Starting phenix.real_space_refine on Fri Feb 14 10:39:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v3f_21035/02_2025/6v3f_21035.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v3f_21035/02_2025/6v3f_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6v3f_21035/02_2025/6v3f_21035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v3f_21035/02_2025/6v3f_21035.map" model { file = "/net/cci-nas-00/data/ceres_data/6v3f_21035/02_2025/6v3f_21035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v3f_21035/02_2025/6v3f_21035.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.61, per 1000 atoms: 0.67 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: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.39 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: 3.75 Time building geometry restraints manager: 2.92 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: 5933 17.21 - 34.42: 288 34.42 - 51.62: 73 51.62 - 68.83: 26 68.83 - 86.04: 5 Dihedral angle restraints: 6325 sinusoidal: 2726 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 6322 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: 2.080 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.340 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 10086 Z= 0.429 Angle : 1.177 18.024 13736 Z= 0.653 Chirality : 0.067 0.620 1641 Planarity : 0.008 0.044 1724 Dihedral : 11.527 86.038 3960 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (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 TRP 0.050 0.003 TRP A 202 HIS 0.010 0.003 HIS A 453 PHE 0.022 0.003 PHE A 411 TYR 0.031 0.003 TYR A 689 ARG 0.011 0.001 ARG A 79 *********************** 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 : 1.084 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: 0.9009 (mt) cc_final: 0.8795 (mt) REVERT: A 1148 MET cc_start: 0.8534 (mtp) cc_final: 0.8314 (mtp) outliers start: 11 outliers final: 8 residues processed: 146 average time/residue: 0.2527 time to fit residues: 50.8397 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 : 1.115 ------------------------------------------------------------------------------- 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 103 optimal weight: 8.9990 chunk 93 optimal weight: 0.0000 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 111 optimal weight: 0.0870 overall best weight: 0.7566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN A 206 GLN A 860 ASN A1010 HIS A1234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088699 restraints weight = 18521.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.089416 restraints weight = 13471.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.090126 restraints weight = 11682.698| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 10086 Z= 0.190 Angle : 0.699 11.939 13736 Z= 0.348 Chirality : 0.044 0.270 1641 Planarity : 0.005 0.051 1724 Dihedral : 7.379 58.100 1783 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.20 % Favored : 97.72 % Rotamer: Outliers : 1.23 % Allowed : 8.61 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.23), residues: 1228 helix: 1.94 (0.20), residues: 640 sheet: 0.46 (0.57), residues: 80 loop : 0.00 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 202 HIS 0.004 0.001 HIS A 126 PHE 0.017 0.001 PHE A 844 TYR 0.019 0.001 TYR A 646 ARG 0.008 0.001 ARG A 75 *********************** 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 110 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 288 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.7060 (mt) REVERT: A 1148 MET cc_start: 0.8476 (mtp) cc_final: 0.7944 (mtp) outliers start: 13 outliers final: 7 residues processed: 108 average time/residue: 0.1832 time to fit residues: 30.5867 Evaluate side-chains 80 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 236 LEU Chi-restraints excluded: chain A residue 288 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 77 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 0.0980 chunk 107 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3605 r_free = 0.3605 target = 0.118522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087800 restraints weight = 18675.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.087674 restraints weight = 12886.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.088528 restraints weight = 13236.136| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10086 Z= 0.190 Angle : 0.648 15.388 13736 Z= 0.320 Chirality : 0.043 0.262 1641 Planarity : 0.004 0.045 1724 Dihedral : 6.762 57.640 1778 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.01 % Favored : 96.91 % Rotamer: Outliers : 2.37 % Allowed : 8.80 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1228 helix: 1.87 (0.20), residues: 644 sheet: 0.32 (0.57), residues: 80 loop : -0.08 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 202 HIS 0.009 0.001 HIS A 124 PHE 0.014 0.001 PHE A 411 TYR 0.017 0.001 TYR A 646 ARG 0.004 0.000 ARG A 63 *********************** 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 105 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 1.070 Fit side-chains REVERT: A 63 ARG cc_start: 0.8013 (mpt180) cc_final: 0.7639 (mpt180) REVERT: A 94 LYS cc_start: 0.8458 (mmmt) cc_final: 0.7676 (tmtt) outliers start: 25 outliers final: 15 residues processed: 97 average time/residue: 0.1741 time to fit residues: 26.8860 Evaluate side-chains 88 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 0.0030 chunk 54 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.086154 restraints weight = 18694.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.086188 restraints weight = 12852.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.086612 restraints weight = 14447.149| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10086 Z= 0.218 Angle : 0.626 14.352 13736 Z= 0.311 Chirality : 0.043 0.262 1641 Planarity : 0.004 0.042 1724 Dihedral : 6.514 57.037 1776 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 96.99 % Rotamer: Outliers : 1.99 % Allowed : 10.03 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1228 helix: 1.82 (0.20), residues: 650 sheet: 0.14 (0.57), residues: 80 loop : -0.13 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 202 HIS 0.011 0.001 HIS A 126 PHE 0.021 0.001 PHE A 839 TYR 0.017 0.001 TYR A 646 ARG 0.003 0.000 ARG A 63 *********************** 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 101 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7935 (mpt180) cc_final: 0.7558 (mpt180) REVERT: A 94 LYS cc_start: 0.8450 (mmmt) cc_final: 0.7661 (tmtt) outliers start: 21 outliers final: 18 residues processed: 92 average time/residue: 0.1737 time to fit residues: 25.2882 Evaluate side-chains 91 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 240 ILE 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 867 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1051 MET 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 30 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 86 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3566 r_free = 0.3566 target = 0.115709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.084390 restraints weight = 18769.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.084241 restraints weight = 14757.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085381 restraints weight = 13147.236| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10086 Z= 0.269 Angle : 0.644 12.465 13736 Z= 0.320 Chirality : 0.044 0.270 1641 Planarity : 0.004 0.037 1724 Dihedral : 6.429 57.419 1775 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.46 % Allowed : 10.41 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1228 helix: 1.70 (0.20), residues: 649 sheet: 0.19 (0.58), residues: 78 loop : -0.23 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 202 HIS 0.007 0.001 HIS A 126 PHE 0.016 0.002 PHE A 717 TYR 0.017 0.002 TYR A 646 ARG 0.003 0.000 ARG A 63 *********************** 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 102 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8444 (mmmt) cc_final: 0.7707 (tmtt) REVERT: A 717 PHE cc_start: 0.9267 (t80) cc_final: 0.9033 (t80) outliers start: 26 outliers final: 16 residues processed: 94 average time/residue: 0.1752 time to fit residues: 25.9721 Evaluate side-chains 88 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 154 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 649 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1109 VAL Chi-restraints excluded: chain A residue 1130 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086414 restraints weight = 18752.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.085993 restraints weight = 12934.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.086725 restraints weight = 14235.464| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10086 Z= 0.175 Angle : 0.616 13.281 13736 Z= 0.296 Chirality : 0.042 0.256 1641 Planarity : 0.004 0.037 1724 Dihedral : 6.235 56.948 1775 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.58 % Favored : 96.34 % Rotamer: Outliers : 2.37 % Allowed : 11.16 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.24), residues: 1228 helix: 1.84 (0.20), residues: 650 sheet: 0.18 (0.56), residues: 78 loop : -0.21 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.003 0.001 HIS A 124 PHE 0.012 0.001 PHE A 411 TYR 0.018 0.001 TYR A 862 ARG 0.002 0.000 ARG A 63 *********************** 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 101 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7578 (ptp90) outliers start: 25 outliers final: 17 residues processed: 93 average time/residue: 0.1793 time to fit residues: 26.2661 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 : 1.080 ------------------------------------------------------------------------------- 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 176 ARG 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 670 LEU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 885 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 94 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3551 r_free = 0.3551 target = 0.114647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.083348 restraints weight = 19109.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.082823 restraints weight = 14166.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.083796 restraints weight = 13549.060| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10086 Z= 0.318 Angle : 0.682 12.469 13736 Z= 0.334 Chirality : 0.045 0.273 1641 Planarity : 0.004 0.035 1724 Dihedral : 6.371 57.448 1775 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 2.18 % Allowed : 12.11 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1228 helix: 1.64 (0.20), residues: 648 sheet: 0.05 (0.55), residues: 78 loop : -0.40 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 960 HIS 0.006 0.001 HIS A1054 PHE 0.026 0.002 PHE A 717 TYR 0.017 0.002 TYR A 646 ARG 0.003 0.000 ARG A 417 *********************** 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: 23 poor density : 73 time to evaluate : 1.090 Fit side-chains REVERT: A 63 ARG cc_start: 0.7904 (mpt180) cc_final: 0.7468 (mpt180) REVERT: A 586 MET cc_start: 0.7871 (mmm) cc_final: 0.7583 (tpp) outliers start: 23 outliers final: 20 residues processed: 88 average time/residue: 0.1789 time to fit residues: 24.6118 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 : 1.046 ------------------------------------------------------------------------------- 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 154 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 407 THR Chi-restraints excluded: chain A residue 538 LEU 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 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 91 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 21 optimal weight: 9.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3578 r_free = 0.3578 target = 0.115997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.084010 restraints weight = 19354.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.083600 restraints weight = 14162.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.084226 restraints weight = 14393.756| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10086 Z= 0.157 Angle : 0.610 12.966 13736 Z= 0.296 Chirality : 0.041 0.248 1641 Planarity : 0.004 0.038 1724 Dihedral : 6.071 57.143 1775 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 2.08 % Allowed : 11.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1228 helix: 1.84 (0.21), residues: 650 sheet: 0.21 (0.57), residues: 78 loop : -0.18 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 284 HIS 0.002 0.000 HIS A 397 PHE 0.019 0.001 PHE A 717 TYR 0.016 0.001 TYR A 646 ARG 0.002 0.000 ARG A 63 *********************** 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 97 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.138 Fit side-chains REVERT: A 63 ARG cc_start: 0.7874 (mpt180) cc_final: 0.7615 (mpt180) REVERT: A 176 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7583 (ptp90) outliers start: 22 outliers final: 19 residues processed: 91 average time/residue: 0.1870 time to fit residues: 26.7184 Evaluate side-chains 87 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 175 VAL Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 ILE 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 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 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 102 optimal weight: 6.9990 chunk 69 optimal weight: 0.0070 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.085128 restraints weight = 19270.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084813 restraints weight = 15305.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085438 restraints weight = 16007.824| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10086 Z= 0.150 Angle : 0.601 12.665 13736 Z= 0.288 Chirality : 0.041 0.245 1641 Planarity : 0.004 0.038 1724 Dihedral : 5.864 57.059 1775 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.99 % Allowed : 12.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1228 helix: 1.99 (0.21), residues: 647 sheet: 0.31 (0.57), residues: 78 loop : -0.15 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 202 HIS 0.002 0.001 HIS A1054 PHE 0.020 0.001 PHE A 717 TYR 0.018 0.001 TYR A 646 ARG 0.002 0.000 ARG A 997 *********************** 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 93 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 1.358 Fit side-chains REVERT: A 63 ARG cc_start: 0.7914 (mpt180) cc_final: 0.7664 (mpt180) REVERT: A 176 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7608 (ptp90) REVERT: A 860 ASN cc_start: 0.8268 (m-40) cc_final: 0.7925 (m-40) outliers start: 21 outliers final: 18 residues processed: 88 average time/residue: 0.2006 time to fit residues: 27.9698 Evaluate side-chains 88 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 176 ARG 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 407 THR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 611 PHE 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 25 optimal weight: 0.0050 chunk 92 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.113222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.081175 restraints weight = 19432.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.080581 restraints weight = 15088.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081229 restraints weight = 15921.268| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10086 Z= 0.285 Angle : 0.665 11.377 13736 Z= 0.326 Chirality : 0.044 0.269 1641 Planarity : 0.004 0.038 1724 Dihedral : 6.091 57.373 1773 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.99 % Allowed : 12.39 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1228 helix: 1.78 (0.20), residues: 648 sheet: 0.22 (0.56), residues: 78 loop : -0.35 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 960 HIS 0.005 0.001 HIS A1054 PHE 0.016 0.002 PHE A 717 TYR 0.017 0.002 TYR A 646 ARG 0.003 0.000 ARG A 417 ********************** 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 88 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 1.179 Fit side-chains REVERT: A 63 ARG cc_start: 0.7977 (mpt180) cc_final: 0.7621 (mpt180) REVERT: A 176 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7625 (ptp90) outliers start: 21 outliers final: 17 residues processed: 82 average time/residue: 0.1798 time to fit residues: 23.2917 Evaluate side-chains 83 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 176 ARG 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 407 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 611 PHE 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 22 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083581 restraints weight = 19297.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.082838 restraints weight = 15525.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.083312 restraints weight = 15566.406| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10086 Z= 0.181 Angle : 0.614 12.102 13736 Z= 0.298 Chirality : 0.042 0.254 1641 Planarity : 0.004 0.037 1724 Dihedral : 5.929 57.068 1773 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.99 % Allowed : 12.49 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1228 helix: 1.87 (0.21), residues: 649 sheet: 0.32 (0.57), residues: 78 loop : -0.25 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 960 HIS 0.003 0.001 HIS A1054 PHE 0.016 0.001 PHE A 717 TYR 0.017 0.001 TYR A 646 ARG 0.002 0.000 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2684.78 seconds wall clock time: 49 minutes 22.83 seconds (2962.83 seconds total)