Starting phenix.real_space_refine on Fri Sep 11 15:35:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v3f_21035/09_2026/6v3f_21035.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v3f_21035/09_2026/6v3f_21035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6v3f_21035/09_2026/6v3f_21035.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v3f_21035/09_2026/6v3f_21035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v3f_21035/09_2026/6v3f_21035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v3f_21035/09_2026/6v3f_21035.map" model { file = "/net/cci-nas-00/data/ceres_data/6v3f_21035/09_2026/6v3f_21035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v3f_21035/09_2026/6v3f_21035.cif" } resolution = 3.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 6351 2.51 5 N 1603 2.21 5 O 1838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 9855 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1234, 9575 Classifications: {'peptide': 1234} Link IDs: {'PTRANS': 68, 'TRANS': 1165} Chain breaks: 2 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: 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: "D" 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: "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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 168 Unusual residues: {'CLR': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 2.11, per 1000 atoms: 0.21 Number of scatterers: 9855 At special positions: 0 Unit cell: (99.992, 149.126, 104.302, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1838 8.00 N 1603 7.00 C 6351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 90 " distance=2.02 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 125 " distance=2.05 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 129 " distance=2.05 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 254 " distance=2.04 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 172 " distance=2.04 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.02 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 263 " distance=2.04 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A 968 " - pdb=" SG CYS A 994 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1401 " - " ASN A 53 " " NAG A1402 " - " ASN A 138 " " NAG A1403 " - " ASN A 244 " " NAG A1404 " - " ASN A 416 " " NAG A1405 " - " ASN A 431 " " NAG A1406 " - " ASN A 464 " " NAG A1411 " - " ASN A 606 " " NAG A1414 " - " ASN A 917 " " NAG A1415 " - " ASN A 996 " " NAG A1418 " - " ASN A1076 " " NAG B 1 " - " ASN A 497 " " NAG C 1 " - " ASN A 506 " " NAG D 1 " - " ASN A 909 " " NAG E 1 " - " ASN A1038 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 349.6 milliseconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 11 sheets defined 60.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 92 through 110 removed outlier: 4.640A pdb=" N ILE A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 130 removed outlier: 3.846A pdb=" N SER A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 162 through 173 removed outlier: 4.216A pdb=" N CYS A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.778A pdb=" N CYS A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 283 through 313 removed outlier: 3.770A pdb=" N VAL A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.521A pdb=" N ILE A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.658A pdb=" N VAL A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 388 through 402 removed outlier: 3.509A pdb=" N LYS A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 436 Processing helix chain 'A' and resid 437 through 454 removed outlier: 3.713A pdb=" N LEU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.533A pdb=" N MET A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.553A pdb=" N HIS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'A' and resid 584 through 607 removed outlier: 3.750A pdb=" N GLN A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 632 removed outlier: 3.818A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.638A pdb=" N PHE A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 665 through 691 Processing helix chain 'A' and resid 695 through 724 Proline residue: A 703 - end of helix removed outlier: 3.962A pdb=" N VAL A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASP A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE A 714 " --> pdb=" O GLY A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 762 Proline residue: A 745 - end of helix removed outlier: 3.762A pdb=" N ALA A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 788 removed outlier: 3.685A pdb=" N ILE A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 804 removed outlier: 3.579A pdb=" N ALA A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 Processing helix chain 'A' and resid 835 through 841 removed outlier: 3.696A pdb=" N PHE A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 864 Processing helix chain 'A' and resid 872 through 877 removed outlier: 3.556A pdb=" N LEU A 875 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 877 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 894 removed outlier: 4.344A pdb=" N ASP A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 Processing helix chain 'A' and resid 929 through 938 Processing helix chain 'A' and resid 952 through 962 Processing helix chain 'A' and resid 963 through 966 Processing helix chain 'A' and resid 1005 through 1017 Proline residue: A1014 - end of helix Processing helix chain 'A' and resid 1059 through 1082 Processing helix chain 'A' and resid 1099 through 1104 removed outlier: 3.531A pdb=" N TYR A1103 " --> pdb=" O SER A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1112 through 1120 removed outlier: 4.584A pdb=" N THR A1116 " --> pdb=" O GLU A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1132 removed outlier: 3.963A pdb=" N PHE A1125 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1160 removed outlier: 3.574A pdb=" N GLY A1139 " --> pdb=" O ASP A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1179 Processing helix chain 'A' and resid 1179 through 1192 removed outlier: 4.848A pdb=" N HIS A1185 " --> pdb=" O GLU A1181 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE A1186 " --> pdb=" O PHE A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1227 removed outlier: 3.652A pdb=" N LYS A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP A1204 " --> pdb=" O GLU A1200 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1205 " --> pdb=" O ARG A1201 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Proline residue: A1223 - end of helix removed outlier: 3.780A pdb=" N ILE A1227 " --> pdb=" O PRO A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1231 Processing helix chain 'A' and resid 1233 through 1240 Processing helix chain 'A' and resid 1240 through 1257 Processing helix chain 'A' and resid 1257 through 1267 removed outlier: 3.868A pdb=" N VAL A1261 " --> pdb=" O VAL A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1281 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 removed outlier: 5.273A pdb=" N GLU A 36 " --> pdb=" O CYS A 56 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS A 56 " --> pdb=" O GLU A 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 Processing sheet with id=AA3, first strand: chain 'A' and resid 137 through 139 Processing sheet with id=AA4, first strand: chain 'A' and resid 277 through 278 Processing sheet with id=AA5, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA7, first strand: chain 'A' and resid 420 through 424 Processing sheet with id=AA8, first strand: chain 'A' and resid 456 through 458 Processing sheet with id=AA9, first strand: chain 'A' and resid 505 through 509 Processing sheet with id=AB1, first strand: chain 'A' and resid 1037 through 1039 removed outlier: 6.993A pdb=" N ASN A1038 " --> pdb=" O ILE A1046 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 980 through 981 removed outlier: 4.442A pdb=" N ARG A 969 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 992 " --> pdb=" O LEU A 970 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1482 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: 1.69 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3080 1.35 - 1.47: 2555 1.47 - 1.60: 4364 1.60 - 1.72: 0 1.72 - 1.85: 87 Bond restraints: 10086 Sorted by residual: bond pdb=" C1 NAG A1404 " pdb=" O5 NAG A1404 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.73e+00 bond pdb=" C17 CLR A1419 " pdb=" C20 CLR A1419 " ideal model delta sigma weight residual 1.535 1.590 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.64e+00 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" C1 NAG A1411 " pdb=" O5 NAG A1411 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.34e+00 ... (remaining 10081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 13517 3.60 - 7.21: 185 7.21 - 10.81: 27 10.81 - 14.42: 6 14.42 - 18.02: 1 Bond angle restraints: 13736 Sorted by residual: angle pdb=" CA CYS A 113 " pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " ideal model delta sigma weight residual 114.40 127.59 -13.19 2.30e+00 1.89e-01 3.29e+01 angle pdb=" CA LEU A 48 " pdb=" CB LEU A 48 " pdb=" CG LEU A 48 " ideal model delta sigma weight residual 116.30 134.32 -18.02 3.50e+00 8.16e-02 2.65e+01 angle pdb=" C HIS A 453 " pdb=" N LEU A 454 " pdb=" CA LEU A 454 " ideal model delta sigma weight residual 121.31 128.66 -7.35 1.49e+00 4.50e-01 2.44e+01 angle pdb=" C SER A 655 " pdb=" N ARG A 656 " pdb=" CA ARG A 656 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C ALA A 228 " pdb=" N LEU A 229 " pdb=" CA LEU A 229 " ideal model delta sigma weight residual 121.80 133.55 -11.75 2.44e+00 1.68e-01 2.32e+01 ... (remaining 13731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 5541 17.21 - 34.42: 270 34.42 - 51.62: 57 51.62 - 68.83: 18 68.83 - 86.04: 5 Dihedral angle restraints: 5891 sinusoidal: 2292 harmonic: 3599 Sorted by residual: dihedral pdb=" CB CYS A 38 " pdb=" SG CYS A 38 " pdb=" SG CYS A 56 " pdb=" CB CYS A 56 " ideal model delta sinusoidal sigma weight residual -86.00 -171.22 85.22 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS A 243 " pdb=" SG CYS A 243 " pdb=" SG CYS A 259 " pdb=" CB CYS A 259 " ideal model delta sinusoidal sigma weight residual 93.00 158.01 -65.01 1 1.00e+01 1.00e-02 5.54e+01 dihedral pdb=" CB CYS A 77 " pdb=" SG CYS A 77 " pdb=" SG CYS A 125 " pdb=" CB CYS A 125 " ideal model delta sinusoidal sigma weight residual 93.00 140.19 -47.19 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 5888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1541 0.124 - 0.248: 93 0.248 - 0.372: 5 0.372 - 0.496: 1 0.496 - 0.620: 1 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A 416 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.60e+00 chirality pdb=" C1 NAG A1405 " pdb=" ND2 ASN A 431 " pdb=" C2 NAG A1405 " pdb=" O5 NAG A1405 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 1638 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 113 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C CYS A 113 " 0.064 2.00e-02 2.50e+03 pdb=" O CYS A 113 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO A 114 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 126 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" O HIS A 126 " -0.023 2.00e-02 2.50e+03 pdb=" N ASN A 127 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 286 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ALA A 286 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA A 286 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A 287 " -0.020 2.00e-02 2.50e+03 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2377 2.81 - 3.33: 9256 3.33 - 3.85: 15447 3.85 - 4.38: 16574 4.38 - 4.90: 30061 Nonbonded interactions: 73715 Sorted by model distance: nonbonded pdb=" O ALA A 108 " pdb=" OG1 THR A 111 " model vdw 2.285 3.040 nonbonded pdb=" O ASN A 119 " pdb=" OG SER A 122 " model vdw 2.288 3.040 nonbonded pdb=" N ASP A 872 " pdb=" OD1 ASP A 872 " model vdw 2.297 3.120 nonbonded pdb=" OG SER A 437 " pdb=" OD1 ASP A 439 " model vdw 2.316 3.040 nonbonded pdb=" OD2 ASP A 956 " pdb=" OH TYR A1033 " model vdw 2.319 3.040 ... (remaining 73710 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 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.880 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 10117 Z= 0.327 Angle : 1.215 18.024 13816 Z= 0.661 Chirality : 0.067 0.620 1641 Planarity : 0.008 0.044 1724 Dihedral : 11.381 86.038 3526 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.44 % Favored : 97.31 % Rotamer: Outliers : 1.04 % Allowed : 4.16 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.23), residues: 1228 helix: 1.42 (0.19), residues: 628 sheet: 0.70 (0.57), residues: 80 loop : 0.04 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 79 TYR 0.031 0.003 TYR A 689 PHE 0.022 0.003 PHE A 411 TRP 0.050 0.003 TRP A 202 HIS 0.010 0.003 HIS A 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.33 (10086) covalent geometry : angle 1.17730 / 0.65 (13736) SS BOND : bond 0.00804 / 0.43 ( 13) SS BOND : angle 3.09272 / 1.76 ( 26) hydrogen bonds : bond 0.19026 / 13.17 ( 525) hydrogen bonds : angle 6.81119 / 4.72 ( 1482) link_BETA1-4 : bond 0.01290 / 0.62 ( 4) link_BETA1-4 : angle 6.22055 / 3.14 ( 12) link_NAG-ASN : bond 0.00580 / 0.31 ( 14) link_NAG-ASN : angle 3.91646 / 2.88 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 124 HIS cc_start: 0.7794 (m-70) cc_final: 0.7578 (m-70) REVERT: A 156 TYR cc_start: 0.8362 (p90) cc_final: 0.7938 (p90) REVERT: A 290 ILE cc_start: 0.8637 (mm) cc_final: 0.8431 (mt) REVERT: A 1144 LEU cc_start: 0.9010 (mt) cc_final: 0.8795 (mt) REVERT: A 1148 MET cc_start: 0.8534 (mtp) cc_final: 0.8313 (mtp) outliers start: 11 outliers final: 8 residues processed: 146 average time/residue: 0.1060 time to fit residues: 21.3160 Evaluate side-chains 83 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 872 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN A 860 ASN A1010 HIS A1142 ASN A1234 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.085990 restraints weight = 18729.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086715 restraints weight = 13332.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087216 restraints weight = 12240.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.089031 restraints weight = 8569.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.088862 restraints weight = 6742.861| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10117 Z= 0.176 Angle : 0.742 11.067 13816 Z= 0.367 Chirality : 0.045 0.282 1641 Planarity : 0.005 0.044 1724 Dihedral : 5.097 53.123 1349 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.36 % Favored : 97.56 % Rotamer: Outliers : 1.42 % Allowed : 8.61 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.23), residues: 1228 helix: 1.82 (0.20), residues: 640 sheet: 0.37 (0.56), residues: 80 loop : -0.10 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 726 TYR 0.018 0.002 TYR A 646 PHE 0.017 0.002 PHE A 411 TRP 0.029 0.002 TRP A 202 HIS 0.004 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (10086) covalent geometry : angle 0.71990 / 0.36 (13736) SS BOND : bond 0.00708 / 0.36 ( 13) SS BOND : angle 1.28236 / 0.70 ( 26) hydrogen bonds : bond 0.06990 / 4.80 ( 525) hydrogen bonds : angle 5.27341 / 3.67 ( 1482) link_BETA1-4 : bond 0.01004 / 0.48 ( 4) link_BETA1-4 : angle 3.48159 / 1.76 ( 12) link_NAG-ASN : bond 0.00409 / 0.23 ( 14) link_NAG-ASN : angle 2.66893 / 1.98 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.370 Fit side-chains REVERT: A 281 MET cc_start: 0.5204 (mmm) cc_final: 0.4945 (mmm) REVERT: A 1148 MET cc_start: 0.8508 (mtp) cc_final: 0.7917 (mtp) REVERT: A 1152 ASP cc_start: 0.8357 (m-30) cc_final: 0.8143 (m-30) outliers start: 15 outliers final: 11 residues processed: 102 average time/residue: 0.0668 time to fit residues: 11.2330 Evaluate side-chains 79 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 1130 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 0.0970 chunk 89 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS A 860 ASN A1010 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087153 restraints weight = 18783.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.086534 restraints weight = 12901.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087432 restraints weight = 13598.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.087897 restraints weight = 8991.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.088470 restraints weight = 7996.081| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10117 Z= 0.144 Angle : 0.663 13.939 13816 Z= 0.324 Chirality : 0.043 0.271 1641 Planarity : 0.004 0.040 1724 Dihedral : 4.639 33.400 1344 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 2.08 % Allowed : 9.37 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.24), residues: 1228 helix: 1.83 (0.20), residues: 644 sheet: 0.37 (0.57), residues: 80 loop : -0.10 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 726 TYR 0.021 0.001 TYR A 936 PHE 0.014 0.001 PHE A 411 TRP 0.024 0.001 TRP A 202 HIS 0.009 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10086) covalent geometry : angle 0.64397 / 0.32 (13736) SS BOND : bond 0.00369 / 0.18 ( 13) SS BOND : angle 1.16035 / 0.62 ( 26) hydrogen bonds : bond 0.05894 / 4.05 ( 525) hydrogen bonds : angle 4.97280 / 3.46 ( 1482) link_BETA1-4 : bond 0.01065 / 0.51 ( 4) link_BETA1-4 : angle 3.36692 / 1.71 ( 12) link_NAG-ASN : bond 0.00310 / 0.18 ( 14) link_NAG-ASN : angle 2.25194 / 1.65 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8466 (mmmt) cc_final: 0.7711 (tmtt) REVERT: A 1148 MET cc_start: 0.8500 (mtp) cc_final: 0.7936 (mtp) outliers start: 22 outliers final: 14 residues processed: 97 average time/residue: 0.0687 time to fit residues: 10.8191 Evaluate side-chains 86 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 126 HIS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 59 optimal weight: 0.6980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 HIS A 626 ASN A1010 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086729 restraints weight = 18924.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.086169 restraints weight = 13285.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.087041 restraints weight = 14197.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087483 restraints weight = 8871.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.089010 restraints weight = 7857.064| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10117 Z= 0.140 Angle : 0.637 12.955 13816 Z= 0.311 Chirality : 0.042 0.267 1641 Planarity : 0.004 0.041 1724 Dihedral : 4.445 32.231 1342 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 96.99 % Rotamer: Outliers : 1.89 % Allowed : 9.74 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1228 helix: 1.84 (0.20), residues: 647 sheet: 0.20 (0.57), residues: 80 loop : -0.14 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.016 0.001 TYR A 646 PHE 0.022 0.001 PHE A 839 TRP 0.015 0.001 TRP A 202 HIS 0.009 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (10086) covalent geometry : angle 0.61933 / 0.31 (13736) SS BOND : bond 0.00298 / 0.15 ( 13) SS BOND : angle 1.21829 / 0.67 ( 26) hydrogen bonds : bond 0.05585 / 3.82 ( 525) hydrogen bonds : angle 4.88949 / 3.39 ( 1482) link_BETA1-4 : bond 0.00979 / 0.47 ( 4) link_BETA1-4 : angle 3.25657 / 1.66 ( 12) link_NAG-ASN : bond 0.00273 / 0.16 ( 14) link_NAG-ASN : angle 2.04090 / 1.47 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7943 (mpt180) cc_final: 0.7541 (mpt180) REVERT: A 94 LYS cc_start: 0.8452 (mmmt) cc_final: 0.7669 (tmtt) outliers start: 20 outliers final: 15 residues processed: 90 average time/residue: 0.0777 time to fit residues: 11.1813 Evaluate side-chains 85 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 95 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 2 optimal weight: 0.0000 chunk 103 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 19 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088057 restraints weight = 18839.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.087525 restraints weight = 13227.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088339 restraints weight = 14140.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088818 restraints weight = 8837.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.090456 restraints weight = 7757.734| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10117 Z= 0.116 Angle : 0.609 12.857 13816 Z= 0.294 Chirality : 0.042 0.260 1641 Planarity : 0.004 0.045 1724 Dihedral : 4.268 33.302 1341 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 2.46 % Allowed : 10.31 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.24), residues: 1228 helix: 1.96 (0.20), residues: 645 sheet: 0.35 (0.57), residues: 78 loop : -0.03 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.017 0.001 TYR A 646 PHE 0.011 0.001 PHE A 411 TRP 0.014 0.001 TRP A 202 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (10086) covalent geometry : angle 0.59298 / 0.29 (13736) SS BOND : bond 0.00200 / 0.10 ( 13) SS BOND : angle 1.04331 / 0.55 ( 26) hydrogen bonds : bond 0.04973 / 3.40 ( 525) hydrogen bonds : angle 4.74518 / 3.29 ( 1482) link_BETA1-4 : bond 0.01033 / 0.50 ( 4) link_BETA1-4 : angle 3.17680 / 1.62 ( 12) link_NAG-ASN : bond 0.00290 / 0.16 ( 14) link_NAG-ASN : angle 1.80668 / 1.29 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8480 (mmmt) cc_final: 0.7687 (tmtt) REVERT: A 632 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.8027 (t0) REVERT: A 1253 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8645 (mm) outliers start: 26 outliers final: 19 residues processed: 96 average time/residue: 0.0744 time to fit residues: 11.3719 Evaluate side-chains 92 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 10 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 HIS A1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.115219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.083975 restraints weight = 19034.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.083500 restraints weight = 14552.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.084398 restraints weight = 14272.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.085119 restraints weight = 9482.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085663 restraints weight = 8379.975| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10117 Z= 0.201 Angle : 0.680 12.072 13816 Z= 0.330 Chirality : 0.045 0.278 1641 Planarity : 0.004 0.041 1724 Dihedral : 4.392 34.349 1341 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.46 % Allowed : 11.16 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1228 helix: 1.72 (0.20), residues: 649 sheet: 0.15 (0.56), residues: 78 loop : -0.25 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 417 TYR 0.016 0.002 TYR A 862 PHE 0.024 0.002 PHE A 717 TRP 0.014 0.001 TRP A 960 HIS 0.006 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (10086) covalent geometry : angle 0.66546 / 0.33 (13736) SS BOND : bond 0.00301 / 0.16 ( 13) SS BOND : angle 1.09776 / 0.58 ( 26) hydrogen bonds : bond 0.05962 / 4.11 ( 525) hydrogen bonds : angle 4.89038 / 3.39 ( 1482) link_BETA1-4 : bond 0.01005 / 0.48 ( 4) link_BETA1-4 : angle 3.20762 / 1.64 ( 12) link_NAG-ASN : bond 0.00239 / 0.14 ( 14) link_NAG-ASN : angle 1.89238 / 1.28 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7944 (mpt180) cc_final: 0.7613 (mpt180) REVERT: A 94 LYS cc_start: 0.8491 (mmmt) cc_final: 0.7727 (tmtt) REVERT: A 586 MET cc_start: 0.7983 (mmm) cc_final: 0.7608 (tpp) REVERT: A 632 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8293 (t0) outliers start: 26 outliers final: 22 residues processed: 89 average time/residue: 0.0752 time to fit residues: 10.7092 Evaluate side-chains 92 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 860 ASN A1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084304 restraints weight = 19164.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.083524 restraints weight = 13862.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.084045 restraints weight = 16417.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.084553 restraints weight = 10421.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085604 restraints weight = 8918.962| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10117 Z= 0.118 Angle : 0.616 12.742 13816 Z= 0.294 Chirality : 0.041 0.262 1641 Planarity : 0.004 0.042 1724 Dihedral : 4.236 35.078 1341 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 2.08 % Allowed : 11.54 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.24), residues: 1228 helix: 1.84 (0.20), residues: 651 sheet: 0.24 (0.57), residues: 78 loop : -0.13 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 75 TYR 0.021 0.001 TYR A 936 PHE 0.018 0.001 PHE A 717 TRP 0.007 0.001 TRP A 960 HIS 0.002 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (10086) covalent geometry : angle 0.60182 / 0.29 (13736) SS BOND : bond 0.00226 / 0.11 ( 13) SS BOND : angle 1.11431 / 0.57 ( 26) hydrogen bonds : bond 0.04913 / 3.36 ( 525) hydrogen bonds : angle 4.71200 / 3.26 ( 1482) link_BETA1-4 : bond 0.01034 / 0.50 ( 4) link_BETA1-4 : angle 3.09821 / 1.58 ( 12) link_NAG-ASN : bond 0.00260 / 0.14 ( 14) link_NAG-ASN : angle 1.68068 / 1.15 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7896 (mpt180) cc_final: 0.7425 (mpt180) REVERT: A 1253 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8708 (mm) outliers start: 22 outliers final: 19 residues processed: 89 average time/residue: 0.0722 time to fit residues: 10.4202 Evaluate side-chains 86 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 0.0980 chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 860 ASN A1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.083156 restraints weight = 19287.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.082619 restraints weight = 15510.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.083032 restraints weight = 14943.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085366 restraints weight = 10649.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.085286 restraints weight = 7860.714| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10117 Z= 0.137 Angle : 0.633 12.252 13816 Z= 0.305 Chirality : 0.042 0.264 1641 Planarity : 0.004 0.041 1724 Dihedral : 4.219 35.776 1341 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 2.18 % Allowed : 11.83 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1228 helix: 1.84 (0.20), residues: 650 sheet: 0.25 (0.56), residues: 78 loop : -0.15 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.017 0.001 TYR A 646 PHE 0.015 0.001 PHE A 717 TRP 0.010 0.001 TRP A 960 HIS 0.004 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (10086) covalent geometry : angle 0.61990 / 0.30 (13736) SS BOND : bond 0.00247 / 0.13 ( 13) SS BOND : angle 0.97788 / 0.51 ( 26) hydrogen bonds : bond 0.05086 / 3.49 ( 525) hydrogen bonds : angle 4.72346 / 3.27 ( 1482) link_BETA1-4 : bond 0.00998 / 0.48 ( 4) link_BETA1-4 : angle 3.09522 / 1.59 ( 12) link_NAG-ASN : bond 0.00220 / 0.13 ( 14) link_NAG-ASN : angle 1.65685 / 1.11 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7874 (mpt180) cc_final: 0.7491 (mpt180) REVERT: A 586 MET cc_start: 0.7963 (mmm) cc_final: 0.7535 (mmm) REVERT: A 1253 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8731 (mm) outliers start: 23 outliers final: 18 residues processed: 85 average time/residue: 0.0784 time to fit residues: 10.5210 Evaluate side-chains 84 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 124 HIS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 111 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.085170 restraints weight = 19171.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.084565 restraints weight = 15253.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085135 restraints weight = 14371.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087592 restraints weight = 10322.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087607 restraints weight = 7571.692| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10117 Z= 0.110 Angle : 0.607 12.443 13816 Z= 0.289 Chirality : 0.041 0.255 1641 Planarity : 0.004 0.043 1724 Dihedral : 4.108 36.296 1341 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.70 % Allowed : 12.02 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.25), residues: 1228 helix: 1.96 (0.21), residues: 650 sheet: 0.34 (0.56), residues: 78 loop : -0.05 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 843 TYR 0.017 0.001 TYR A 646 PHE 0.014 0.001 PHE A 717 TRP 0.007 0.001 TRP A 284 HIS 0.002 0.000 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (10086) covalent geometry : angle 0.59495 / 0.29 (13736) SS BOND : bond 0.00243 / 0.12 ( 13) SS BOND : angle 0.87540 / 0.46 ( 26) hydrogen bonds : bond 0.04429 / 3.03 ( 525) hydrogen bonds : angle 4.61421 / 3.20 ( 1482) link_BETA1-4 : bond 0.01028 / 0.49 ( 4) link_BETA1-4 : angle 3.02920 / 1.55 ( 12) link_NAG-ASN : bond 0.00268 / 0.15 ( 14) link_NAG-ASN : angle 1.50648 / 1.02 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7890 (mpt180) cc_final: 0.7567 (mpt180) REVERT: A 860 ASN cc_start: 0.8154 (m-40) cc_final: 0.7812 (m-40) REVERT: A 1253 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8684 (mm) outliers start: 18 outliers final: 15 residues processed: 85 average time/residue: 0.0761 time to fit residues: 10.2775 Evaluate side-chains 84 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 10 optimal weight: 5.9990 chunk 91 optimal weight: 0.0770 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.080316 restraints weight = 19274.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.079757 restraints weight = 15122.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.080077 restraints weight = 15333.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.082261 restraints weight = 10871.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.082186 restraints weight = 8028.248| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10117 Z= 0.211 Angle : 0.699 12.121 13816 Z= 0.339 Chirality : 0.045 0.280 1641 Planarity : 0.004 0.039 1724 Dihedral : 4.370 37.146 1339 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.70 % Allowed : 12.49 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.24), residues: 1228 helix: 1.75 (0.20), residues: 642 sheet: 0.16 (0.55), residues: 78 loop : -0.32 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 417 TYR 0.018 0.002 TYR A 646 PHE 0.017 0.002 PHE A 411 TRP 0.016 0.001 TRP A 960 HIS 0.006 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (10086) covalent geometry : angle 0.68646 / 0.34 (13736) SS BOND : bond 0.00304 / 0.17 ( 13) SS BOND : angle 1.04359 / 0.56 ( 26) hydrogen bonds : bond 0.06070 / 4.19 ( 525) hydrogen bonds : angle 4.85200 / 3.37 ( 1482) link_BETA1-4 : bond 0.00953 / 0.46 ( 4) link_BETA1-4 : angle 3.12219 / 1.60 ( 12) link_NAG-ASN : bond 0.00236 / 0.15 ( 14) link_NAG-ASN : angle 1.80081 / 1.17 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7842 (mpt180) cc_final: 0.7429 (mpt180) REVERT: A 586 MET cc_start: 0.8074 (mmm) cc_final: 0.7760 (tpp) outliers start: 18 outliers final: 15 residues processed: 82 average time/residue: 0.0775 time to fit residues: 10.1921 Evaluate side-chains 81 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 56 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 HIS A1142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.083903 restraints weight = 19211.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.083566 restraints weight = 14282.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.084009 restraints weight = 13746.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.086267 restraints weight = 9951.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.086255 restraints weight = 7475.800| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10117 Z= 0.113 Angle : 0.615 12.315 13816 Z= 0.293 Chirality : 0.041 0.256 1641 Planarity : 0.004 0.042 1724 Dihedral : 4.162 37.519 1339 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.23 % Allowed : 12.87 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.25), residues: 1228 helix: 1.92 (0.21), residues: 647 sheet: 0.31 (0.56), residues: 78 loop : -0.15 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.017 0.001 TYR A 646 PHE 0.012 0.001 PHE A 717 TRP 0.008 0.001 TRP A 284 HIS 0.002 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10086) covalent geometry : angle 0.60292 / 0.29 (13736) SS BOND : bond 0.00223 / 0.11 ( 13) SS BOND : angle 0.87032 / 0.46 ( 26) hydrogen bonds : bond 0.04549 / 3.11 ( 525) hydrogen bonds : angle 4.63785 / 3.21 ( 1482) link_BETA1-4 : bond 0.01030 / 0.49 ( 4) link_BETA1-4 : angle 3.01544 / 1.54 ( 12) link_NAG-ASN : bond 0.00278 / 0.16 ( 14) link_NAG-ASN : angle 1.52647 / 1.01 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1475.62 seconds wall clock time: 26 minutes 18.91 seconds (1578.91 seconds total)