Starting phenix.real_space_refine on Wed Jun 11 15:55:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kya_23073/06_2025/7kya_23073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kya_23073/06_2025/7kya_23073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kya_23073/06_2025/7kya_23073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kya_23073/06_2025/7kya_23073.map" model { file = "/net/cci-nas-00/data/ceres_data/7kya_23073/06_2025/7kya_23073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kya_23073/06_2025/7kya_23073.cif" } resolution = 3.5 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= 0.003 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 62 5.16 5 Be 1 3.05 5 C 8163 2.51 5 N 2074 2.21 5 O 2352 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 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: 12656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 9384 Classifications: {'peptide': 1174} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1134} Chain breaks: 3 Chain: "B" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2989 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Unusual residues: {' MG': 1, 'BEF': 1, 'CLR': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.33, per 1000 atoms: 0.66 Number of scatterers: 12656 At special positions: 0 Unit cell: (139.594, 118.944, 138.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 62 16.00 Mg 1 11.99 F 3 9.00 O 2352 8.00 N 2074 7.00 C 8163 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B2002 " - " ASN B 113 " " NAG C 1 " - " ASN B 298 " " NAG D 1 " - " ASN B 240 " " NAG E 1 " - " ASN B 256 " " NAG F 1 " - " ASN B 332 " Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.9 seconds 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2902 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 44.7% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 243 through 253 Processing helix chain 'A' and resid 255 through 270 removed outlier: 3.621A pdb=" N ILE A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 removed outlier: 3.778A pdb=" N PHE A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 281 through 312 removed outlier: 4.310A pdb=" N LEU A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.864A pdb=" N ILE A 500 " --> pdb=" O CYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.526A pdb=" N THR A 574 " --> pdb=" O GLY A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.808A pdb=" N GLU A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 617 " --> pdb=" O GLY A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 640 through 654 removed outlier: 3.914A pdb=" N ILE A 652 " --> pdb=" O TRP A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 701 through 704 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 753 through 779 removed outlier: 3.745A pdb=" N SER A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 789 removed outlier: 3.519A pdb=" N ASP A 788 " --> pdb=" O CYS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 removed outlier: 3.502A pdb=" N GLU A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 820 removed outlier: 3.781A pdb=" N GLN A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 856 removed outlier: 3.667A pdb=" N LEU A 856 " --> pdb=" O THR A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.593A pdb=" N ARG A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 948 removed outlier: 3.741A pdb=" N THR A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 978 removed outlier: 3.812A pdb=" N ALA A 978 " --> pdb=" O ASP A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 4.401A pdb=" N GLU A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1025 removed outlier: 3.656A pdb=" N ALA A1019 " --> pdb=" O PRO A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1046 removed outlier: 3.902A pdb=" N ALA A1039 " --> pdb=" O LYS A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1084 Processing helix chain 'A' and resid 1096 through 1101 Processing helix chain 'A' and resid 1102 through 1104 No H-bonds generated for 'chain 'A' and resid 1102 through 1104' Processing helix chain 'A' and resid 1116 through 1124 Processing helix chain 'A' and resid 1126 through 1139 removed outlier: 3.790A pdb=" N ASN A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1163 Processing helix chain 'A' and resid 1174 through 1176 No H-bonds generated for 'chain 'A' and resid 1174 through 1176' Processing helix chain 'A' and resid 1177 through 1183 Processing helix chain 'A' and resid 1208 through 1210 No H-bonds generated for 'chain 'A' and resid 1208 through 1210' Processing helix chain 'A' and resid 1211 through 1216 Processing helix chain 'A' and resid 1218 through 1248 Proline residue: A1232 - end of helix removed outlier: 3.691A pdb=" N ASN A1238 " --> pdb=" O PHE A1234 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A1239 " --> pdb=" O PHE A1235 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A1241 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER A1244 " --> pdb=" O ILE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1250 No H-bonds generated for 'chain 'A' and resid 1249 through 1250' Processing helix chain 'A' and resid 1251 through 1255 removed outlier: 4.007A pdb=" N PHE A1254 " --> pdb=" O TYR A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1283 removed outlier: 3.971A pdb=" N VAL A1277 " --> pdb=" O THR A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1295 Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing helix chain 'A' and resid 1299 through 1304 Processing helix chain 'A' and resid 1309 through 1336 Proline residue: A1331 - end of helix Processing helix chain 'A' and resid 1350 through 1373 Processing helix chain 'A' and resid 1380 through 1401 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1418 through 1444 removed outlier: 3.849A pdb=" N TRP A1422 " --> pdb=" O GLN A1418 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) Proline residue: A1435 - end of helix Processing helix chain 'A' and resid 1449 through 1461 Processing helix chain 'B' and resid 75 through 98 Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.547A pdb=" N ALA B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.800A pdb=" N LEU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 231 through 237 removed outlier: 4.625A pdb=" N ALA B 235 " --> pdb=" O CYS B 231 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.973A pdb=" N GLU B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 372 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 210 Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 441 removed outlier: 3.930A pdb=" N HIS A 316 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE A 451 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET A 564 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 458 through 459 removed outlier: 3.761A pdb=" N ASP A 458 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AA5, first strand: chain 'A' and resid 693 through 694 removed outlier: 3.919A pdb=" N THR A 693 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A1205 " --> pdb=" O THR A 693 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1027 through 1030 removed outlier: 6.667A pdb=" N MET A1167 " --> pdb=" O ILE A 706 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 732 through 734 removed outlier: 5.776A pdb=" N ARG A1009 " --> pdb=" O GLN A 719 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 721 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU A1007 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU A 723 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA A1005 " --> pdb=" O GLU A 723 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS A 725 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N GLY A1003 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N CYS A 727 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 11.895A pdb=" N LEU A1001 " --> pdb=" O CYS A 727 " (cutoff:3.500A) removed outlier: 11.741A pdb=" N ILE A 729 " --> pdb=" O ILE A 999 " (cutoff:3.500A) removed outlier: 14.739A pdb=" N ILE A 999 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU A1000 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLN A 958 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A1006 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS A 899 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 881 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 826 through 829 Processing sheet with id=AA9, first strand: chain 'A' and resid 858 through 861 Processing sheet with id=AB1, first strand: chain 'A' and resid 1054 through 1058 Processing sheet with id=AB2, first strand: chain 'A' and resid 1377 through 1378 Processing sheet with id=AB3, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.345A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 119 through 120 removed outlier: 5.905A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1560 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: 4.78 Time building geometry restraints manager: 3.95 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: 3984 1.34 - 1.46: 2013 1.46 - 1.57: 6858 1.57 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 12948 Sorted by residual: bond pdb=" F1 BEF A1703 " pdb="BE BEF A1703 " ideal model delta sigma weight residual 1.476 1.766 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" F3 BEF A1703 " pdb="BE BEF A1703 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" F2 BEF A1703 " pdb="BE BEF A1703 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.97e+00 ... (remaining 12943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 17178 1.71 - 3.43: 325 3.43 - 5.14: 59 5.14 - 6.85: 25 6.85 - 8.57: 5 Bond angle restraints: 17592 Sorted by residual: angle pdb=" N HIS A1336 " pdb=" CA HIS A1336 " pdb=" C HIS A1336 " ideal model delta sigma weight residual 112.38 120.95 -8.57 1.22e+00 6.72e-01 4.93e+01 angle pdb=" N HIS A 254 " pdb=" CA HIS A 254 " pdb=" C HIS A 254 " ideal model delta sigma weight residual 111.36 104.98 6.38 1.09e+00 8.42e-01 3.43e+01 angle pdb=" C TYR A1251 " pdb=" N ASN A1252 " pdb=" CA ASN A1252 " ideal model delta sigma weight residual 126.45 119.14 7.31 1.77e+00 3.19e-01 1.70e+01 angle pdb=" N ASN A1252 " pdb=" CA ASN A1252 " pdb=" CB ASN A1252 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" N LEU A1243 " pdb=" CA LEU A1243 " pdb=" C LEU A1243 " ideal model delta sigma weight residual 111.71 108.27 3.44 1.15e+00 7.56e-01 8.96e+00 ... (remaining 17587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.36: 7584 24.36 - 48.73: 419 48.73 - 73.09: 49 73.09 - 97.46: 10 97.46 - 121.82: 6 Dihedral angle restraints: 8068 sinusoidal: 3556 harmonic: 4512 Sorted by residual: dihedral pdb=" CA LYS B 170 " pdb=" C LYS B 170 " pdb=" N ASN B 171 " pdb=" CA ASN B 171 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ILE A1250 " pdb=" C ILE A1250 " pdb=" N TYR A1251 " pdb=" CA TYR A1251 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C5 NAG C 2 " ideal model delta sinusoidal sigma weight residual -62.96 58.86 -121.82 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 8065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1815 0.075 - 0.150: 166 0.150 - 0.224: 7 0.224 - 0.299: 9 0.299 - 0.374: 7 Chirality restraints: 2004 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.61e+00 chirality pdb=" C14 CLR A1701 " pdb=" C13 CLR A1701 " pdb=" C15 CLR A1701 " pdb=" C8 CLR A1701 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C14 CLR A1705 " pdb=" C13 CLR A1705 " pdb=" C15 CLR A1705 " pdb=" C8 CLR A1705 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 2001 not shown) Planarity restraints: 2202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.081 2.00e-02 2.50e+03 6.65e-02 5.53e+01 pdb=" C7 NAG D 1 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.061 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.105 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 240 " -0.017 2.00e-02 2.50e+03 6.23e-02 4.86e+01 pdb=" CG ASN B 240 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 240 " 0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN B 240 " -0.100 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1335 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C TYR A1335 " -0.037 2.00e-02 2.50e+03 pdb=" O TYR A1335 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS A1336 " 0.013 2.00e-02 2.50e+03 ... (remaining 2199 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 1 2.19 - 2.86: 4694 2.86 - 3.54: 17327 3.54 - 4.22: 29035 4.22 - 4.90: 51447 Nonbonded interactions: 102504 Sorted by model distance: nonbonded pdb=" OG1 THR A 714 " pdb="MG MG A1702 " model vdw 1.508 2.170 nonbonded pdb=" CG2 ILE A 869 " pdb=" OE2 GLU A 878 " model vdw 2.199 3.460 nonbonded pdb=" OG SER A 779 " pdb=" O GLN A 873 " model vdw 2.215 3.040 nonbonded pdb=" O GLU A 997 " pdb=" CD1 LEU A 998 " model vdw 2.240 3.460 nonbonded pdb=" OH TYR A1264 " pdb=" OG1 THR A1396 " model vdw 2.252 3.040 ... (remaining 102499 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 'C' and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or name O6 or n \ ame O7 )) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 32.620 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 38.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 0.290 12960 Z= 0.275 Angle : 0.663 24.715 17626 Z= 0.336 Chirality : 0.050 0.374 2004 Planarity : 0.003 0.067 2197 Dihedral : 14.653 121.824 5160 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.24 % Favored : 92.63 % Rotamer: Outliers : 1.03 % Allowed : 12.98 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -3.21 (0.19), residues: 1533 helix: -1.11 (0.19), residues: 615 sheet: -2.35 (0.33), residues: 208 loop : -3.00 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1247 HIS 0.003 0.000 HIS A 520 PHE 0.012 0.001 PHE A1357 TYR 0.013 0.001 TYR B 280 ARG 0.002 0.000 ARG B 316 Details of bonding type rmsd link_NAG-ASN : bond 0.04567 ( 5) link_NAG-ASN : angle 7.26247 ( 15) link_ALPHA1-4 : bond 0.00458 ( 1) link_ALPHA1-4 : angle 2.22221 ( 3) link_BETA1-4 : bond 0.00616 ( 4) link_BETA1-4 : angle 1.48234 ( 12) hydrogen bonds : bond 0.15655 ( 557) hydrogen bonds : angle 6.14207 ( 1560) SS BOND : bond 0.00050 ( 2) SS BOND : angle 0.32047 ( 4) covalent geometry : bond 0.00548 (12948) covalent geometry : angle 0.62653 (17592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 237 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.7932 (t80) cc_final: 0.7633 (t80) REVERT: A 761 LYS cc_start: 0.8150 (tptp) cc_final: 0.7940 (tptp) REVERT: A 809 GLN cc_start: 0.6699 (tm-30) cc_final: 0.6403 (tm-30) REVERT: A 813 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6314 (pt0) REVERT: A 928 ARG cc_start: 0.5214 (OUTLIER) cc_final: 0.3335 (mmt-90) REVERT: A 935 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7270 (pt) REVERT: B 111 MET cc_start: 0.7872 (ttp) cc_final: 0.7657 (ttp) outliers start: 14 outliers final: 9 residues processed: 247 average time/residue: 0.2733 time to fit residues: 95.0461 Evaluate side-chains 186 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1408 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 0.0000 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 73 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 232 ASN A 248 ASN A 311 ASN A 433 ASN A 527 GLN A 579 ASN A 655 GLN A 720 ASN A 876 GLN A1176 ASN A1269 ASN A1297 GLN A1374 GLN B 50 ASN B 60 GLN B 96 GLN B 246 GLN B 341 GLN B 366 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116350 restraints weight = 13402.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116597 restraints weight = 9063.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117883 restraints weight = 7016.294| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12960 Z= 0.128 Angle : 0.595 11.198 17626 Z= 0.296 Chirality : 0.044 0.260 2004 Planarity : 0.004 0.048 2197 Dihedral : 8.960 95.939 2244 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.39 % Allowed : 15.56 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -2.24 (0.21), residues: 1533 helix: -0.30 (0.20), residues: 649 sheet: -1.81 (0.34), residues: 215 loop : -2.59 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 648 HIS 0.003 0.001 HIS A 520 PHE 0.015 0.001 PHE B 320 TYR 0.018 0.001 TYR B 136 ARG 0.006 0.000 ARG A 925 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 5) link_NAG-ASN : angle 1.77349 ( 15) link_ALPHA1-4 : bond 0.00890 ( 1) link_ALPHA1-4 : angle 2.33880 ( 3) link_BETA1-4 : bond 0.00710 ( 4) link_BETA1-4 : angle 1.56206 ( 12) hydrogen bonds : bond 0.04434 ( 557) hydrogen bonds : angle 4.71920 ( 1560) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.33951 ( 4) covalent geometry : bond 0.00282 (12948) covalent geometry : angle 0.59062 (17592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 809 GLN cc_start: 0.6602 (tm-30) cc_final: 0.6157 (tm-30) REVERT: A 813 GLU cc_start: 0.6535 (tm-30) cc_final: 0.5873 (pp20) REVERT: A 928 ARG cc_start: 0.5657 (OUTLIER) cc_final: 0.3813 (mpt180) REVERT: B 111 MET cc_start: 0.7944 (ttp) cc_final: 0.7694 (ttp) outliers start: 46 outliers final: 25 residues processed: 234 average time/residue: 0.2593 time to fit residues: 88.5540 Evaluate side-chains 196 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1185 ASP Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 373 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 87 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN A 873 GLN ** A1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113468 restraints weight = 13644.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115448 restraints weight = 9291.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116608 restraints weight = 6827.671| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12960 Z= 0.143 Angle : 0.601 10.626 17626 Z= 0.300 Chirality : 0.044 0.220 2004 Planarity : 0.004 0.049 2197 Dihedral : 7.880 87.362 2235 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.32 % Allowed : 17.40 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.76 (0.21), residues: 1533 helix: 0.15 (0.21), residues: 638 sheet: -1.59 (0.35), residues: 216 loop : -2.32 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 648 HIS 0.003 0.001 HIS B 347 PHE 0.019 0.001 PHE A1313 TYR 0.020 0.001 TYR A1447 ARG 0.008 0.000 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 5) link_NAG-ASN : angle 2.22649 ( 15) link_ALPHA1-4 : bond 0.01124 ( 1) link_ALPHA1-4 : angle 2.57096 ( 3) link_BETA1-4 : bond 0.00641 ( 4) link_BETA1-4 : angle 2.01977 ( 12) hydrogen bonds : bond 0.04262 ( 557) hydrogen bonds : angle 4.55850 ( 1560) SS BOND : bond 0.00114 ( 2) SS BOND : angle 0.27576 ( 4) covalent geometry : bond 0.00326 (12948) covalent geometry : angle 0.59439 (17592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8034 (t160) cc_final: 0.7629 (t0) REVERT: A 809 GLN cc_start: 0.6733 (tm-30) cc_final: 0.6455 (tm-30) REVERT: A 928 ARG cc_start: 0.5822 (OUTLIER) cc_final: 0.3981 (mmt-90) REVERT: A 930 GLN cc_start: 0.3863 (OUTLIER) cc_final: 0.3598 (pp30) REVERT: B 111 MET cc_start: 0.7879 (ttp) cc_final: 0.7643 (ttp) REVERT: B 292 MET cc_start: 0.7414 (ttt) cc_final: 0.7122 (ttt) outliers start: 45 outliers final: 29 residues processed: 212 average time/residue: 0.2393 time to fit residues: 75.6091 Evaluate side-chains 195 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 928 ARG Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 373 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 91 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 579 ASN A1238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.153494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114202 restraints weight = 13714.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113103 restraints weight = 9695.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115184 restraints weight = 7924.476| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12960 Z= 0.147 Angle : 0.594 10.213 17626 Z= 0.296 Chirality : 0.043 0.190 2004 Planarity : 0.004 0.046 2197 Dihedral : 7.332 80.760 2235 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.98 % Allowed : 17.77 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.63 (0.22), residues: 1533 helix: 0.22 (0.20), residues: 646 sheet: -1.48 (0.36), residues: 216 loop : -2.26 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 648 HIS 0.003 0.001 HIS B 347 PHE 0.019 0.001 PHE A1313 TYR 0.017 0.001 TYR B 136 ARG 0.005 0.000 ARG A 925 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 5) link_NAG-ASN : angle 2.08763 ( 15) link_ALPHA1-4 : bond 0.01215 ( 1) link_ALPHA1-4 : angle 2.71406 ( 3) link_BETA1-4 : bond 0.00781 ( 4) link_BETA1-4 : angle 2.59169 ( 12) hydrogen bonds : bond 0.04184 ( 557) hydrogen bonds : angle 4.49530 ( 1560) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.29628 ( 4) covalent geometry : bond 0.00338 (12948) covalent geometry : angle 0.58629 (17592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3066 Ramachandran restraints generated. 1533 Oldfield, 0 Emsley, 1533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 ASN cc_start: 0.8043 (t160) cc_final: 0.7778 (t0) REVERT: A 809 GLN cc_start: 0.6599 (tm-30) cc_final: 0.6397 (tm-30) REVERT: A 813 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5988 (pt0) REVERT: A 930 GLN cc_start: 0.3761 (OUTLIER) cc_final: 0.3477 (pp30) REVERT: B 111 MET cc_start: 0.7935 (ttp) cc_final: 0.7695 (ttp) REVERT: B 137 ASN cc_start: 0.5701 (OUTLIER) cc_final: 0.5302 (p0) outliers start: 54 outliers final: 37 residues processed: 207 average time/residue: 0.2340 time to fit residues: 72.7659 Evaluate side-chains 198 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1252 ASN Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1336 HIS Chi-restraints excluded: chain A residue 1349 ASP Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain A residue 1370 VAL Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1408 PHE Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 373 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 61.5855 > 50: distance: 16 - 116: 13.145 distance: 19 - 113: 26.201 distance: 91 - 95: 29.309 distance: 95 - 96: 33.496 distance: 96 - 97: 25.447 distance: 96 - 99: 35.168 distance: 97 - 98: 17.725 distance: 97 - 103: 37.550 distance: 99 - 100: 20.434 distance: 100 - 101: 34.110 distance: 100 - 102: 28.206 distance: 103 - 104: 19.382 distance: 104 - 105: 20.458 distance: 104 - 107: 10.331 distance: 105 - 106: 19.290 distance: 105 - 108: 8.416 distance: 108 - 109: 26.806 distance: 109 - 110: 33.125 distance: 109 - 112: 23.122 distance: 110 - 111: 17.212 distance: 110 - 113: 23.190 distance: 113 - 114: 17.428 distance: 114 - 115: 22.155 distance: 114 - 117: 39.646 distance: 115 - 116: 24.656 distance: 115 - 121: 7.687 distance: 117 - 118: 42.229 distance: 117 - 119: 55.628 distance: 118 - 120: 49.260 distance: 121 - 122: 16.897 distance: 122 - 123: 26.488 distance: 122 - 125: 29.257 distance: 123 - 124: 32.231 distance: 123 - 129: 26.013 distance: 125 - 126: 32.687 distance: 126 - 127: 11.292 distance: 126 - 128: 11.827 distance: 129 - 130: 36.041 distance: 129 - 135: 25.423 distance: 130 - 131: 27.989 distance: 130 - 133: 33.484 distance: 131 - 132: 41.656 distance: 131 - 136: 18.813 distance: 133 - 134: 36.361 distance: 134 - 135: 22.759 distance: 136 - 137: 13.598 distance: 137 - 138: 29.196 distance: 137 - 140: 17.402 distance: 138 - 139: 23.522 distance: 138 - 143: 18.013 distance: 140 - 141: 21.791 distance: 140 - 142: 35.329 distance: 143 - 144: 22.905 distance: 144 - 145: 10.158 distance: 144 - 147: 17.245 distance: 145 - 146: 40.935 distance: 145 - 151: 22.896 distance: 147 - 148: 17.609 distance: 148 - 149: 28.003 distance: 148 - 150: 38.110 distance: 151 - 152: 7.107 distance: 152 - 153: 7.555 distance: 152 - 155: 33.698 distance: 153 - 154: 14.412 distance: 153 - 158: 15.262 distance: 155 - 156: 49.525 distance: 155 - 157: 22.116 distance: 158 - 159: 10.854 distance: 158 - 164: 34.425 distance: 159 - 160: 28.420 distance: 159 - 162: 40.937 distance: 160 - 165: 26.531 distance: 162 - 163: 40.408 distance: 163 - 164: 51.243