 0.82 ( 3) link_ALPHA1-4 : bond 0.00841 / 0.44 ( 1) link_ALPHA1-4 : angle 3.41815 / 1.87 ( 3) link_BETA1-4 : bond 0.00857 / 0.43 ( 4) link_BETA1-4 : angle 2.36589 / 1.27 ( 12) link_NAG-ASN : bond 0.00456 / 0.21 ( 13) link_NAG-ASN : angle 2.04412 / 1.72 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3181.71 seconds wall clock time: 54 minutes 53.17 seconds (3293.17 seconds total)