Starting phenix.real_space_refine on Tue Feb 13 20:35:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df8_30662/02_2024/7df8_30662_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df8_30662/02_2024/7df8_30662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df8_30662/02_2024/7df8_30662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df8_30662/02_2024/7df8_30662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df8_30662/02_2024/7df8_30662_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7df8_30662/02_2024/7df8_30662_neut_trim_updated.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 41 5.16 5 C 4915 2.51 5 N 1171 2.21 5 O 1378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 391": "NH1" <-> "NH2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 605": "NH1" <-> "NH2" Residue "A PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A ARG 726": "NH1" <-> "NH2" Residue "A ARG 727": "NH1" <-> "NH2" Residue "A ARG 738": "NH1" <-> "NH2" Residue "A ASP 783": "OD1" <-> "OD2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1081": "NH1" <-> "NH2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1187": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7505 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7148 Classifications: {'peptide': 918} Link IDs: {'PTRANS': 46, 'TRANS': 871} Chain breaks: 2 Chain: "H" 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: "K" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Unusual residues: {'CLR': 4, 'LMT': 1, 'NAG': 7} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.72, per 1000 atoms: 0.63 Number of scatterers: 7505 At special positions: 0 Unit cell: (94.429, 77.453, 131.564, 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 41 16.00 O 1378 8.00 N 1171 7.00 C 4915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 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 920 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A 989 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 H 1 " - " NAG H 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " NAG K 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " NAG R 3 " NAG-ASN " NAG A1301 " - " ASN A 431 " " NAG A1302 " - " ASN A 464 " " NAG A1303 " - " ASN A 506 " " NAG A1304 " - " ASN A 416 " " NAG A1305 " - " ASN A 479 " " NAG A1306 " - " ASN A 927 " " NAG A1307 " - " ASN A1075 " " NAG H 1 " - " ASN A 497 " " NAG K 1 " - " ASN A 909 " " NAG R 1 " - " ASN A1037 " Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.4 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 6 sheets defined 52.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.736A pdb=" N LEU A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 370 removed outlier: 3.697A pdb=" N ILE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix removed outlier: 4.331A pdb=" N GLY A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 438 through 452 removed outlier: 4.076A pdb=" N GLU A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 518 through 527 removed outlier: 3.636A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 584 through 606 removed outlier: 3.647A pdb=" N GLN A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.626A pdb=" N ILE A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 646 removed outlier: 3.863A pdb=" N LEU A 633 " --> pdb=" O THR A 629 " (cutoff:3.500A) Proline residue: A 634 - end of helix removed outlier: 4.234A pdb=" N THR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 689 removed outlier: 3.590A pdb=" N LEU A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 679 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A 688 " --> pdb=" O MET A 684 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 705 removed outlier: 3.733A pdb=" N VAL A 702 " --> pdb=" O ILE A 698 " (cutoff:3.500A) Proline residue: A 703 - end of helix No H-bonds generated for 'chain 'A' and resid 698 through 705' Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.703A pdb=" N ILE A 716 " --> pdb=" O ASP A 712 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 744 through 763 removed outlier: 4.692A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 789 removed outlier: 3.530A pdb=" N THR A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 803 removed outlier: 3.557A pdb=" N ARG A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 802 " --> pdb=" O ASP A 798 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 840 Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 845 through 866 removed outlier: 4.305A pdb=" N LEU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 854 " --> pdb=" O LEU A 850 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N HIS A 866 " --> pdb=" O TYR A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 876 removed outlier: 3.603A pdb=" N ALA A 876 " --> pdb=" O GLN A 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 873 through 876' Processing helix chain 'A' and resid 883 through 893 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.768A pdb=" N ALA A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 937 Processing helix chain 'A' and resid 953 through 960 Processing helix chain 'A' and resid 1005 through 1015 removed outlier: 3.549A pdb=" N LEU A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1059 through 1082 removed outlier: 3.596A pdb=" N THR A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1102 No H-bonds generated for 'chain 'A' and resid 1099 through 1102' Processing helix chain 'A' and resid 1104 through 1106 No H-bonds generated for 'chain 'A' and resid 1104 through 1106' Processing helix chain 'A' and resid 1108 through 1124 removed outlier: 3.520A pdb=" N CYS A1119 " --> pdb=" O MET A1115 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A1120 " --> pdb=" O LEU A1116 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A1121 " --> pdb=" O SER A1117 " (cutoff:3.500A) Proline residue: A1122 - end of helix Processing helix chain 'A' and resid 1127 through 1130 No H-bonds generated for 'chain 'A' and resid 1127 through 1130' Processing helix chain 'A' and resid 1138 through 1159 removed outlier: 4.183A pdb=" N LEU A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1175 removed outlier: 3.598A pdb=" N ILE A1169 " --> pdb=" O ALA A1165 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A1170 " --> pdb=" O VAL A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1190 removed outlier: 4.556A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1215 removed outlier: 3.505A pdb=" N MET A1208 " --> pdb=" O ALA A1204 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER A1210 " --> pdb=" O ILE A1206 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA A1211 " --> pdb=" O SER A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1228 removed outlier: 4.614A pdb=" N LEU A1227 " --> pdb=" O GLY A1223 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A1228 " --> pdb=" O ILE A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1238 Processing helix chain 'A' and resid 1241 through 1254 removed outlier: 3.513A pdb=" N LEU A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1265 removed outlier: 3.977A pdb=" N TYR A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 570 through 576 Processing sheet with id= B, first strand: chain 'A' and resid 420 through 423 Processing sheet with id= C, first strand: chain 'A' and resid 455 through 458 removed outlier: 4.119A pdb=" N ARG A 463 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 505 through 508 Processing sheet with id= E, first strand: chain 'A' and resid 1050 through 1052 Processing sheet with id= F, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.914A pdb=" N ALA A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2172 1.34 - 1.46: 1551 1.46 - 1.58: 3907 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 7694 Sorted by residual: bond pdb=" C ASP A 378 " pdb=" N PRO A 379 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.11e+00 bond pdb=" C3' LMT A1308 " pdb=" O3' LMT A1308 " ideal model delta sigma weight residual 1.404 1.350 0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" C6' LMT A1308 " pdb=" O6' LMT A1308 " ideal model delta sigma weight residual 1.407 1.356 0.051 2.00e-02 2.50e+03 6.43e+00 bond pdb=" C2B LMT A1308 " pdb=" O2B LMT A1308 " ideal model delta sigma weight residual 1.410 1.362 0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C3B LMT A1308 " pdb=" O3B LMT A1308 " ideal model delta sigma weight residual 1.406 1.358 0.048 2.00e-02 2.50e+03 5.67e+00 ... (remaining 7689 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.73: 155 104.73 - 112.04: 3929 112.04 - 119.35: 2528 119.35 - 126.66: 3775 126.66 - 133.97: 111 Bond angle restraints: 10498 Sorted by residual: angle pdb=" N ASP A 378 " pdb=" CA ASP A 378 " pdb=" C ASP A 378 " ideal model delta sigma weight residual 109.81 121.02 -11.21 2.21e+00 2.05e-01 2.57e+01 angle pdb=" N VAL A 371 " pdb=" CA VAL A 371 " pdb=" C VAL A 371 " ideal model delta sigma weight residual 113.53 109.42 4.11 9.80e-01 1.04e+00 1.76e+01 angle pdb=" CA ASP A 378 " pdb=" C ASP A 378 " pdb=" N PRO A 379 " ideal model delta sigma weight residual 118.44 124.68 -6.24 1.59e+00 3.96e-01 1.54e+01 angle pdb=" N ALA A 744 " pdb=" CA ALA A 744 " pdb=" C ALA A 744 " ideal model delta sigma weight residual 109.81 117.67 -7.86 2.21e+00 2.05e-01 1.26e+01 angle pdb=" N ARG A 801 " pdb=" CA ARG A 801 " pdb=" C ARG A 801 " ideal model delta sigma weight residual 111.33 115.62 -4.29 1.21e+00 6.83e-01 1.26e+01 ... (remaining 10493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 4653 22.77 - 45.55: 275 45.55 - 68.32: 23 68.32 - 91.09: 14 91.09 - 113.87: 5 Dihedral angle restraints: 4970 sinusoidal: 2299 harmonic: 2671 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -156.34 70.34 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CB CYS A 920 " pdb=" SG CYS A 920 " pdb=" SG CYS A 925 " pdb=" CB CYS A 925 " ideal model delta sinusoidal sigma weight residual -86.00 -125.37 39.37 1 1.00e+01 1.00e-02 2.18e+01 dihedral pdb=" CA GLU A 381 " pdb=" C GLU A 381 " pdb=" N LEU A 382 " pdb=" CA LEU A 382 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 4967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1035 0.061 - 0.122: 197 0.122 - 0.183: 23 0.183 - 0.244: 12 0.244 - 0.305: 7 Chirality restraints: 1274 Sorted by residual: chirality pdb=" CA ASP A 378 " pdb=" N ASP A 378 " pdb=" C ASP A 378 " pdb=" CB ASP A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C13 CLR A1312 " pdb=" C12 CLR A1312 " pdb=" C14 CLR A1312 " pdb=" C17 CLR A1312 " both_signs ideal model delta sigma weight residual False -2.93 -2.63 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB THR A 377 " pdb=" CA THR A 377 " pdb=" OG1 THR A 377 " pdb=" CG2 THR A 377 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1271 not shown) Planarity restraints: 1282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 3 " -0.336 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG K 3 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG K 3 " -0.047 2.00e-02 2.50e+03 pdb=" N2 NAG K 3 " 0.511 2.00e-02 2.50e+03 pdb=" O7 NAG K 3 " -0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " -0.329 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG A1306 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " -0.057 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " 0.505 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.292 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" C7 NAG K 1 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.418 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.015 2.00e-02 2.50e+03 ... (remaining 1279 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 41 2.57 - 3.15: 6013 3.15 - 3.73: 11050 3.73 - 4.32: 15560 4.32 - 4.90: 26276 Nonbonded interactions: 58940 Sorted by model distance: nonbonded pdb=" NH2 ARG A 801 " pdb=" OE1 GLN A 802 " model vdw 1.986 2.520 nonbonded pdb=" OG1 THR A1039 " pdb=" OD1 ASP A1041 " model vdw 2.187 2.440 nonbonded pdb=" OE1 GLU A 624 " pdb=" OG SER A 881 " model vdw 2.188 2.440 nonbonded pdb=" OG SER A1192 " pdb=" OE1 GLU A1203 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR A 407 " pdb=" O6B LMT A1308 " model vdw 2.248 2.440 ... (remaining 58935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'R' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 0.020 Extract box with map and model: 2.200 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.120 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.006 0.067 7694 Z= 0.383 Angle : 0.880 11.208 10498 Z= 0.435 Chirality : 0.056 0.305 1274 Planarity : 0.017 0.291 1272 Dihedral : 14.527 113.869 3233 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.26 % Allowed : 0.13 % Favored : 99.61 % 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: -4.03 (0.20), residues: 912 helix: -2.75 (0.15), residues: 496 sheet: -1.24 (0.56), residues: 78 loop : -2.63 (0.27), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 953 HIS 0.013 0.002 HIS A1053 PHE 0.037 0.002 PHE A 832 TYR 0.012 0.001 TYR A 546 ARG 0.003 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 425 LEU cc_start: 0.8743 (tp) cc_final: 0.8506 (tp) REVERT: A 517 ASP cc_start: 0.8532 (t0) cc_final: 0.8193 (t0) REVERT: A 543 MET cc_start: 0.7947 (mtp) cc_final: 0.7619 (mtm) REVERT: A 705 LEU cc_start: 0.8308 (tt) cc_final: 0.7661 (mp) REVERT: A 727 ARG cc_start: 0.7302 (mtt-85) cc_final: 0.7081 (mpt-90) REVERT: A 742 ARG cc_start: 0.8706 (ttm-80) cc_final: 0.8491 (ttm-80) REVERT: A 788 MET cc_start: 0.8361 (tpp) cc_final: 0.8138 (tpp) REVERT: A 798 ASP cc_start: 0.8176 (t70) cc_final: 0.7897 (t0) REVERT: A 955 ASP cc_start: 0.7881 (t0) cc_final: 0.7637 (t0) REVERT: A 970 TYR cc_start: 0.8061 (m-80) cc_final: 0.7576 (m-80) REVERT: A 1043 GLN cc_start: 0.6920 (tp-100) cc_final: 0.6693 (tt0) REVERT: A 1050 MET cc_start: 0.9153 (ttt) cc_final: 0.8849 (ttt) outliers start: 2 outliers final: 0 residues processed: 101 average time/residue: 0.2199 time to fit residues: 29.6319 Evaluate side-chains 65 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.0050 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 0.0770 overall best weight: 1.0158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7694 Z= 0.168 Angle : 0.604 9.497 10498 Z= 0.278 Chirality : 0.043 0.334 1274 Planarity : 0.004 0.052 1272 Dihedral : 11.241 109.741 1621 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.90 % Allowed : 5.91 % Favored : 93.20 % 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: -1.94 (0.25), residues: 912 helix: -0.70 (0.22), residues: 500 sheet: -0.99 (0.56), residues: 78 loop : -2.14 (0.29), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 351 HIS 0.008 0.001 HIS A1053 PHE 0.021 0.001 PHE A 930 TYR 0.009 0.001 TYR A 886 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7226 (mt) cc_final: 0.6938 (mp) REVERT: A 517 ASP cc_start: 0.8593 (t0) cc_final: 0.8221 (t0) REVERT: A 543 MET cc_start: 0.7938 (mtp) cc_final: 0.7706 (mtm) REVERT: A 705 LEU cc_start: 0.8018 (tt) cc_final: 0.7332 (mt) REVERT: A 742 ARG cc_start: 0.8828 (ttm-80) cc_final: 0.8599 (ttm170) REVERT: A 747 MET cc_start: 0.8025 (mtp) cc_final: 0.7611 (mtp) REVERT: A 766 MET cc_start: 0.7951 (mmm) cc_final: 0.7344 (mmt) REVERT: A 955 ASP cc_start: 0.7816 (t0) cc_final: 0.7436 (t0) REVERT: A 970 TYR cc_start: 0.8021 (m-80) cc_final: 0.7746 (m-80) REVERT: A 1050 MET cc_start: 0.8979 (ttt) cc_final: 0.8778 (ttt) REVERT: A 1252 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7922 (mp) outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.1923 time to fit residues: 21.5795 Evaluate side-chains 73 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 0.0970 chunk 56 optimal weight: 8.9990 chunk 22 optimal weight: 0.0980 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7694 Z= 0.130 Angle : 0.545 9.442 10498 Z= 0.248 Chirality : 0.040 0.276 1274 Planarity : 0.003 0.036 1272 Dihedral : 9.897 106.981 1621 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.03 % Allowed : 8.99 % Favored : 89.99 % 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: -0.96 (0.27), residues: 912 helix: 0.21 (0.24), residues: 495 sheet: -0.71 (0.56), residues: 78 loop : -1.84 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 351 HIS 0.006 0.001 HIS A1053 PHE 0.014 0.001 PHE A 930 TYR 0.009 0.001 TYR A 886 ARG 0.001 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7184 (mt) cc_final: 0.6895 (mp) REVERT: A 607 MET cc_start: 0.7572 (mmt) cc_final: 0.7294 (mmm) REVERT: A 705 LEU cc_start: 0.7967 (tt) cc_final: 0.7290 (mt) REVERT: A 766 MET cc_start: 0.7994 (mmm) cc_final: 0.7784 (mmt) REVERT: A 955 ASP cc_start: 0.7764 (t0) cc_final: 0.7403 (t0) REVERT: A 970 TYR cc_start: 0.8113 (m-80) cc_final: 0.7775 (m-80) REVERT: A 1252 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7909 (mp) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 0.1828 time to fit residues: 20.8353 Evaluate side-chains 72 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7694 Z= 0.164 Angle : 0.543 9.635 10498 Z= 0.248 Chirality : 0.041 0.272 1274 Planarity : 0.003 0.032 1272 Dihedral : 9.214 104.856 1621 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.41 % Allowed : 11.17 % Favored : 87.42 % 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: -0.45 (0.28), residues: 912 helix: 0.72 (0.25), residues: 490 sheet: -0.69 (0.54), residues: 88 loop : -1.69 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 960 HIS 0.005 0.001 HIS A1053 PHE 0.017 0.001 PHE A 930 TYR 0.008 0.001 TYR A 546 ARG 0.001 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7148 (mt) cc_final: 0.6865 (mp) REVERT: A 378 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7519 (p0) REVERT: A 517 ASP cc_start: 0.8554 (t0) cc_final: 0.8235 (t0) REVERT: A 607 MET cc_start: 0.7671 (mmt) cc_final: 0.7428 (mmt) REVERT: A 705 LEU cc_start: 0.8051 (tt) cc_final: 0.7323 (mt) REVERT: A 720 GLU cc_start: 0.7880 (tp30) cc_final: 0.7274 (tp30) REVERT: A 766 MET cc_start: 0.8037 (mmm) cc_final: 0.7707 (mmm) REVERT: A 851 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 955 ASP cc_start: 0.7778 (t0) cc_final: 0.7390 (t0) REVERT: A 970 TYR cc_start: 0.8059 (m-80) cc_final: 0.7747 (m-80) REVERT: A 1208 MET cc_start: 0.8856 (tpp) cc_final: 0.8575 (tpt) REVERT: A 1252 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7922 (mp) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.1725 time to fit residues: 19.1665 Evaluate side-chains 76 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7694 Z= 0.161 Angle : 0.529 9.604 10498 Z= 0.242 Chirality : 0.040 0.263 1274 Planarity : 0.003 0.030 1272 Dihedral : 8.797 103.174 1621 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.05 % Allowed : 11.94 % Favored : 86.01 % 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: -0.21 (0.28), residues: 912 helix: 0.91 (0.24), residues: 496 sheet: -0.71 (0.52), residues: 88 loop : -1.58 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 960 HIS 0.004 0.001 HIS A1053 PHE 0.017 0.001 PHE A 930 TYR 0.008 0.001 TYR A 546 ARG 0.001 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7115 (mt) cc_final: 0.6836 (mp) REVERT: A 517 ASP cc_start: 0.8500 (t0) cc_final: 0.8179 (t0) REVERT: A 607 MET cc_start: 0.7720 (mmt) cc_final: 0.7453 (mmt) REVERT: A 720 GLU cc_start: 0.7840 (tp30) cc_final: 0.7263 (tp30) REVERT: A 766 MET cc_start: 0.8093 (mmm) cc_final: 0.7846 (mmm) REVERT: A 851 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8280 (tt) REVERT: A 955 ASP cc_start: 0.7779 (t0) cc_final: 0.7380 (t0) REVERT: A 970 TYR cc_start: 0.8047 (m-80) cc_final: 0.7753 (m-80) REVERT: A 1208 MET cc_start: 0.8872 (tpp) cc_final: 0.8552 (tpt) REVERT: A 1252 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7904 (mp) outliers start: 16 outliers final: 8 residues processed: 76 average time/residue: 0.1560 time to fit residues: 17.6599 Evaluate side-chains 73 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7694 Z= 0.131 Angle : 0.516 9.593 10498 Z= 0.234 Chirality : 0.040 0.271 1274 Planarity : 0.003 0.029 1272 Dihedral : 8.292 100.891 1621 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.80 % Allowed : 13.22 % Favored : 84.98 % 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: 0.01 (0.29), residues: 912 helix: 1.10 (0.25), residues: 496 sheet: -0.37 (0.56), residues: 78 loop : -1.55 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 960 HIS 0.005 0.001 HIS A1053 PHE 0.013 0.001 PHE A 930 TYR 0.008 0.001 TYR A 886 ARG 0.001 0.000 ARG A1241 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7086 (mt) cc_final: 0.6812 (mp) REVERT: A 517 ASP cc_start: 0.8453 (t0) cc_final: 0.8100 (t0) REVERT: A 720 GLU cc_start: 0.7865 (tp30) cc_final: 0.7351 (tp30) REVERT: A 851 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 955 ASP cc_start: 0.7744 (t0) cc_final: 0.7352 (t0) REVERT: A 970 TYR cc_start: 0.8013 (m-80) cc_final: 0.7754 (m-80) REVERT: A 1252 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7831 (mp) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.1678 time to fit residues: 20.1180 Evaluate side-chains 77 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 998 MET Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7694 Z= 0.315 Angle : 0.616 11.753 10498 Z= 0.282 Chirality : 0.044 0.248 1274 Planarity : 0.003 0.031 1272 Dihedral : 8.505 100.604 1621 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.57 % Allowed : 12.84 % Favored : 84.60 % 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: -0.17 (0.28), residues: 912 helix: 0.91 (0.24), residues: 498 sheet: -0.65 (0.54), residues: 80 loop : -1.51 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 960 HIS 0.002 0.001 HIS A1053 PHE 0.022 0.002 PHE A 930 TYR 0.010 0.001 TYR A 546 ARG 0.002 0.000 ARG A1241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7130 (mt) cc_final: 0.6855 (mp) REVERT: A 517 ASP cc_start: 0.8500 (t0) cc_final: 0.8137 (t0) REVERT: A 720 GLU cc_start: 0.7915 (tp30) cc_final: 0.7339 (tp30) REVERT: A 955 ASP cc_start: 0.7914 (t0) cc_final: 0.7605 (t0) REVERT: A 970 TYR cc_start: 0.8089 (m-80) cc_final: 0.7710 (m-80) REVERT: A 1252 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7920 (mp) outliers start: 20 outliers final: 14 residues processed: 81 average time/residue: 0.1712 time to fit residues: 20.0782 Evaluate side-chains 84 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 998 MET Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7694 Z= 0.134 Angle : 0.544 10.326 10498 Z= 0.244 Chirality : 0.040 0.264 1274 Planarity : 0.003 0.028 1272 Dihedral : 8.029 98.932 1621 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.05 % Allowed : 13.09 % Favored : 84.85 % 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: 0.13 (0.29), residues: 912 helix: 1.18 (0.25), residues: 496 sheet: -0.36 (0.55), residues: 78 loop : -1.46 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 960 HIS 0.006 0.001 HIS A1053 PHE 0.012 0.001 PHE A 930 TYR 0.007 0.001 TYR A 546 ARG 0.001 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7113 (mt) cc_final: 0.6836 (mp) REVERT: A 517 ASP cc_start: 0.8504 (t0) cc_final: 0.8176 (t0) REVERT: A 720 GLU cc_start: 0.7889 (tp30) cc_final: 0.7365 (tp30) REVERT: A 955 ASP cc_start: 0.7794 (t0) cc_final: 0.7375 (t0) REVERT: A 970 TYR cc_start: 0.8030 (m-80) cc_final: 0.7734 (m-80) REVERT: A 1252 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7871 (mp) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.1618 time to fit residues: 18.3727 Evaluate side-chains 77 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 64 optimal weight: 0.0270 chunk 25 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7694 Z= 0.165 Angle : 0.541 9.861 10498 Z= 0.245 Chirality : 0.041 0.253 1274 Planarity : 0.003 0.028 1272 Dihedral : 7.800 97.736 1621 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.80 % Allowed : 13.22 % Favored : 84.98 % 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: 0.21 (0.29), residues: 912 helix: 1.20 (0.24), residues: 496 sheet: 0.03 (0.58), residues: 68 loop : -1.41 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 960 HIS 0.006 0.001 HIS A1053 PHE 0.014 0.001 PHE A 930 TYR 0.008 0.001 TYR A 546 ARG 0.001 0.000 ARG A1241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7104 (mt) cc_final: 0.6827 (mp) REVERT: A 517 ASP cc_start: 0.8470 (t0) cc_final: 0.8147 (t0) REVERT: A 720 GLU cc_start: 0.7930 (tp30) cc_final: 0.7411 (tp30) REVERT: A 955 ASP cc_start: 0.7811 (t0) cc_final: 0.7391 (t0) REVERT: A 970 TYR cc_start: 0.8030 (m-80) cc_final: 0.7745 (m-80) REVERT: A 1252 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7857 (mp) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.1609 time to fit residues: 18.7846 Evaluate side-chains 81 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.0030 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7694 Z= 0.118 Angle : 0.519 9.536 10498 Z= 0.235 Chirality : 0.039 0.268 1274 Planarity : 0.003 0.027 1272 Dihedral : 7.431 95.590 1621 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.67 % Allowed : 13.86 % Favored : 84.47 % 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: 0.32 (0.29), residues: 912 helix: 1.29 (0.25), residues: 497 sheet: 0.14 (0.58), residues: 68 loop : -1.38 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 960 HIS 0.007 0.001 HIS A1053 PHE 0.012 0.001 PHE A 930 TYR 0.009 0.001 TYR A 886 ARG 0.002 0.000 ARG A1002 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7076 (mt) cc_final: 0.6803 (mp) REVERT: A 517 ASP cc_start: 0.8501 (t0) cc_final: 0.8166 (t0) REVERT: A 955 ASP cc_start: 0.7743 (t0) cc_final: 0.7342 (t0) REVERT: A 970 TYR cc_start: 0.7987 (m-80) cc_final: 0.7750 (m-80) REVERT: A 1252 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7848 (mp) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.1592 time to fit residues: 18.6545 Evaluate side-chains 81 residues out of total 779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.0000 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.091336 restraints weight = 11618.648| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.62 r_work: 0.2970 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7694 Z= 0.118 Angle : 0.519 9.575 10498 Z= 0.235 Chirality : 0.039 0.264 1274 Planarity : 0.003 0.027 1272 Dihedral : 7.185 93.693 1621 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.54 % Allowed : 13.99 % Favored : 84.47 % 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: 0.39 (0.29), residues: 912 helix: 1.36 (0.25), residues: 497 sheet: 0.07 (0.58), residues: 70 loop : -1.34 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 960 HIS 0.007 0.001 HIS A1053 PHE 0.013 0.001 PHE A 832 TYR 0.009 0.001 TYR A 886 ARG 0.002 0.000 ARG A1002 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1739.80 seconds wall clock time: 32 minutes 20.55 seconds (1940.55 seconds total)