Starting phenix.real_space_refine on Fri Jun 6 16:03:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7df8_30662/06_2025/7df8_30662_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7df8_30662/06_2025/7df8_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/cci-nas-00/data/ceres_data/7df8_30662/06_2025/7df8_30662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7df8_30662/06_2025/7df8_30662.map" model { file = "/net/cci-nas-00/data/ceres_data/7df8_30662/06_2025/7df8_30662_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7df8_30662/06_2025/7df8_30662_neut_trim.cif" } 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. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.20, per 1000 atoms: 0.69 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 - 3.00 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 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: 2.33 Conformation dependent library (CDL) restraints added in 984.8 milliseconds 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... Secondary structure from input PDB file: 46 helices and 7 sheets defined 58.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 332 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 351 through 368 removed outlier: 3.697A pdb=" N ILE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 437 through 453 removed outlier: 4.076A pdb=" N GLU A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.659A pdb=" N TYR A 493 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.692A pdb=" N HIS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.516A pdb=" N GLU A 566 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 607 removed outlier: 4.349A pdb=" N ALA A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) 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 619 through 626 removed outlier: 3.626A pdb=" N ILE A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.863A pdb=" N LEU A 633 " --> pdb=" O THR A 629 " (cutoff:3.500A) Proline residue: A 634 - end of helix Processing helix chain 'A' and resid 637 through 647 removed outlier: 3.933A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 690 removed outlier: 3.543A pdb=" N GLY A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) 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) removed outlier: 3.733A pdb=" N LEU A 690 " --> pdb=" O PHE A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.733A pdb=" N VAL A 702 " --> pdb=" O ILE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 724 removed outlier: 3.563A pdb=" N PHE A 715 " --> pdb=" O ALA A 711 " (cutoff:3.500A) 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 731 through 742 Processing helix chain 'A' and resid 743 through 761 Processing helix chain 'A' and resid 762 through 764 No H-bonds generated for 'chain 'A' and resid 762 through 764' Processing helix chain 'A' and resid 766 through 790 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 790 through 802 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) Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 844 through 864 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) Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 872 through 877 removed outlier: 3.603A pdb=" N ALA A 876 " --> pdb=" O GLN A 873 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 877 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 894 removed outlier: 3.637A pdb=" N TYR A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 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 929 through 938 removed outlier: 3.620A pdb=" N THR A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 1004 through 1016 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 1058 through 1081 removed outlier: 3.827A pdb=" N TYR A1062 " --> pdb=" O ASN A1058 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1103 removed outlier: 4.055A pdb=" N TYR A1102 " --> pdb=" O THR A1098 " (cutoff:3.500A) 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 1107 through 1118 removed outlier: 3.794A pdb=" N GLU A1111 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1125 Processing helix chain 'A' and resid 1126 through 1131 Processing helix chain 'A' and resid 1140 through 1160 Processing helix chain 'A' and resid 1164 through 1176 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) removed outlier: 3.569A pdb=" N GLY A1176 " --> pdb=" O VAL A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1191 removed outlier: 3.830A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) 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 1196 through 1216 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 1220 through 1226 Processing helix chain 'A' and resid 1227 through 1229 No H-bonds generated for 'chain 'A' and resid 1227 through 1229' Processing helix chain 'A' and resid 1232 through 1239 Processing helix chain 'A' and resid 1240 through 1255 removed outlier: 3.513A pdb=" N LEU A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1266 removed outlier: 3.977A pdb=" N TYR A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA3, first strand: chain 'A' and resid 420 through 423 Processing sheet with id=AA4, 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=AA5, first strand: chain 'A' and resid 505 through 508 Processing sheet with id=AA6, first strand: chain 'A' and resid 946 through 951 removed outlier: 6.707A pdb=" N TYR A1052 " --> pdb=" O ALA A 947 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET A1050 " --> pdb=" O PRO A 949 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.914A pdb=" N ALA A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 969 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: 2.20 Time building geometry restraints manager: 2.70 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: 0.00 - 2.24: 10139 2.24 - 4.48: 306 4.48 - 6.72: 41 6.72 - 8.97: 10 8.97 - 11.21: 2 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: 5990 3.15 - 3.73: 11000 3.73 - 4.32: 15457 4.32 - 4.90: 26240 Nonbonded interactions: 58728 Sorted by model distance: nonbonded pdb=" NH2 ARG A 801 " pdb=" OE1 GLN A 802 " model vdw 1.986 3.120 nonbonded pdb=" OG1 THR A1039 " pdb=" OD1 ASP A1041 " model vdw 2.187 3.040 nonbonded pdb=" OE1 GLU A 624 " pdb=" OG SER A 881 " model vdw 2.188 3.040 nonbonded pdb=" OG SER A1192 " pdb=" OE1 GLU A1203 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR A 407 " pdb=" O6B LMT A1308 " model vdw 2.248 3.040 ... (remaining 58723 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 '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: 0.520 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.940 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- 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 7714 Z= 0.283 Angle : 0.914 14.373 10553 Z= 0.443 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 10) link_NAG-ASN : angle 4.44123 ( 30) link_BETA1-4 : bond 0.00415 ( 5) link_BETA1-4 : angle 1.20722 ( 15) hydrogen bonds : bond 0.22560 ( 329) hydrogen bonds : angle 7.71946 ( 969) SS BOND : bond 0.00248 ( 5) SS BOND : angle 2.73473 ( 10) covalent geometry : bond 0.00608 ( 7694) covalent geometry : angle 0.88009 (10498) *********************** 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 to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.901 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: 0.2258 time to fit residues: 30.5974 Evaluate side-chains 65 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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: 0.0030 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.088832 restraints weight = 11644.050| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.61 r_work: 0.2938 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7714 Z= 0.122 Angle : 0.663 11.390 10553 Z= 0.303 Chirality : 0.043 0.323 1274 Planarity : 0.005 0.052 1272 Dihedral : 10.824 108.329 1621 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.77 % Allowed : 5.52 % Favored : 93.71 % 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: -1.75 (0.26), residues: 912 helix: -0.49 (0.22), residues: 494 sheet: -1.12 (0.55), residues: 84 loop : -2.07 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 960 HIS 0.007 0.001 HIS A1053 PHE 0.020 0.001 PHE A 930 TYR 0.009 0.001 TYR A 886 ARG 0.002 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 10) link_NAG-ASN : angle 3.82021 ( 30) link_BETA1-4 : bond 0.00743 ( 5) link_BETA1-4 : angle 1.77580 ( 15) hydrogen bonds : bond 0.04402 ( 329) hydrogen bonds : angle 4.64951 ( 969) SS BOND : bond 0.00179 ( 5) SS BOND : angle 1.07639 ( 10) covalent geometry : bond 0.00264 ( 7694) covalent geometry : angle 0.62796 (10498) *********************** 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 89 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7549 (mt) cc_final: 0.7263 (mp) REVERT: A 430 LYS cc_start: 0.8559 (mttm) cc_final: 0.8337 (mttt) REVERT: A 543 MET cc_start: 0.8544 (mtp) cc_final: 0.8307 (mtm) REVERT: A 705 LEU cc_start: 0.8500 (tt) cc_final: 0.7843 (mt) REVERT: A 727 ARG cc_start: 0.7412 (mtt-85) cc_final: 0.7197 (mpt-90) REVERT: A 766 MET cc_start: 0.8311 (mmm) cc_final: 0.7771 (mmt) REVERT: A 955 ASP cc_start: 0.8574 (t0) cc_final: 0.8236 (t0) REVERT: A 970 TYR cc_start: 0.8079 (m-80) cc_final: 0.7706 (m-80) REVERT: A 1252 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8409 (mp) outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 0.1889 time to fit residues: 22.5981 Evaluate side-chains 70 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 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 74 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** A 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.084421 restraints weight = 11982.671| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.61 r_work: 0.2869 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 7714 Z= 0.271 Angle : 0.730 10.371 10553 Z= 0.337 Chirality : 0.047 0.254 1274 Planarity : 0.004 0.038 1272 Dihedral : 10.493 107.347 1621 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.54 % Allowed : 9.24 % Favored : 89.22 % 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: -1.08 (0.27), residues: 912 helix: 0.11 (0.24), residues: 496 sheet: -1.04 (0.54), residues: 84 loop : -1.81 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 960 HIS 0.003 0.001 HIS A1053 PHE 0.028 0.002 PHE A 930 TYR 0.011 0.001 TYR A 546 ARG 0.002 0.000 ARG A 627 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 10) link_NAG-ASN : angle 3.77752 ( 30) link_BETA1-4 : bond 0.00718 ( 5) link_BETA1-4 : angle 1.79498 ( 15) hydrogen bonds : bond 0.04984 ( 329) hydrogen bonds : angle 4.47098 ( 969) SS BOND : bond 0.00422 ( 5) SS BOND : angle 1.19262 ( 10) covalent geometry : bond 0.00662 ( 7694) covalent geometry : angle 0.69947 (10498) *********************** 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 82 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7597 (mt) cc_final: 0.7311 (mp) REVERT: A 727 ARG cc_start: 0.7495 (mtt-85) cc_final: 0.7264 (mpt-90) REVERT: A 851 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8569 (tt) REVERT: A 955 ASP cc_start: 0.8640 (t0) cc_final: 0.8303 (t0) REVERT: A 970 TYR cc_start: 0.8139 (m-80) cc_final: 0.7755 (m-80) REVERT: A 1252 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8476 (mp) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.1635 time to fit residues: 18.9116 Evaluate side-chains 75 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 513 THR 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 859 VAL Chi-restraints excluded: chain A residue 1175 VAL 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 79 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.112101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.088308 restraints weight = 11725.320| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.60 r_work: 0.2929 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7714 Z= 0.107 Angle : 0.596 9.535 10553 Z= 0.271 Chirality : 0.041 0.263 1274 Planarity : 0.003 0.032 1272 Dihedral : 9.695 106.064 1621 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.54 % Allowed : 11.68 % Favored : 86.78 % 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: -0.52 (0.28), residues: 912 helix: 0.59 (0.24), residues: 501 sheet: -0.86 (0.55), residues: 84 loop : -1.63 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 960 HIS 0.006 0.001 HIS A1053 PHE 0.012 0.001 PHE A 704 TYR 0.008 0.001 TYR A 886 ARG 0.001 0.000 ARG A 693 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 10) link_NAG-ASN : angle 3.18136 ( 30) link_BETA1-4 : bond 0.00635 ( 5) link_BETA1-4 : angle 1.55939 ( 15) hydrogen bonds : bond 0.03545 ( 329) hydrogen bonds : angle 4.17316 ( 969) SS BOND : bond 0.00176 ( 5) SS BOND : angle 0.71924 ( 10) covalent geometry : bond 0.00243 ( 7694) covalent geometry : angle 0.56914 (10498) *********************** 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 83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7529 (mt) cc_final: 0.7252 (mp) REVERT: A 517 ASP cc_start: 0.8572 (t0) cc_final: 0.8307 (t0) REVERT: A 607 MET cc_start: 0.8096 (mmt) cc_final: 0.7887 (mmt) REVERT: A 727 ARG cc_start: 0.7445 (mtt-85) cc_final: 0.7227 (mpt-90) REVERT: A 955 ASP cc_start: 0.8533 (t0) cc_final: 0.8235 (t0) REVERT: A 970 TYR cc_start: 0.8285 (m-80) cc_final: 0.7872 (m-80) REVERT: A 1208 MET cc_start: 0.9133 (tpp) cc_final: 0.8927 (tpt) REVERT: A 1252 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8467 (mp) outliers start: 12 outliers final: 8 residues processed: 79 average time/residue: 0.1749 time to fit residues: 19.9370 Evaluate side-chains 75 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.637 ------------------------------------------------------------------------------- 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 631 GLU 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 1226 VAL 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 88 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 0.0020 overall best weight: 1.5192 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.111819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.087654 restraints weight = 11717.558| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.61 r_work: 0.2909 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7714 Z= 0.127 Angle : 0.601 9.622 10553 Z= 0.272 Chirality : 0.042 0.252 1274 Planarity : 0.003 0.029 1272 Dihedral : 9.220 105.104 1621 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.18 % Allowed : 13.22 % 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: -0.24 (0.28), residues: 912 helix: 0.85 (0.24), residues: 501 sheet: -0.80 (0.54), residues: 84 loop : -1.52 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.004 0.001 HIS A1053 PHE 0.016 0.001 PHE A 930 TYR 0.007 0.001 TYR A 546 ARG 0.001 0.000 ARG A 723 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 10) link_NAG-ASN : angle 3.12873 ( 30) link_BETA1-4 : bond 0.00596 ( 5) link_BETA1-4 : angle 1.70319 ( 15) hydrogen bonds : bond 0.03616 ( 329) hydrogen bonds : angle 4.07518 ( 969) SS BOND : bond 0.00218 ( 5) SS BOND : angle 0.72507 ( 10) covalent geometry : bond 0.00302 ( 7694) covalent geometry : angle 0.57483 (10498) *********************** 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 87 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7477 (mt) cc_final: 0.7198 (mp) REVERT: A 607 MET cc_start: 0.8090 (mmt) cc_final: 0.7881 (mmt) REVERT: A 727 ARG cc_start: 0.7411 (mtt-85) cc_final: 0.7209 (mpt-90) REVERT: A 955 ASP cc_start: 0.8528 (t0) cc_final: 0.8253 (t0) REVERT: A 970 TYR cc_start: 0.8281 (m-80) cc_final: 0.7879 (m-80) REVERT: A 1252 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8453 (mp) outliers start: 17 outliers final: 11 residues processed: 83 average time/residue: 0.1614 time to fit residues: 19.6957 Evaluate side-chains 80 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER 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 705 LEU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1226 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 72 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.111344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.087195 restraints weight = 11699.700| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.60 r_work: 0.2908 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7714 Z= 0.145 Angle : 0.613 11.423 10553 Z= 0.276 Chirality : 0.042 0.246 1274 Planarity : 0.003 0.028 1272 Dihedral : 9.000 104.507 1621 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.05 % Allowed : 13.86 % Favored : 84.08 % 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: -0.12 (0.29), residues: 912 helix: 0.95 (0.25), residues: 501 sheet: -0.73 (0.54), residues: 84 loop : -1.49 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 960 HIS 0.004 0.001 HIS A1053 PHE 0.016 0.001 PHE A 930 TYR 0.008 0.001 TYR A 654 ARG 0.002 0.000 ARG A1200 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 10) link_NAG-ASN : angle 3.09504 ( 30) link_BETA1-4 : bond 0.00603 ( 5) link_BETA1-4 : angle 1.74784 ( 15) hydrogen bonds : bond 0.03688 ( 329) hydrogen bonds : angle 4.08492 ( 969) SS BOND : bond 0.00238 ( 5) SS BOND : angle 0.72761 ( 10) covalent geometry : bond 0.00349 ( 7694) covalent geometry : angle 0.58749 (10498) *********************** 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 83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7489 (mt) cc_final: 0.7210 (mp) REVERT: A 727 ARG cc_start: 0.7397 (mtt-85) cc_final: 0.7176 (mpt-90) REVERT: A 955 ASP cc_start: 0.8536 (t0) cc_final: 0.8255 (t0) REVERT: A 970 TYR cc_start: 0.8293 (m-80) cc_final: 0.7879 (m-80) REVERT: A 1252 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8455 (mp) outliers start: 16 outliers final: 14 residues processed: 79 average time/residue: 0.1794 time to fit residues: 20.6759 Evaluate side-chains 81 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER 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 550 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1226 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8613 > 50: distance: 13 - 23: 3.069 distance: 15 - 32: 3.230 distance: 86 - 100: 35.606 distance: 90 - 111: 32.212 distance: 95 - 116: 34.028 distance: 98 - 100: 35.246 distance: 99 - 124: 33.606 distance: 100 - 101: 56.473 distance: 101 - 102: 57.111 distance: 101 - 104: 39.545 distance: 102 - 103: 40.271 distance: 102 - 111: 68.671 distance: 103 - 128: 3.853 distance: 104 - 105: 68.192 distance: 105 - 106: 39.416 distance: 106 - 107: 56.860 distance: 107 - 108: 38.915 distance: 108 - 109: 56.531 distance: 108 - 110: 40.324 distance: 111 - 112: 39.468 distance: 112 - 113: 41.160 distance: 112 - 115: 41.480 distance: 113 - 114: 39.846 distance: 113 - 116: 56.453 distance: 116 - 117: 55.339 distance: 117 - 118: 41.284 distance: 117 - 120: 39.297 distance: 118 - 119: 40.635 distance: 118 - 124: 39.915 distance: 121 - 122: 39.657 distance: 124 - 125: 39.135 distance: 126 - 127: 39.648 distance: 126 - 128: 39.535 distance: 129 - 130: 69.542 distance: 129 - 132: 41.047 distance: 130 - 139: 55.798 distance: 132 - 133: 40.686 distance: 136 - 137: 57.234 distance: 136 - 138: 39.406 distance: 140 - 141: 40.263 distance: 140 - 143: 68.840 distance: 142 - 164: 38.203 distance: 143 - 145: 41.108 distance: 146 - 147: 40.125 distance: 147 - 148: 39.696 distance: 147 - 150: 40.302 distance: 148 - 151: 55.801 distance: 149 - 172: 35.777 distance: 151 - 152: 55.911 distance: 151 - 157: 57.654 distance: 152 - 153: 41.100 distance: 152 - 155: 39.487 distance: 153 - 154: 38.836 distance: 153 - 158: 69.972 distance: 154 - 180: 35.360 distance: 155 - 156: 55.220 distance: 156 - 157: 39.546 distance: 159 - 162: 55.277 distance: 160 - 161: 41.092 distance: 160 - 164: 40.401 distance: 161 - 187: 34.280 distance: 162 - 163: 39.884 distance: 165 - 166: 40.756 distance: 165 - 168: 39.760 distance: 166 - 172: 34.786 distance: 167 - 192: 34.197 distance: 168 - 169: 56.525