Starting phenix.real_space_refine on Mon Aug 25 14:13:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xx4_38745/08_2025/8xx4_38745.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xx4_38745/08_2025/8xx4_38745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xx4_38745/08_2025/8xx4_38745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xx4_38745/08_2025/8xx4_38745.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xx4_38745/08_2025/8xx4_38745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xx4_38745/08_2025/8xx4_38745.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 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 Zn 6 6.06 5 P 43 5.49 5 Mg 1 5.21 5 S 164 5.16 5 C 18116 2.51 5 N 4951 2.21 5 O 5404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28685 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 11091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1391, 11091 Classifications: {'peptide': 1391} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1325} Chain breaks: 6 Chain: "B" Number of atoms: 9255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1171, 9255 Classifications: {'peptide': 1171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1118} Chain breaks: 7 Chain: "C" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2907 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 338} Chain: "D" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1669 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "H" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 569 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain breaks: 1 Chain: "P" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 472 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "E" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 854 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "N" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 450 SG CYS A 59 99.369 106.912 66.614 1.00 78.19 S ATOM 471 SG CYS A 62 96.703 109.169 67.898 1.00 61.50 S ATOM 531 SG CYS A 69 96.432 105.309 68.125 1.00 71.28 S ATOM 775 SG CYS A 99 92.498 93.060 22.447 1.00107.11 S ATOM 797 SG CYS A 102 92.503 96.792 21.594 1.00103.81 S ATOM 1049 SG CYS A 134 90.243 94.405 19.686 1.00110.87 S ATOM 1074 SG CYS A 137 94.119 94.251 19.360 1.00121.37 S ATOM 19865 SG CYS B1180 88.986 116.268 55.930 1.00 74.91 S ATOM 19890 SG CYS B1183 89.223 113.197 53.875 1.00 65.71 S ATOM 20006 SG CYS B1198 92.258 114.793 55.441 1.00 68.56 S ATOM 20028 SG CYS B1201 90.439 116.604 52.425 1.00 71.93 S ATOM 25597 SG CYS G 4 77.478 36.205 22.341 1.00126.71 S ATOM 25617 SG CYS G 7 80.086 37.735 24.507 1.00128.67 S ATOM 25751 SG CYS G 24 77.542 40.038 22.845 1.00126.50 S ATOM 25763 SG CYS G 26 80.143 38.331 20.703 1.00131.63 S ATOM 26133 SG CYS G 73 47.257 22.657 61.356 1.00 83.87 S ATOM 26154 SG CYS G 76 49.625 20.158 63.630 1.00 90.80 S ATOM 26311 SG CYS G 96 50.524 23.676 62.779 1.00 88.93 S ATOM 26328 SG CYS G 98 50.339 21.198 59.988 1.00 84.61 S ATOM 26417 SG CYS H 7 64.883 66.419 114.441 1.00 56.44 S ATOM 26441 SG CYS H 10 62.788 68.052 117.164 1.00 53.01 S ATOM 26798 SG CYS H 65 61.169 65.947 114.391 1.00 41.60 S ATOM 26804 SG CYS H 66 63.118 64.469 117.371 1.00 54.69 S Time building chain proxies: 5.60, per 1000 atoms: 0.20 Number of scatterers: 28685 At special positions: 0 Unit cell: (138.58, 147.6, 151.7, 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) Zn 6 29.99 S 164 16.00 P 43 15.00 Mg 1 11.99 O 5404 8.00 N 4951 7.00 C 18116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 901.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 69 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 99 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 137 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 134 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 4 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 7 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 26 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 24 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 96 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 98 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 73 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 76 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " Number of angles added : 33 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6586 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 43 sheets defined 41.7% alpha, 17.1% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 116 through 126 removed outlier: 4.296A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.550A pdb=" N HIS A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 226 through 238 Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.680A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.562A pdb=" N ARG A 302 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 303 " --> pdb=" O MET A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 303' Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.170A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 625 through 648 removed outlier: 3.979A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.507A pdb=" N LEU A 657 " --> pdb=" O ALA A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 686 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 722 removed outlier: 3.919A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 781 through 785 Processing helix chain 'A' and resid 797 through 834 removed outlier: 3.861A pdb=" N THR A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.782A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 953 through 970 Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1015 through 1032 Processing helix chain 'A' and resid 1040 through 1059 Proline residue: A1052 - end of helix removed outlier: 3.923A pdb=" N GLN A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1063 Processing helix chain 'A' and resid 1074 through 1082 Processing helix chain 'A' and resid 1085 through 1089 Processing helix chain 'A' and resid 1106 through 1118 Processing helix chain 'A' and resid 1151 through 1162 Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1310 through 1314 removed outlier: 3.755A pdb=" N THR A1313 " --> pdb=" O ASP A1310 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A1314 " --> pdb=" O PRO A1311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1310 through 1314' Processing helix chain 'A' and resid 1318 through 1327 Processing helix chain 'A' and resid 1327 through 1344 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.878A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.670A pdb=" N MET B 26 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 61 removed outlier: 3.718A pdb=" N ILE B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Proline residue: B 56 - end of helix Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 175 through 182 removed outlier: 3.519A pdb=" N ILE B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.565A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 removed outlier: 3.674A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 314 removed outlier: 4.448A pdb=" N ASN B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 340 removed outlier: 3.875A pdb=" N ILE B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.589A pdb=" N ASP B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 383 through 402 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.504A pdb=" N THR B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 458 through 471 removed outlier: 3.725A pdb=" N ILE B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 513 through 521 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.528A pdb=" N ASP B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 Processing helix chain 'B' and resid 603 through 610 removed outlier: 3.595A pdb=" N VAL B 608 " --> pdb=" O ASN B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 642 Processing helix chain 'B' and resid 679 through 697 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 742 through 747 removed outlier: 3.690A pdb=" N GLU B 747 " --> pdb=" O PRO B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 782 through 786 removed outlier: 3.526A pdb=" N SER B 786 " --> pdb=" O ALA B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 804 Processing helix chain 'B' and resid 814 through 818 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 1030 through 1033 Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.704A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1158 Processing helix chain 'B' and resid 1163 through 1169 Processing helix chain 'B' and resid 1214 through 1226 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.568A pdb=" N PHE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 259 removed outlier: 3.672A pdb=" N ILE C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 302 Processing helix chain 'C' and resid 328 through 359 Processing helix chain 'D' and resid 2 through 17 removed outlier: 4.484A pdb=" N TYR D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU D 12 " --> pdb=" O THR D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 Processing helix chain 'D' and resid 62 through 66 removed outlier: 3.698A pdb=" N VAL D 65 " --> pdb=" O GLY D 62 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS D 66 " --> pdb=" O LYS D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 66' Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 93 through 98 Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.522A pdb=" N LEU D 125 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 35 Processing helix chain 'G' and resid 33 through 36 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'H' and resid 13 through 16 removed outlier: 3.546A pdb=" N THR H 16 " --> pdb=" O PRO H 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 13 through 16' Processing helix chain 'H' and resid 17 through 33 Processing helix chain 'H' and resid 51 through 59 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.609A pdb=" N THR H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 removed outlier: 3.582A pdb=" N TYR H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'E' and resid 137 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 6.327A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASP B1211 " --> pdb=" O GLY A 4 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ALA A 6 " --> pdb=" O ASP B1211 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N ARG B1213 " --> pdb=" O ALA A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 83 removed outlier: 6.220A pdb=" N LYS A 199 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N ALA A 80 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N VAL A 197 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.395A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA7, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 7.363A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.856A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 386 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AB1, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AB2, first strand: chain 'A' and resid 567 through 569 removed outlier: 3.613A pdb=" N GLU A 600 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG A 594 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AB4, first strand: chain 'A' and resid 836 through 838 removed outlier: 6.425A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB6, first strand: chain 'A' and resid 1268 through 1278 removed outlier: 6.505A pdb=" N ARG A1275 " --> pdb=" O ASP A1288 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP A1288 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG A1277 " --> pdb=" O ARG A1286 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ARG A1286 " --> pdb=" O ARG A1277 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A1094 " --> pdb=" O THR A1295 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB8, first strand: chain 'A' and resid 1206 through 1210 removed outlier: 6.367A pdb=" N CYS A1175 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A1131 " --> pdb=" O CYS A1175 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG A1177 " --> pdb=" O TRP A1129 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TRP A1129 " --> pdb=" O ARG A1177 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU A1179 " --> pdb=" O LEU A1127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 6.850A pdb=" N ILE E 132 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL E 125 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN E 130 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE B1239 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE E 59 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.675A pdb=" N VAL B 65 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.675A pdb=" N VAL B 65 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 131 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL B 94 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN B 129 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 96 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 158 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 130 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLN B 156 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC4, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC5, first strand: chain 'B' and resid 416 through 420 removed outlier: 3.738A pdb=" N LEU B 204 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 213 through 216 Processing sheet with id=AC7, first strand: chain 'B' and resid 492 through 495 Processing sheet with id=AC8, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC9, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.511A pdb=" N LEU B 674 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 596 through 598 removed outlier: 6.796A pdb=" N VAL B 615 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS B 624 " --> pdb=" O ALA B 613 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA B 613 " --> pdb=" O CYS B 624 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 823 through 826 removed outlier: 6.047A pdb=" N ARG B 985 " --> pdb=" O VAL B 965 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL B 965 " --> pdb=" O ARG B 985 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLU B 987 " --> pdb=" O ALA B 963 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N ALA B 963 " --> pdb=" O GLU B 987 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD4, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.011A pdb=" N VAL B 865 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B1008 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 895 through 896 Processing sheet with id=AD6, first strand: chain 'B' and resid 932 through 933 removed outlier: 3.723A pdb=" N VAL B 955 " --> pdb=" O ILE B 933 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD8, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD9, first strand: chain 'C' and resid 5 through 12 removed outlier: 4.327A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N CYS C 222 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS C 181 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 68 through 73 removed outlier: 4.813A pdb=" N ILE C 159 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER C 115 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLU C 161 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C 113 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL C 110 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AE3, first strand: chain 'C' and resid 267 through 269 Processing sheet with id=AE4, first strand: chain 'D' and resid 20 through 21 removed outlier: 6.293A pdb=" N ILE D 52 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE D 89 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER D 54 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE D 91 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE D 56 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 138 through 142 removed outlier: 3.863A pdb=" N LYS D 138 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET D 162 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR D 201 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 3 through 10 removed outlier: 6.057A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 67 through 69 removed outlier: 4.207A pdb=" N CYS G 67 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU G 94 " --> pdb=" O SER G 102 " (cutoff:3.500A) 1219 hydrogen bonds defined for protein. 3336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9104 1.34 - 1.46: 5513 1.46 - 1.58: 14353 1.58 - 1.70: 85 1.70 - 1.82: 269 Bond restraints: 29324 Sorted by residual: bond pdb=" CB PRO B 12 " pdb=" CG PRO B 12 " ideal model delta sigma weight residual 1.492 1.616 -0.124 5.00e-02 4.00e+02 6.17e+00 bond pdb=" C ARG A 419 " pdb=" N GLN A 420 " ideal model delta sigma weight residual 1.331 1.292 0.039 2.07e-02 2.33e+03 3.54e+00 bond pdb=" CB PRO B 440 " pdb=" CG PRO B 440 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.44e+00 bond pdb=" CG PRO B 12 " pdb=" CD PRO B 12 " ideal model delta sigma weight residual 1.503 1.563 -0.060 3.40e-02 8.65e+02 3.12e+00 bond pdb=" CB GLU A 476 " pdb=" CG GLU A 476 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.91e+00 ... (remaining 29319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 39504 2.62 - 5.23: 332 5.23 - 7.85: 17 7.85 - 10.46: 8 10.46 - 13.08: 3 Bond angle restraints: 39864 Sorted by residual: angle pdb=" CA PRO B 440 " pdb=" N PRO B 440 " pdb=" CD PRO B 440 " ideal model delta sigma weight residual 112.00 101.47 10.53 1.40e+00 5.10e-01 5.66e+01 angle pdb=" CA PRO B 12 " pdb=" N PRO B 12 " pdb=" CD PRO B 12 " ideal model delta sigma weight residual 112.00 103.85 8.15 1.40e+00 5.10e-01 3.39e+01 angle pdb=" N ILE A1074 " pdb=" CA ILE A1074 " pdb=" C ILE A1074 " ideal model delta sigma weight residual 112.17 107.00 5.17 9.50e-01 1.11e+00 2.96e+01 angle pdb=" C SER B 488 " pdb=" CA SER B 488 " pdb=" CB SER B 488 " ideal model delta sigma weight residual 117.23 110.11 7.12 1.36e+00 5.41e-01 2.74e+01 angle pdb=" CA SER B 488 " pdb=" C SER B 488 " pdb=" N GLY B 489 " ideal model delta sigma weight residual 119.98 116.63 3.35 8.50e-01 1.38e+00 1.55e+01 ... (remaining 39859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.68: 14943 18.68 - 37.36: 1986 37.36 - 56.04: 632 56.04 - 74.71: 143 74.71 - 93.39: 43 Dihedral angle restraints: 17747 sinusoidal: 7564 harmonic: 10183 Sorted by residual: dihedral pdb=" CA ARG A1228 " pdb=" C ARG A1228 " pdb=" N GLU A1229 " pdb=" CA GLU A1229 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA THR B1163 " pdb=" C THR B1163 " pdb=" N ILE B1164 " pdb=" CA ILE B1164 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA THR B 904 " pdb=" C THR B 904 " pdb=" N LYS B 905 " pdb=" CA LYS B 905 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 17744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3078 0.041 - 0.082: 1057 0.082 - 0.123: 353 0.123 - 0.164: 46 0.164 - 0.204: 2 Chirality restraints: 4536 Sorted by residual: chirality pdb=" CB VAL A1103 " pdb=" CA VAL A1103 " pdb=" CG1 VAL A1103 " pdb=" CG2 VAL A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO B 12 " pdb=" N PRO B 12 " pdb=" C PRO B 12 " pdb=" CB PRO B 12 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA TYR F 69 " pdb=" N TYR F 69 " pdb=" C TYR F 69 " pdb=" CB TYR F 69 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 4533 not shown) Planarity restraints: 4975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 439 " 0.091 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO B 440 " -0.225 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1100 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO A1101 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A1101 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A1101 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 235 " -0.071 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO B 236 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.056 5.00e-02 4.00e+02 ... (remaining 4972 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 202 2.50 - 3.10: 20383 3.10 - 3.70: 46364 3.70 - 4.30: 71473 4.30 - 4.90: 116191 Nonbonded interactions: 254613 Sorted by model distance: nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A1503 " model vdw 1.899 2.170 nonbonded pdb=" O3' A P 30 " pdb="MG MG A1503 " model vdw 1.949 2.170 nonbonded pdb=" OD1 ASP A 461 " pdb="MG MG A1503 " model vdw 1.983 2.170 nonbonded pdb=" OD1 ASP A 457 " pdb="MG MG A1503 " model vdw 2.004 2.170 nonbonded pdb=" OG1 THR G 14 " pdb=" O ILE G 21 " model vdw 2.110 3.040 ... (remaining 254608 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.820 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 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 : 0.005 0.124 29348 Z= 0.224 Angle : 0.627 13.777 39897 Z= 0.328 Chirality : 0.046 0.204 4536 Planarity : 0.005 0.130 4975 Dihedral : 19.163 93.392 11161 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.94 % Favored : 94.77 % Rotamer: Outliers : 2.39 % Allowed : 27.69 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.14), residues: 3444 helix: 0.76 (0.14), residues: 1287 sheet: -0.43 (0.23), residues: 503 loop : -0.41 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1228 TYR 0.021 0.002 TYR F 69 PHE 0.027 0.002 PHE B 304 TRP 0.015 0.001 TRP A 466 HIS 0.005 0.001 HIS A1203 Details of bonding type rmsd covalent geometry : bond 0.00542 (29324) covalent geometry : angle 0.61492 (39864) hydrogen bonds : bond 0.16219 ( 1256) hydrogen bonds : angle 6.81554 ( 3430) metal coordination : bond 0.00834 ( 24) metal coordination : angle 4.38373 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 364 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 126 SER cc_start: 0.8285 (t) cc_final: 0.8077 (m) REVERT: A 954 GLU cc_start: 0.7032 (tt0) cc_final: 0.6763 (tm-30) REVERT: A 1179 GLU cc_start: 0.7247 (tt0) cc_final: 0.6684 (mt-10) REVERT: A 1346 LYS cc_start: 0.7607 (tptp) cc_final: 0.7343 (tppt) REVERT: B 721 ASP cc_start: 0.8132 (m-30) cc_final: 0.7805 (m-30) REVERT: D 72 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7656 (ttp-110) outliers start: 74 outliers final: 67 residues processed: 426 average time/residue: 0.5282 time to fit residues: 268.0663 Evaluate side-chains 425 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 358 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 417 PHE Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 996 SER Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1160 GLU Chi-restraints excluded: chain A residue 1211 SER Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1402 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 558 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1198 CYS Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 146 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4366 > 50: distance: 130 - 176: 26.773 distance: 133 - 173: 21.257 distance: 155 - 162: 15.270 distance: 162 - 163: 25.932 distance: 163 - 164: 21.725 distance: 163 - 166: 12.810 distance: 164 - 165: 41.971 distance: 164 - 173: 21.723 distance: 166 - 167: 38.854 distance: 167 - 168: 42.675 distance: 167 - 169: 32.391 distance: 168 - 170: 24.856 distance: 169 - 171: 19.815 distance: 170 - 172: 5.846 distance: 173 - 174: 38.394 distance: 174 - 175: 41.599 distance: 174 - 177: 38.298 distance: 175 - 176: 42.809 distance: 175 - 181: 26.476 distance: 177 - 178: 7.833 distance: 177 - 179: 15.047 distance: 178 - 180: 11.516 distance: 181 - 182: 27.245 distance: 182 - 183: 49.223 distance: 182 - 185: 36.385 distance: 183 - 184: 11.833 distance: 183 - 188: 16.152 distance: 184 - 213: 16.062 distance: 185 - 186: 19.627 distance: 185 - 187: 29.187 distance: 188 - 189: 5.976 distance: 188 - 194: 11.556 distance: 189 - 190: 7.456 distance: 189 - 192: 7.169 distance: 190 - 191: 11.456 distance: 190 - 195: 9.005 distance: 192 - 193: 9.006 distance: 193 - 194: 7.635 distance: 195 - 196: 10.141 distance: 196 - 197: 25.378 distance: 196 - 199: 5.882 distance: 197 - 198: 5.636 distance: 197 - 204: 41.988 distance: 199 - 200: 10.061 distance: 200 - 201: 5.440 distance: 204 - 205: 11.858 distance: 205 - 206: 19.967 distance: 205 - 208: 4.141 distance: 206 - 207: 24.687 distance: 206 - 213: 9.389 distance: 208 - 209: 8.104 distance: 209 - 210: 3.499 distance: 210 - 211: 3.804 distance: 213 - 214: 9.512 distance: 214 - 215: 13.227 distance: 214 - 217: 13.149 distance: 215 - 216: 12.574 distance: 215 - 218: 34.143 distance: 218 - 219: 24.299 distance: 219 - 220: 8.979 distance: 219 - 222: 3.700 distance: 220 - 221: 8.912 distance: 220 - 227: 10.218 distance: 222 - 223: 4.212 distance: 223 - 224: 6.649 distance: 224 - 226: 3.266 distance: 227 - 228: 20.992 distance: 228 - 229: 17.091 distance: 228 - 231: 11.141 distance: 229 - 230: 18.228 distance: 229 - 235: 17.629 distance: 231 - 232: 16.169 distance: 232 - 233: 10.188 distance: 232 - 234: 12.248 distance: 235 - 236: 12.507 distance: 236 - 237: 3.968 distance: 236 - 239: 7.726 distance: 237 - 238: 12.218 distance: 237 - 241: 3.399 distance: 239 - 240: 11.646